ECO (https://github.com/evidenceontology/evidenceontology) is released into the public domain under CC0 1.0 Universal (CC0 1.0). Anyone is free to copy, modify, or distribute the work, even for commercial purposes, without asking permission. Please see the Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/) for an easy-to-read description of CC0 1.0 or the full legal code (https://creativecommons.org/publicdomain/zero/1.0/legalcode) for more detailed information. To get a sense of why ECO is CC0 as opposed to licensed under CC-BY, please read this thoughtful discussion (https://github.com/OBOFoundry/OBOFoundry.github.io/issues/285) on the OBO Foundry GitHub site.
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.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
BFO CLIF specification label
editor preferred label
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
example of usage
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
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.
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.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
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
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
curator note
An administrative note of use for a curator but of no use for a user
The 'term requester' can credit the person, organization or project who request the ontology term.,The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
imported from
For external terms/classes, the ontology from which the term was imported
elucidation
person:Alan Ruttenberg
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
has associated axiom(nl)
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
ISA tools project (http://isa-tools.org)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
GO biological process terms should be used in the GO with/from field
GO cellular component terms should be used in the GO with/from field
Chemical entity IDs should be used in the GO with/from field
Gene IDs should be used in the GO with/from field
GO molecular function terms should be used in the GO with/from field
Protein IDs should be used in the GO with/from field
Protein complex IDs should be used in the GO with/from field
Transcript IDs should be used in the GO with/from field
Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
An account of the content of the resource.
Description
The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
A reference to a resource from which the present resource is derived.
Source
A legal document giving official permission to do something with the resource.
A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence.
In the future we may use a more generic relation with weaker domain and range constraints taken from IAO, RO or OBI.
has_specified_input
see is_input_of example_of_usage
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
Alan Ruttenberg
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
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
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
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.
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])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
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])
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)
(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]
process
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
A type of information that is used to support an assertion.
A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator.
inference from background scientific knowledge
A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature.
A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology.
A type of protein assay evidence where the catalytic activity of an enzyme is determined.
A type of evidence resulting from manipulation of variables in order to discover cause and effect.
A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell.
A type of experimental evidence that is based on characterization of gene expression.
Use this evidence type when the annotation is inferred from the timing or location of expression of a gene. It may be difficult to determine whether the expression pattern truly indicates that a gene plays a role in a given process.
A type of expression pattern evidence where abundance of a transcript is analyzed.
A type of expression pattern evidence resulting from protein abundance quantification techniques.
A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products.
A type of genetic interaction evidence where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background.
A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
A type of experimental phenotypic evidence derived from the difference in two alleles of a corresponding gene that result from one or more changes in the genome.
A type of mutant phenotype evidence where a phenotype is associated with altered gene product which lacks the molecular function of the wild-type gene.
loss-of-function mutant phenotype evidence
A type of experimental phenotypic evidence where a transgenic strain carrying the construct of a promoter cDNA fusion in which a gene of interest is driven by a defined promoter or enhancer is ectopically expressed in the defined pattern to characterize potential cellular properties and functions of a protein of interest.
IMP: analysis of overexpression/ectopic expression phenotype
A type of mutant phenotype evidence where a phenotype is observed while expressing an anti-sense version of a gene product in a wild-type (for that gene product) background.
A type of mutant phenotype evidence where an RNA construct is introduced into a cell and the expression of the gene bearing its complementary sequence is suppressed.
A type of protein assay evidence based on the inhibition of the molecular function of a protein.
A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
Molecules interacted with might include protein, nucleic acid, ion, or complex.
A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
A type of physical interaction evidence that depends on the strength of the interaction between two entities.
A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex.
A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein.
Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode.
A type of experimental genomic evidence resulting from a process in which single stranded nucleic acids are allowed to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences.
A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
For GO annotation, in the case of a single gene, an accession for the related gene's sequence is entered in the evidence_with field.
A type of match to sequence model evidence that is based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence.
A type of match to sequence model evidence resulting from a positive match of a protein, or set of proteins to a predictive model (signature) in the InterPro database.
match to InterPro member signature evidence
A type of BLAST evidence that is used in a manual assertion.
A type of protein BLAST evidence that is used in a manual assertion.
protein BLAST evidence used in manual assertion
BLAST search criteria for ISS assignment in PAMGO_GAT
A type of nucleotide BLAST evidence that is used in a manual assertion.
nucleotide BLAST evidence used in manual assertion
A type of author statement that is based on a cited reference.
The traceable author statement (TAS) evidence code covers author statements that are attributed to a cited source. Typically this type of information comes from review articles. Material from the introductions and discussion sections of non-review papers may also be suitable if another reference is cited as the source of experimental work or analysis. When annotating with this code the curator should use caution and be aware that authors often cite papers dealing with experiments that were performed in organisms different from the one being discussed in the paper at hand. Thus a problem with the TAS code is that it may turn out from following up the references in the paper that no experiments were performed on the gene in the organism actually being characterized in the primary paper. For this reason we recommend (when time and resources allow) that curators track down the cited paper and annotate directly from the experimental paper using the appropriate experimental evidence code. When this is not possible and it is necessary to annotate from reviews, the TAS code is the appropriate code to use for statements that are associated with a cited reference. Once an annotation has been made to a given term using an experimental evidence code, we recommend removing any annotations made to the same term using the TAS evidence code.
A type of author statement that is not associated with results presented or a cited reference.
The non-traceable author statement evidence code should be used in all cases where the author makes a statement that a curator wants to capture but for which there are neither results presented nor a specific reference cited in the source used to make the annotation. The source of the information may be peer reviewed papers, textbooks, database records or vouchered specimens.
A curator inference that results from research where no information about a biological feature was found in the scientific literature, at biological databases, or within other resources.
An assertion of "no biological data found" carries the assumption that a more-or-less exhaustive search has been conducted.
The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations.
A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins.
A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
A type of evidence resulting from comparing likeness of distinct biological entities.
A type of mutant phenotype evidence resulting from a phenotype that is associated with the altered gene product which possesses a new molecular function or a new pattern of gene expression.
gain-of-function mutant phenotype evidence
A type of similarity based on biomolecular sequence.
A sequence similarity analysis may involve a gene or a gene product, and it could be based on similarity to a single other gene or to a group of other genes.
spatial pattern of protein expression evidence
A type of protein expression evidence resulting from the quantification of protein production in a sample.
spatial pattern of transcript expression evidence
A type of experimental phenotypic evidence that is based on the expression pattern of a reporter gene.
A type of phenotypic evidence based on an author's phenotypic description of a species or higher level group explicitly referencing an observation of a voucher specimen, a specimen with a permanent museum catalog.
A type of similarity based on genotype without respect to expression.
A genetic similarity analysis might consider genetic markers, polymorphisms, alleles, or other characteristics sometimes considered as part of the field of traditional genetics. Although an attempt has been made to treat as distinct the concepts of "genetic", "genotypic", "genomic", and "sequence", there is considerable overlap in usage throughout the field of biology.
A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)
suppressor/enhancer interaction evidence
A type of combinatorial analysis where data are combined and evaluated by an algorithm.
Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
A type of genetic interaction evidence that is based on the phenotypic outcome of two mutations in unrelated genetic loci.
This general 'array experiment' term should not be used - replace with the specific type of array (e.g. ECO:0000097, ECO:0000062, ECO:0000104, etc.)
A type of genetic interaction evidence that is based on the suppression of one allelic effect by an allele at another genetic locus.
Epistasis' can be used in different contexts in different areas of genetics. It is sometimes used to mean 'genetic interaction', whereas other times it may be specific to mutations that block the effects of other mutations.
A type of similarity based on the expression of a genotype in an environment.
Phenotype is defined as the outcome of the expression of a genotype in a given environment. A comparison might involve whole organisms or sub-parts of organisms.
A type of transcript expression evidence resulting from simultaneous profiling of the expression levels of thousands of genes in a single experiment allowing analysis of genes and their networks.
differential gene expression evidence from microarray experiment
A type of experimental evidence that is based on the expression of a genotype in an environment.
A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements.
A type of phenotypic evidence that is based on a gene product that is associated with a quantitative trait locus, but has not been cloned.
A type of expression microarray evidence where expression level is quantified by sample biotin-labeled cRNA (transcribed from an unknown RNA sample) hybridized to DNA oligonuclotides immoblized on a solid surface.
cRNA to DNA expression microarray evidence
A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures.
A type of functional complementation evidence that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene.
IGI: functional complementation in heterologous system
functional complementation in heterologous system evidence
A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
The assay involves screening a library of candidate proteins for the ability bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to a yeast reporter gene (TAIR:TED).
A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures.
A type of hybrid interaction evidence that is based on detection of protein-protein interaction by activation of a yeast reporter gene after a bait protein fused to a DNA-binding domain (which has been transfected into a yeast cell) is used to screen a cDNA library of clones fused to an activation domain.
A type of nucleic acid hybridization evidence where methylation-sensitive restriction enzymes are utilized to analyze methylated DNA fragments by hybridizing them to a CpG island microarray.
differential methylation hybridization evidence
A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification.
If performing GO annotation, the interacting protein is referenced in the evidence_with column.
A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures.
A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product.
A type of physical interaction evidence that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein.
The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquitin (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough to reconstitute.TAIR:TED
A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles.
A type of physical interaction evidence that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes.
The interacting protein is referenced in the evidence_with column.
A type of polymerase chain reaction evidence resulting from initial modification of DNA by sodium bisulfite, converting all unmethylated cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA.
methylation-specific polymerase chain reaction evidence
A type of DNA detection assay evidence that is based on detection of a specific DNA sequence by hybridization of labeled probes to any immobilized DNA fragment with sequence similarity.
The DNA fragments are prepared through gel electrophoresis then transferred to a filter membrane.
A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound.
"Used when an annotation is made based on affinity chromatography, which is a selective separation technique by which a compound (e.g., an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components, the bound compound is displaced by changing the concentration of protons, salts, or cofactors in the eluent" (from original definition by TAIR:TED). Types of highly specific interaction might include those of antigen and antibody, enzyme and substrate, or receptor and ligand.
A type of similarity that indicates common ancestry.
A type of motif similarity evidence that is based on detection of a targeting sequence in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand.
A type of motif similarity evidence that is based on detection of one, or more, transmembrane domains in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
transmembrane domain prediction evidence
A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes.
Genomic cluster analyses include synteny and operon structure.
A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding.
A type of experimental genomic evidence resulting from a genome-wide estimate of DNA methylation by differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences.
intermethylated site amplification evidence
A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues.
A type of evidence that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system.
The biological system in question might be a multi-step process or pathway or a physical complex comprising several components. The components in the experimental evidence can come from the same species or a mix of species. The experimental evidences may be only partial or weak.
biological system reconstruction evidence
A type of DNA detection assay evidence resulting from the use of restriction enzymes for direct end-labeling of DNA (creating landmarks), followed by high-resolution two-dimensional electrophoresis to visualize the landmarks.
restriction landmark genome scanning evidence
restriction landmark genomic scanning evidence
A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy.
A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies.
IDA: immunolocalization of epitope-tagged protein
epitope-tagged protein immunolocalization evidence
A type of experimental genomic evidence where gene sequence or variation is determined or detected by fluorescently-labeled DNA fragments hybridized to sequence-specific oligonucleotides immobilized on an array.
single nucleotide polymorphism array evidence
The children of 'biological assay evidence' have been moved under 'direct assay evidence', and this term has been deprecated with no children left.
A type of cell growth assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect.
Cell growth aspects can include growth rate and extent of growth. A cell growth curve acts as a natural reporter.
A type of direct assay evidence based on an electrophoretic mobility shift of macromolecules, compounds, and proteins where solutions of protein and nucleic acid are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect protein-nucleic acid interactions.
EMSA: electrophoretic mobility shift assay
IDA: electrophoretic mobility shift assay
EMSA is often used for assessing TF-binding with fluorophore labelling. Protein-nucleic acid complexes generally migrate at a slower rate than the corresponding non-bonded nucleic acid.
electrophoretic mobility shift assay evidence
A type of expression microarray evidence where expression level is quantified by fluroescently-labeled cDNA (reverse transcribed from an unknown RNA sample) hybridized to DNA immobilized on a solid surface.
cDNA to DNA expression microarray evidence
A type of nucleic acid hybridization evidence based on localization of a specific segment of DNA or RNA by the application of a complementary strand of nucleic acid to which a reporter molecule is attached.
A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions.
A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information.
A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules.
A type of expression microarray evidence where expression levels are quantified by hybridization of fluorescently-labeled DNA to cDNA (reverse transcribed from an unknown RNA sample) immobilized on a solid surface.
microarray RNA expression level evidence
IEP: transcript levels (e.g. microarray data)
REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that.
DNA to cDNA expression microarray evidence
A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels.
A type of transcript expression evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples.
A type of transcript expression evidence in which expression levels are determined through RT-PCR (quantitative or otherwise).
reverse transcription polymerase chain reaction transcription evidence
A type of polymerase chain reaction evidence where RNA is reverse transcribed into cDNA and amplified for product measurement in real time for transcription analysis i.e. qPCR.
The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate.
reverse transcription polymerase chain reaction evidence
A type of nuclease protection assay evidence where mRNA is hybridized with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions, later the remaining probe target hybrids are purified and resolved on denaturing polyacrylamide gel, and quantified by autoradiography.
A type of gel electrophoresis evidence where proteins are separated using gel electrophoresis and then they are blotted on a nitrocellulose or polyvinylidene difluoride (PVDF) membrane, later an antibody with a dye or an enzyme is added to the solution which is able to bind to its specific protein and this product is detected either by chemiluminescent detection technique or fluorescence imaging technique.
IEP: protein levels (e.g. Western blots)
Western blot is used for protein detection and analysis. A mixed protein sample is separated through polyacrylamide gel electrophoresis then transferred to a membrane, such as polyvinylidene fluoride (PVDF), and labeled with protein-specific antibodies.
A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein.
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue is compared to another cell type or tissue when mRNA from each sample is reverse transcribed, labeled, and hybridized to a cDNA library to compare hybridization patterns.
Differential hybridization identifies differentially expressed cloned genes. Two different mRNA-derived probes are used to demonstrate RNA expression under a specific condition.
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue are compared to another cell type or tissue when denatured ds-cDNA from the two samples are hybridized, and the common sequences are 'subtracted'.
Subtractive hybridization is used for isolation and identification of transcripts involving the removal of any sequences present in the control from the test probe to detect only transcripts present in the sample. The method is PCR-based for the comparison of two cDNA libraries.
A type of experimental phenotypic evidence in which a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product.
A type of protein assay evidence where sub-cellular localization of a protein within a cell is determined.
A type of protein localization evidence resulting from the fusion of a protein of interest to a labeling protein which has enzymatic activity or fluorescence properties.
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with green fluorescent protein (GFP) from the jellyfish Aequorea victoria.
GFP fusion protein localization evidence
IDA: localization of GFP/YFP fusion protein
green fluorescent protein fusion protein localization evidence
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with yellow fluorescent protein (YFP), which was created by mutating green fluorescent protein (GFP) of the Aequorea victoria.
YFP fusion protein localization evidence
yellow fluorescent protein fusion protein localization evidence
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-glucuronidase (GUS) coding gene as a reporter gene for the localization of a particular gene product.
GUS fusion protein localization evidence
beta-glucuronidase fusion protein localization evidence
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-galactosidase coding gene (lacZ) into a specific gene to create a beta-galactosidase-tagged fusion protein.
LacZ fusion protein localization evidence
beta-galactosidase fusion protein localization evidence
A type of direct assay evidence resulting from the activity assessment of transport proteins.
A type of affinity evidence resulting from the binding of a molecule to a nucleic acid.
A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer.
A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site.
A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis.
IDA: in vitro reconstitution assay with recombinant protein
in vitro transcription reconstitution assay evidence
A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system.
in vitro recombinant protein transcription reconstitution assay evidence
A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed.
IDA: protein expression in heterologous system
heterologous protein expression evidence
A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture.
IDA: protein separation and direct sequencing
protein separation followed by direct sequencing evidence
IDA: protein separation and fragment identification
protein separation followed by fragment identification evidence
A type of transport assay evidence in which the uptake mechanism of a transporter is investigated in a cell that does not normally express that protein.
IDA: uptake assay in heterologous system
The transporter is a recombinant protein.
A type of direct assay evidence where electrical properties of cells or tissues are studied.
The scale of electrophysiology assays can range from small, e.g. a single ion channel, to large, e.g. an entire organ such as a heart.
A type of voltage clamp recording evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current.
IDA: two-electrode voltage clamp technique
two-electrode voltage clamp recording evidence
A type of direct assay evidence resulting from the detection and quantification of transcribed RNA.
A type of transcription assay evidence in which sequence-specific binding proteins that increase transcription of a specific target gene or genes are identified, quantified, and/or analyzed.
A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed.
For example, the accumulation of a biosynthetic intermediate.
A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined.
Examples include: abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions.
A type of mutant phenotype evidence in which traits arising from a mutation are visually examined.
A type of evidence in which the location of the gene within the genome provides insight into its function, or provides evolutionary insight.
This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis.
A type of direct assay evidence resulting from a sample of microorganisms or living tissue grown in a medium.
A type of experimental evidence arising from the investigation of an animal model system.
A type of experimental evidence arising from a controlled investigation that uses human subjects.
A type of direct assay evidence resulting from a process performed outside the living organism, where the components of an organism have been isolated from their usual biological context, to permit a more detailed or more convenient analysis in an artificial setting.
Use ECO:0001563 (cell growth assay evidence) in place of this term.
A type of direct assay evidence resulting from studies in which cytoplasmic and/or nuclear cellular components from resting, nonstimulated cells, are isolated by ultracentrifugation to provide molecular machinery that can be used in reactions in the absence of many of the other cellular components for the purpose of in vitro protein synthesis, transcription, DNA replication, etc.
A type of specific protein inhibition evidence where the protein under study is an enzyme.
A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment
Such alignments may be pairwise alignments or multiple alignments.
A type of sequence similarity evidence in which orthology is established by multiple criteria, including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors.
Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor.
A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model.
Used when evidence from any kind of statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Examples of relevant evidence are: Hidden Markov Models, PROSITE motifs, and tools such as tRNASCAN.
An assertion method that does not involve human review.
An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically.
An evidence type that is based on an assertion by the author of a paper, which is read by a curator.
A type of inferential evidence that is based on a conclusion drawn by a curator.
A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST).
A type of BLAST evidence in which nucleotide sequences are aligned.
A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned.
A type of BLAST evidence that is used in an automatic assertion.
BLAST evidence used in automatic assertion
A type of nucleotide BLAST evidence that is used in an automatic assertion.
nucleotide BLAST evidence used in automatic assertion
A type of protein BLAST evidence that is used in an automatic assertion.
protein BLAST evidence used in automatic assertion
A type of evidence that arises out of the integration of more than one line of evidence.
A key aspect of this type of evidence is that two or more pieces of information are combined to generate an emergent type of evidence not possible with the constituent pieces of evidence alone. A combinatorial analysis typically involves incorporation of different types of evidence.
A type of combinatorial analysis that is used in an automatic assertion.
combinatorial evidence used in automatic assertion
A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
This type of evidence can be used in support of both positive and "not" GO annotations. It should be used to annotate ancestral genes but not extant ones.
biological aspect of descendant evidence
A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence.
rapid divergence from ancestral sequence evidence
A type of phylogenetic evidence characterized by the absence of key sequence residues.
The loss of certain residues important for function can indicate that a sequence lacks a particular function.
phylogenetic determination of loss of key residues evidence
A means by which a statement is made about an entity.
An assertion method that involves human review.
A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information.
A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides.
A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique.
Typically thousands to millions of reads are produced in parallel.
high throughput nucleotide sequencing assay evidence
A type of high throughput nucleotide sequencing evidence in which sequence is determined through hybridization of adaptor-ligated DNA to a glass slide on which each fragment is simultaneously clonally amplified, followed by progressive rounds of base incorporation with fluorescently-tagged nucleotides, washing, imaging, and cleavage.
In Illumina sequencing technology, adapters are ligated onto the ends of randomly fragmented DNA. After single-stranded fragments are bound to the inside surface of a flow cell channel, they undergo in-place bridge PCR amplification. To begin the sequencing cycle, labeled reversible terminators, primers and DNA polymerase are added, followed by laser excitation of the fluorescent label and high resolution scanning. After non-incorporated nucleotides are washed away and the dye is chemically removed, the next cycle repeats with four labeled reversible terminators, primers and DNA polymerase, again followed by imaging.
A type of high throughput nucleotide sequencing evidence in which the sequence for a ssDNA is determined by addition of primers and then nucleotides, one base pair at a time (which generate a specific fluorescence), to the target strand.
454 pyrosequencing technology amplifies individual DNA fragments inside water droplets within an oil solution (emulsion PCR). Within each droplet, a single DNA template is attached to a single primer-coated bead. Each bead is subsequently captured in a picolitre well within the sequencing machine. A luciferase-based readout system is used to identify individual nucleotides added to the nascent DNA. The target strand is usually prepared by fragmentation, adaptor ligation, and amplification by emulsion PCR.
A type of high throughput nucleotide sequencing evidence in which sequence is determined through rounds of ligation-based sequencing with fluorescently-labeled Di-base probes and cleavage, after which the template is reset, with a primer offset by one base, for subsequent rounds of ligation.
SOLiD sequencing technology is based on sequencing by ligation. After library preparation, emulsion PCR and bead enrichment are performed, including 3' modification of templates on selected beads to allow covalent bonding to a slide. 3' modified beads are attached to a glass slide and primers are added. Four fluorescently labeled di-base probes are added and multiple cycles of ligation, detection and cleavage are performed. The number of cycles determines read length. After a number of ligation cycles, the extension product is removed and another round of ligation cycles is performed with a new primer complimentary to the n-1 position of the template. Five rounds of primer reset are performed for each sequence tag. Samples are prepared by fragmentation of a sample library, adaptor ligation, emulsion PCR, and attachment of resultant beads to glass slides.
A type of nucleotide sequencing assay in which DNA sequence is determined by addition of a primed DNA template to a reaction mixture, followed by addition of DNA polymerase, deoxynucleosidetriphosphates (dNTPs - one of which may be radiolabeled), and one of four di-deoxynucleotidetriphosphates (ddNTPs), after which DNA elongation is terminated and the DNA is separated by size and imaged.
Chain termination sequencing, also called Sanger sequencing after its developer, uses dideoxynucleotide triphosphates (ddNTPs) as DNA chain terminators. Single-stranded DNA template, DNA primer, DNA polymerase, fluorescently or radioactively labeled nucleotides, and one of four ddNTPs are added together in each of four separate sequencing reactions. The synthesized and labeled DNA fragments from each of the four reactions are denatured, separated by size by gel electrophoresis, and visualized by autoradiography or UV light. The ddNTPs lack an OH group so the next dNTP cannot be attached, causing chain termination.
A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
Chromatin immunoprecipitation (ChIP) is used to investigate protein-DNA interactions in vivo. DNA and proteins are chemically cross-linked in vivo to form chromatin complexes, followed by cell lysis and DNA shearing. Fragmented DNA-protein complexes are selectively enriched for a protein of interest using a specific antibody (immunoprecipitation). Protein digestion and DNA purification are performed prior to DNA detection via molecular cloning and sequencing, polymerase chain reaction (PCR), microarray analysis (ChIP-on-chip), or direct high-throughput sequencing (ChIP-seq).
A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection.
ChIP-PCR is often used to validate ChIP-chip results and less frequently,ChIP-Seq results.
chromatin immunoprecipitation-PCR evidence
A type of chromatin immunoprecipitation evidence in which protein-DNA interactions are investigated at known genomic binding sites through a process of ChIP, DNA purification, and finally quantitative polymerase chain reaction (qPCR) for DNA detection.
chromatin immunoprecipitation-qPCR evidence
A type of chromatin immunoprecipitation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins.
ChIP-Seq experiments often use the input as a control to eliminate biases. To obtain similar results, ChIP-chip with high-density tiling arrays can be used.
chromatin immunoprecipitation-seq evidence
A type of chromatin immunoprecipitation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions.
A fixating agent such as formaldehyde is used to cross link proteins and DNA. Sonication is applied for DNA shearing. For transcription factor tagging, an antibody or epitope is employed. After cross-linking is reversed, the DNA is amplified and labeled with a flourophore for microarray which produces a resolution of aproximately 500 bp.
chromatin immunoprecipitation-chip evidence
A type of polymerase chain reaction evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes for detection and quantification of specific sequences in a DNA sample.
real-time polymerase chain reaction evidence
Quantitative PCR enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. The dye is activated upon binding double-stranded DNA. Although qRT-PCR is commonly found in literature synonymous to qPCR, it is preferable not to use this synonym as it is the accepted abbreviation for reverse transcription PCR. qPCR should be used instead (ISBN 978-0-470-68386-6 page 173).
quantitative polymerase chain reaction evidence
A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, and DNA processing and quantitation.
Chromosome conformation capture technologies are used to study the structural properties and spatial organization of chromosomes inside cells. All types of chromosome conformation capture technology involve five primary steps: cross-linking of DNA in vivo, restriction digestion, intramolecular ligation, reversing cross-linkages, and DNA enrichment and quantitation. The last step is different for each type of chromosome conformation capture technology, and may include PCR (3C), inverse PCR (4C), or ligation-mediated amplification (5C). Methods for product quantitation can include agarose gel detection or real-time quantitative PCR in the case of 3C, or high-throughput sequencing or microarray analysis for 4C and 5C.
chromosome conformation capture-based evidence
A type of chromosome conformation capture-based evidence that is derived by performing a type of polymerase chain reaction (PCR) in the final product quantitation step.
3C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C differs only in the fifth step, which involves performing either standard polymerase chain reaction (PCR) or quantitative PCR (qPCR) for product quantitation.
chromosome conformation capture evidence
A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray.
4C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 4C differs only in the fifth step, which involves inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation.
circularized chromosome conformation capture evidence
A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
5C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 5C differs only in the fifth step, which involves ligation-mediated amplification (LMA) followed by product quantitation.
carbon-copy chromosome conformation capture evidence
A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
chromosome conformation capture-PCR evidence
A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step.
chromosome conformation capture-qPCR evidence
A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation.
Hi-C is used to study the structural properties and spatial organization of chromosomes inside cells. Hi-C is similar to other types of chromosome conformation capture technology, but involves the addition of biotinylated nucleotides during the second or fourth step and enrichment for ligated fragments using immunoprecipitation after the fourth step.
A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with high-throughput (HT) sequencing.
3C-seq is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C-seq differs only in the fifth step, which involves inverse polymerase chain reaction (PCR) on a circularized 3C library prior to product quantitation.
chromosome conformation capture sequencing evidence
A type of experimental phenotypic evidence in which the phenotype of an organism is observed after the disruption of a structural feature.
A type of experimental phenotypic evidence in which the phenotype of an organism is observed after modification of the extra-organismal context.
Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth.
A type of anatomical perturbation that is based on disruption of tissue.
A tissue ablation experiment involves observing the phenotype of an entity whose tissues have been disrupted through genetic or biochemical manipulation, physical destruction, or some other means.
A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure.
A type of combinatorial analysis that is used in a manual assertion.
combinatorial evidence used in manual assertion
A type of computational combinatorial analysis that is used in a manual assertion.
inferred from reviewed computational analysis
computational combinatorial evidence used in manual assertion
A type of computational combinatorial analysis that is used in an automatic assertion.
computational combinatorial evidence used in automatic assertion
A type of sequence alignment evidence that is used in a manual assertion.
sequence alignment evidence used in manual assertion
A type of sequence alignment evidence that is used in an automatic assertion.
sequence alignment evidence used in automatic assertion
A type of sequence similarity evidence that is used in an automatic assertion.
sequence similarity evidence used in automatic assertion
A type of sequence similarity evidence that is used in a manual assertion.
inferred from sequence or structural similarity
sequence similarity evidence used in manual assertion
A type of similarity evidence that is used in an automatic assertion.
similarity evidence used in automatic assertion
A type of similarity evidence that is used in a manual assertion.
similarity evidence used in manual assertion
A type of genetic similarity evidence that is used in a manual assertion.
genetic similarity evidence used in manual assertion
A type of genetic similarity evidence that is used in an automatic assertion.
genetic similarity evidence used in automatic assertion
A type of match to sequence model evidence that is used in a manual assertion.
match to sequence model evidence used in manual assertion
A type of match to sequence model evidence that is used in an automatic assertion.
match to sequence model evidence used in automatic assertion
Gene Ontology annotation through association of InterPro records with GO terms.
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl
A type of motif similarity evidence that is used in a manual assertion.
motif similarity evidence used in manual assertion
A type of motif similarity evidence that is used in an automatic assertion.
motif similarity evidence used in automatic assertion
A type of match to InterPro member signature evidence that is used in an automatic assertion.
match to InterPro member signature evidence used in automatic assertion
A type of match to InterPro member signature evidence that is used in a manual assertion.
match to InterPro member signature evidence used in manual assertion
A type of targeting sequence prediction that is used in an automatic assertion.
targeting sequence prediction evidence used in automatic assertion
A type of targeting sequence prediction that is used in a manual assertion.
targeting sequence prediction evidence used in manual assertion
A type of transmembrane domain prediction that is used in an automatic assertion.
transmembrane domain prediction evidence used in automatic assertion
A type of transmembrane domain prediction that is used in a manual assertion.
transmembrane domain prediction evidence used in manual assertion
A type of sequence orthology evidence that is used in an automatic assertion.
sequence orthology evidence used in automatic assertion
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins.
Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara
Automatic transfer of experimentally verified manual GO annotation data to fungal orthologs using Ensembl Compara
A type of sequence orthology evidence that is used in a manual assertion.
sequence orthology evidence used in manual assertion
A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate.
ELISA is sometimes used in the study of transcriptional regulation to identify a produced protein, especially secreted protein.
enzyme-linked immunoabsorbent assay evidence
A type of direct assay evidence in which cells or particles are characterized by passing them through a light source and monitoring the resultant light scatter or fluorochrome excitation.
A type of experimental evidence that is used in a manual assertion.
experimental evidence used in manual assertion
A type of expression pattern evidence that is used in a manual assertion.
expression evidence used in manual assertion
This general 'array experiment' term should not be used - replace with the specific type of array (e.g. ECO:0000273, ECO:0000276, ECO:0000285, etc.)
array experiment evidence used in manual assertion
A type of Affymetrix GeneChip evidence that is used in a manual assertion.
Affymetrix GeneChip evidence used in manual assertion
A type of cDNA to DNA expression microarray evidence that is used in a manual assertion.
cDNA to DNA expression microarray evidence used in manual assertion
A type of differential methylation hybridization evidence that is used in a manual assertion.
CpG island microarray evidence used in manual assertion
differential methylation hybridization evidence used in manual assertion
A type of expression microarray evidence that is used in a manual assertion.
expression microarray evidence used in manual assertion
A type of cRNA to DNA expression microarray evidence that is used in a manual assertion.
genomic microarray evidence used in manual assertion
cRNA to DNA expression microarray evidence used in manual assertion
A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
Nimblegen array evidence used in manual assertion
A type of array-based sequence capture evidence that is used in a manual assertion.
oligonucleotide microarray evidence used in manual assertion
array-based sequence capture evidence used in manual assertion
A type of Western blot assay that is used in a manual assertion.
western blot evidence used in manual assertion
A type of protein expression level analysis that is used in a manual assertion.
protein expression level evidence used in manual assertion
A type of expression library screen evidence that is used in a manual assertion.
expression library screen evidence used in manual assertion
A type of heterologous protein expression analysis that is used in a manual assertion.
heterologous protein expression evidence used in manual assertion
A type of protein expression spatial pattern analysis that is used in a manual assertion.
spatial pattern of protein expression evidence used in manual assertion
A type of protein expression analysis that is used in a manual assertion.
protein expression evidence used in manual assertion
A type of DNA to cDNA expression microarray evidence that is used in a manual assertion.
DNA to cDNA expression microarray evidence used in manual assertion
A type of differential hybridization experiment that is used in a manual assertion.
differential hybridization evidence used in manual assertion
A type of RNA protection assay that is used in a manual assertion.
RNA protection assay evidence used in manual assertion
A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
spatial pattern of transcript expression evidence used in manual assertion
A type of subtractive hybridization experiment that is used in a manual assertion.
subtractive hybridization evidence used in manual assertion
A type of transcript expression evidence that is used in a manual assertion.
transcript expression evidence used in manual assertion
A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
Morpholino oligonucleotides modify gene expression by blocking access of other molecules to specific, approximately 25-base-long regions of the base-pairing surfaces of ribonucleic acid (RNA). To achieve this anti-sense knockdown technique, delivery of the morpholino can be achieved via microinjection, electroporation, or another method.
A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
SELEX begins with the synthesis of a large oligonucleotide library, either single-stranded DNA or RNA, which consists of random fixed-length sequences flanked by constant 5' and 3' ends that serve as primers. The library is exposed to a target ligand, typically a protein or small organic compound. Unbound sequences are removed, typically with affinity chromatography. Bound sequences are eluted and the nucleic acid is extracted, followed by PCR amplification (RNA is first reverse transcribed). PCR product is converted to single stranded (DNA) or transcribed (RNA). Oligonucleotides are bound to the ligand again and the process is repeated with increasing elution stringency. After several rounds of the process, recovered oligonucleotides are sequenced and analyzed to reveal the binding specificity of the protein.
systematic evolution of ligands by exponential amplification evidence
systematic evolution of ligands by exponential enrichment
A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
Bacterial one-hybrid assay is a method for screening a library of candidate proteins (prey plasmid) for the ability to bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to reporter genes (bait plasmid). Transformation of a bacterial host with two different plasmids is required: One is designed to express the "bait". The other plasmid contains a "prey" which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes.
A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
differential gene expression evidence from RNA-seq experiment
Total RNA is isolated from cells and mRNA is purified by targeting the 3' polyadenylated (poly(A)) tail with poly(T) oligos covalently attached to a substrate. Next, cDNA fragments are generated either by hydrolysis of RNA into 200-300 base oligonucleotides, preceded by reverse transcription, or by reverse transcription initiated by random primers. The cDNA second strand is synthesized, fragments are adapter ligated and high-throughput sequencing is performed by Roche 454, Illumina, ABI-SOLiD, or another HT sequencing technology. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
A type of transcriptional activation assay evidence that is based on transcriptional activation of a green fluorescent protein (GFP) reporter gene.
This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of green fluorescent protein".
green fluorescent protein transcript localization evidence
A type of transcriptional activation assay evidence that is based on transcriptional activation of a LacZ reporter gene.
This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of LacZ protein".
A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
In the embryos of some organisms, inhibition of cytokinesis blocks neither the cell cycle nor the unfolding of the developmental program. As such, embryonic morphology can be frozen, allowing analysis of the developmental fate of each cell present at the time of cleavage arrest.
A type of cleavage arrested development that arises after treatment with cytochalasin.
Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments.
A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript".
green fluorescent protein immunolocalization evidence
A type of immunolocalization evidence that was generated using LacZ protein as a marker.
LacZ protein immunolocalization evidence
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript".
beta-galactosidase protein immunolocalization evidence
A type of author statement that is used in a manual assertion.
author statement used in manual assertion
A type of non-traceable author statement that is used in a manual assertion.
non-traceable author statement used in manual assertion
A type of traceable author statement that is used in a manual assertion.
traceable author statement used in manual assertion
A type of curator inference that is used in a manual assertion.
curator inference used in manual assertion
A type of inference from background scientific knowledge that is used in a manual assertion.
inference from background scientific knowledge used in manual assertion
A type of no biological data found that is used in a manual assertion.
no biological data found used in manual assertion
A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
First, a characteristic of the most recent common ancestor (MRCA) is inferred from experimental evidence in descendants; this is followed by inferring a characteristic of a descendant of the MRCA. This type of evidence can be used in support of both positive and "not" GO annotations.
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system.
Complementary DNA (cDNA) is synthesized from microgram quantities of mRNA using first-strand cDNA primer (oligo dT12-18) and reverse transcriptase in the presence of trehalose and sorbitol, followed by selection of full-length cDNA with biotinylated cap-trapper. Linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI, which creates a two base overhang. After amplification, sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
cap analysis of gene expression evidence
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching.
NanoCAGE captures the 5' ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5' full length cDNAs is extended upon hybridization of the riboguanosine-tailed template switching oligonucleotides to these extra cytosines. In semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers, which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template switching, semisuppressive PCR, and EcoP151 cleavage, 25-bp tags are ligated to bar code-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. NanoCAGE requires as little as 10 nanograms of total RNA.
nano-cap analysis of gene expression evidence
A type of evidence that is based on work performed by a person or group prior to a use by a different person or group.
A type of imported information that is used in a manual assertion.
imported information used in manual assertion
A type of imported information that is used in an automatic assertion.
imported information used in automatic assertion
A type of direct assay evidence that is used in a manual assertion.
direct assay evidence used in manual assertion
A type of mutant phenotype evidence that is used in a manual assertion.
mutant phenotype evidence used in manual assertion
A type of genetic interaction experiment evidence that is used in a manual assertion.
genetic interaction evidence used in manual assertion
A type of genomic context evidence that is used in a manual assertion.
genomic context evidence used in manual assertion
A type of biological aspect of ancestor evidence that is used in a manual assertion.
inferred from biological aspect of ancestor
biological aspect of ancestor evidence used in manual assertion
A type of biological aspect of descendant evidence that is used in a manual assertion.
inferred from biological aspect of descendant
biological aspect of descendant evidence used in manual assertion
A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
phylogenetic determination of loss of key residues evidence used in manual assertion
A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
rapid divergence from ancestral sequence evidence used in manual assertion
Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
imported manually asserted information used in automatic assertion
Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.
Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.
A type of imported information used in automatic assertion that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
imported automatically asserted information used in automatic assertion
Gene Ontology annotation based on automatic assignment of UniProtKB keywords in UniProtKB/TrEMBL entries.
Gene Ontology annotation based on the automatic assignment of UniProtKB Subcellular Location terms in UniProtKB/TrEMBL entries.
A type of direct assay evidence in which an image is created and analyzed.
A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase.
A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript.
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child.
whole transcript splice pattern evidence
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript.
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child.
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion.
whole transcript splice pattern evidence used in manual assertion
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion.
coding sequence splice pattern evidence used in manual assertion
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion.
coding sequence splice pattern evidence used in automatic assertion
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion.
whole transcript splice pattern evidence used in automatic assertion
A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
Electrophoretic mobility is a function of both the length and charge of a protein. The protein sample is linearized with sodium dodecyl sulfate (SDS), an anionic detergent. Typically, polypeptides bound with SDS possess an even distribution of charge per unit mass, and subsequent fractionation is by size.
sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence
A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined.
An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system.
A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
Two examples of substance quantification assay are (i) measuring how much of a radiolabelled compound is taken up by a cell and (ii) measuring how much of a substrate is turned over by a given enzyme.
A type of cell proliferation assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed usually by means of a fluorescent marker and flow cytometric analysis.
A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field.
Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch.
A type of gel electrophoresis evidence in which large DNA molecules are separated on agarose gel by alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous.
pulsed-field gel electrophoresis evidence
A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide.
The first dimension gel is intentionally run at low voltage in low percentage agarose to separate DNA molecules in proportion to their mass. The second dimension is run at high voltage in a gel of higher agarose concentration in the presence of ethidium bromide so that the mobility of a non-linear molecule is drastically influenced by its shape.
two-dimensional agarose gel electrophoresis evidence
A type of experimental evidence in which retention of an introduced plasmid is determined when a mitotically stable plasmid (or minichromosome) is introduced into cells, which are grown without selection for several generations.
minichromosome maintenance assay evidence
Loss per generation is determined by comparing colony numbers on selective and non-selective media.
A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
specific protein inhibition by antibody evidence
A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
RNA-seq alignment intron location evidence is used by NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq). Exon-exon boundaries (or intron locations) of a RefSeq transcript, as determined by aligning the transcript to a reference chromosome, are compared to intron locations supported by RNAseq data.
Support of intron position by RNA-seq alignment evidence
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
Full support entails that all exon pairs represented in the transcript are supported. For example, for a transcript containing five exons, if liver RNA-seq reads support all four introns but brain RNA-seq supports only three introns, then the liver data fully support the transcript exons whereas the brain data do not.
Full support of intron position by RNA-seq alignment evidence
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript.
Partial support can occur in two ways. First, one or more exon-exon pair (intron) is not supported by any RNA-seq sample included in the analysis. Second, no single RNA-seq sample provides support for all exon-exon pairs (introns) represented in a transcript, but all represented exons are supported by at least one sample.
Partial support of intron position by RNA-seq alignment evidence
single exon transcript confirmation via alignment evidence
A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
Support of intron position by RNA-seq alignment evidence used in manual assertion
A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
Support of intron position by RNA-seq alignment evidence used in automatic assertion
A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
Full support of intron position by RNA-seq alignment evidence used in automatic assertion
A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
Full support of intron position by RNA-seq alignment evidence used in manual assertion
A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
Partial support of intron position by RNA-seq alignment evidence used in automatic assertion
A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
Partial support of intron position by RNA-seq alignment evidence used in manual assertion
A type of evidence that is used in an manual assertion.
A type of physical interaction evidence that is used in a manual assertion.
physical interaction evidence used in manual assertion
A type of gene neighbors evidence that is used in a manual assertion.
gene neighbors evidence used in manual assertion
A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
Example of use: "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor." PMID: 7013637. Northcutt RG. (1981) Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci.
A type of transcript expression evidence resulting from a microarray analysis with the use of the Gene Set Enrichment Analysis (GSEA) method or the Fisher's-Exact (FE) method to assess the differential expression.
differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact)
A type of transcript expression evidence resulting from the use of the Gene Set Enrichment Analysis (GSEA) method or Fisher's-Exact (FE) method to assess an RNA-seq dataset for differential gene expression.
differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact)
biological target-disease association via drug
A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
Inference is the process of deriving logical conclusions from premises known or assumed to be true, or alternatively, arriving at conclusions via some non-logical means of observation of patterns of facts, which can result in identifying new meanings and contexts for understanding. Given the evidence provided by a set of premises, deductive reasoning involves drawing conclusions that necessarily follow, i.e. are certain, whereas inductive reasoning generates conclusions that are likely to be, but are not necessarily, true.
A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is computationally derived.
evidence based on computational logical inference
A type of evidence based on computational logical inference that is used in automatic assertion.
evidence based on computational logical inference used in automatic assertion
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
evidence based on logical inference from manual annotation used in automatic assertion
A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
evidence based on logical inference from automatic annotation used in automatic assertion
A type of evidence that is used in an automatic assertion.
Gene Ontology annotation based on Enzyme Commission mapping.
Gene Ontology annotation based on Swiss-Prot keyword mapping.
Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.
A type of cell proliferation assay evidence resulting from the growth of cells in a micro-environment that mimics real tissue and establishes physiological cell-cell and cell-substrate interactions that regulate proliferation and differentiation.
A type of cell-based assay evidence resulting from labeling cells with [3H]arachidonic acid and subsequently determining the release of the arachidonic acid by the cells.
[3H]arachidonic acid release assay evidence
A type of DNA synthesis cell proliferation assay evidence resulting from the measurement of cell proliferation rate by determining the incorporation of [3H]-thymidine into cellular nucleic acids.
[3H]-thymidine incorporation assay evidence
A type of cytotoxicity assay evidence resulting from the measurement of the amount of radioactive 51Cr released in the supernatant of a sample of 51Cr pre-labeled cells via cytolysis by effector cells (cytotoxic T-cells).
A type of apoptotic assay evidence resulting from the use of 7-aminoactinomycin D (7-AAD) to distinguish viable, apoptotic, and dead cells, using the fact that permeability of the cell membrane, and fluorescence intensity, is low in early apoptotic cells and high in late apoptotic and dead cells.
A type of cell-based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells.
A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host.
A type of cell viability assay evidence resulting from the continuous measurement of fluorescence intensity from the viable cells, where a cell permeable compound, resazurin (the active ingredient of alamarBlue), is reduced to fluorescent resorufin.
A type of anatomical perturbation evidence where an organ or tissue is transplanted from one individual to another of the same species with a different genotype.
allograft transplantation experiment evidence
A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules.
A type of apoptotic assay evidence resulting from the addition and subsequent binding of Annexin V to phosphatidylserine in cells to detect if they are viable, apoptotic, or necrotic.
A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning.
A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies.
A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets.
A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the number of cells that migrate from the upper compartment of a chamber (separated by a micro-porous membrane) to the lower compartment, in which chemotactic agents are present.
A type of nucleotide analog incorporation evidence resulting from the incorporation of bromodeoxyuridine (BrdU) as a thymidine analog into nuclear DNA, resulting in a label that can be tracked using antibody probes.
cell proliferation marker detection assay evidence
5-bromo-2'-deoxyuridine incorporation assay evidence
bromodeoxyuridine incorporation assay evidence
A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis.
A type of cell-based assay evidence resulting from the quantification of a sample of cells.
A type of cell-based assay evidence resulting from the quantification of cell permeability.
A type of staining evidence resulting from monitoring division by the use of carboxyfluorescein diacetate succinimidyl ester (CFSE) to label intracellular molecules with carboxyfluorescein; when a labeled cell divides, the number of carboxyfluorescein-tagged molecules is split.
carboxyfluorescein diacetate succinimidyl ester staining evidence
A type of protein detection assay evidence resulting from a complex (a chemiluminescent compound, protein and a steroidal hapten) utilized as a labeled antigen, which emits light when treated with hydrogen peroxide and copper acetate at a high pH.
chemiluminescence-linked immunoassay evidence
A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product.
A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions.
A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location.
A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish.
A type of physical interaction evidence resulting from the separation of a mixture of molecules under the influence of a force such as artificial gravity, where molecules sedimenting together are assumed to interact.
A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration.
A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal.
A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation.
A type of experimental phenotypic evidence resulting from a constitutively active mutant (CAM), resulting in mutant proteins that remain active in the absence of upstream signals.
A type of protein binding evidence resulting from the identification of two interacting proteins (that exist in close proximity) by linking through covalent bonds followed by identification
A type of structure determination evidence resulting from the use of a narrow beam of x-rays to identify molecular structures by creating a diffraction pattern.
A type of histochemistry evidence resulting from localizing chemical components of cells and organelles on histological sections.
A type of apoptotic assay evidence resulting from the identification of an accumulation of cytochrome C in the cytoplasm after its release from the mitochondria, an early event in apoptosis.
A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence.
4',6-diamidino-2-phenylindole staining evidence
A type of experimental phenotypic evidence resulting from a mutation in which there is a removal of one or more contiguous nucleotides.
A type of apoptotic assay evidence resulting from the visualization via gel electrophoresis of the fragmented DNA (DNA ladder) which is the result of apoptotic DNA fragmentation.
A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments.
A type of experimental phenotypic evidence resulting from the analysis of a mutated gene producing mutant polypeptides that disrupt the activity of the wild-type genes.
A type of Edman degradation evidence that is used in a manual assertion.
Edman degradation evidence used in manual assertion
A type of protein detection assay evidence resulting from labeling a termonal amino acid residue and cleaving it from a peptide by sequentially removing one residue at a time from the amino end of the peptide, without disrupting the bonds.
A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters.
A type of physical interaction evidence resulting from a mixture of two molecules passed through a nitrocellulose filter, where one may be immobilized on the filter, and if the immobilized molecule is capable of binding to the other, it will be retained on the filter as well.
A type of expression pattern evidence and in situ hybridization evidence resulting from the use of fluorescent probes to detect complementary sequences of nucleic acids.
fluorescence in situ hybridization evidence
A type of physical interaction evidence resulting from the measurement of the proximity of two fluorophores, where the energy from an excited molecular fluorophore to another fluorophore can only occur within ~10nm.
fluorescence resonance energy transfer evidence
A type of chromatography evidence resulting from the exclusion of proteins based on molecular size by filtration through a porous matrix (swollen gel), from which larger molecules are excluded.
A type of histology evidence resulting from the identification of chemical components in cells and tissues.
A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues.
A type of chromatography evidence resulting from the separation of molecules in a solute by forcing the solvent containing the sample through a column packed with nonporous particles at high pressure.
high-performance liquid chromatography evidence
A type of protein detection assay evidence resulting from the use of antibodies linked to coloring agents to localize structures in cell cultures to identify proteins.
A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample.
A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections.
A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation.
A type of acetylation assay evidence used in an in vitro experiment.
A type of cleavage assay evidence used in an in vitro experiment.
A type of deubiquitination assay evidence used in an in vitro experiment.
in vitro deubiquitination assay evidence
A type of deacetylation assay evidence used in an in vitro experiment.
A type of defarnesylation assay evidence used in an in vitro experiment.
A type of demethylation assay evidence used in an in vitro experiment.
A type of desumoylation assay evidence used in an in vitro experiment.
A type of farnesylation assay evidence used in an in vitro experiment.
A type of methylation assay evidence used in an in vitro experiment.
A type of palmitoylation assay evidence used in an in vitro experiment.
A type of phosphatase assay evidence used in an in vitro experiment.
A type of protein kinase assay evidence used in an in vitro experiment.
A type of polyADP-ribosylation assay evidence used in an in vitro experiment.
in vitro polyADP-ribosylation assay evidence
A type of sumoylation assay evidence used in an in vitro experiment.
A type of transcription assay evidence used in an in vitro experiment.
A type of translation assay evidence used in an in vitro experiment.
A type of ubiquitination assay evidenceused in an in vitro experiment.
A type of acetylation assay evidence used in an in vivo experiment.
A type of cleavage assay evidence used in an in vivo experiment.
A type of deacetylation assay evidence used in an in vivo experiment.
A type of defarnesylation assay evidence used in an in vivo experiment.
A type of demethylation assay evidence used in an in vivo experiment.
A type of deubiquitination assay evidence used in an in vivo experiment.
A type of desumoylation assay evidence used in an in vivo experiment.
A type of farnesylation assay evidence used in an in vivo experiment.
A type of methylation assay evidence used in an in vivo experiment.
A type of palmitoylation assay evidence used in an in vivo experiment.
A type of phosphatase assay evidence used in an in vivo experiment.
A type of protein kinase assay evidence used in an in vivo experiment.
A type of sumoylation assay evidence used in an in vivo experiment.
A type of transcription assay evidence used in an in vivo experiment.
A type of translation assay evidence used in an in vivo experiment.
A type of ubiquitination assay evidence used in an in vivo experiment.
A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence.
A type of genetic transformation evidence resulting from the removal of a particular gene (or genes), disrupting the function and allowing for functional analysis.
A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid.
A type of physical interaction evidence resulting from the analysis of protein-protein interactions by use of a luciferase enzyme fused to a particular protein (or proteins), which are coexpressed with epitope-tagged partners in mammalian cells.
luminescence-based mammalian interactome mapping assay evidence
A type of hybrid interaction evidence resulting from the analysis of proteins of interest attached to two portions of the transcriptional activator, and in interaction bring the two portions together to increase expression of the reporter gene.
A type of spectrometry evidence resulting from identifying the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles.
A type of imaging assay evidence resulting from the use of technology to visualize and provide information about the body to diagnose, treat, or monitor medical conditions.
A type of direct assay evidence where a microscope was used to view a sample.
A type of cell-based assay evidence to measure cell motility in which a "wound" is created in a cell monolayer and the migration of the cells is captured by imaging at regular intervals during cell migration to close the wound.
A type of apoptotic assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) in combination with phenazine methyl sulfate (PMS) as an intermediate electron acceptor reagent to produce a soluble formazan dye in viable cells.
A type of apoptotic assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to its insoluble purple formazan dye in viable cells and measures cell viability / metabolic activity.
3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
A type of protein detection assay evidence resulting from determination of analyte concentration by fluorescent bead sets attached to an antibody (to a specific analyte) with a fluorescent reporter dye label attached to a second antibody (to a specific analyte).
multiplex bead-based immunoassay evidence
A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits.
A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death.
A type of structure determination evidence resulting from the use of an MRI to provide chemical information about tissue metabolites.
nuclear magnetic resonance spectroscopy evidence
A type of RNA detection assay evidence resulting from the detection and quantitation of specific RNAs (from a sample of total cellular RNA) that are bound by antisense RNA or DNA probes and therefore protected from nucleases.
A type of DNA synthesis cell proliferation assay evidence resulting from the analysis and measurement of the incorporation of fluorescently labeled nucleotide analog(s) into the DNA.
nucleotide analog incorporation assay evidence
A type of protein binding evidence resulting from the panning of a phage library where the individual phage displayed a different peptide or protein by fusion to coat proteins on the capsid.
A type of protein assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis.
phosphopeptide affinity enrichment evidence
A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample.
A type of protein assay evidence resulting from protein-bound peptides detected from a collection of peptides arranged as an array and incubated with the partner protein in order to map protein-protein interaction sites.
A type of experimental phenotypic evidence resulting from the change in a single nucleotide.
A type of staining evidence resulting from the binding and labeling of DNA (during apoptosis, when there is a loss of nuclear DNA content) with propidium iodide (PI) to identify the cells from which it originated.
A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore.
A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged.
A type of protein detection assay evidence resulting from proteins immobilized to prepare protein chips, or microwells, that can be utilized to determine presence of proteins, monitor differential expression profiles, and/or study protein interactions.
A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein.
A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes.
A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant.
A type of protein detection assay evidence resulting from the use of a radioligand to measure the binding of a substance to a specific antibody or other receptor system.
A type of direct assay evidence from the analysis of the real-time interaction between an analyte in solution and its interactant linked to the surface of the resonant mirror.
A type of DNA detection assay evidence resulting from homologous DNA fragments digested by restriction enzymes, and the resulting restriction fragments are sorted by length to illustrate differences.
A type of spectrometry evidence resulting from the evaluation of a molecule in a fluid by its ability to alter the transmission of light at specific wavelengths.
A type of physical interaction evidence based on real-time, rapid plasmon generation on the interface between a planar surface and vacuum that measures changes in refractive index close to the sensor surface when an analyte and its immobilized ligand bind to observe and characterize molecular interaction.
Plasmons are generated by an incident light beam.
A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin.
syngeneic transplantation experiment evidence
A type of enzyme assay evidence resulting from the analysis of tumor necrosis factor (TNF)-a converting enzyme (TACE), which releases a soluble TNF-a from the membrane-bound precursor protein.
Tumor necrosis factor - alpha converting enzyme activity assay
A type of cytochemistry evidence resulting from the analysis of section(s) of a paraffin block containing embedded tissues cores arranged in an array pattern.
A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification.
A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate.
tryptic phosphopeptide mapping assay evidence
A type of apoptotic assay evidence resulting from the visualization of DNA fragmentation by detection of exposed 3'-OH ends, localized by terminal deoxynucleotidyl transferase (TdT) which then catalyzes the addition of labeled dUTPs.
TdT-mediated dUTP-biotin nick end labeling assay
terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence
A type of direct assay evidence resulting from the analysis of a urine sample.
A type of cell proliferation assay evidence resulting from the assessment of metabolic activity from a water-soluble tetrazolium salt WST-1 being reduced outside the cell (by reacting with mitochondrial succinate-tetrazolium reductase) to form a formazan dye.
metabolic cell proliferation assay evidence
A type of anatomical perturbation evidence where live cells, tissues, or organs from a non-human animal source are transplanted, implanted or infused into a human recipient.
A type of 3D cell culture evidence that is used in a manual assertion.
3D cell culture evidence used in manual assertion
A type of 51Cr release assay evidence that is used in a manual assertion.
51Cr release assay evidence used in manual assertion
A type of 7-aminoactinomycin staining evidence that is used in a manual assertion.
7-aminoactinomycin staining evidence used in manual assertion
A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion.
[3H]-thymidine incorporation assay evidence used in manual assertion
A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion.
[3H]arachidonic acid release assay evidence used in manual assertion
A type of adhesion assay evidence that is used in a manual assertion.
adhesion assay evidence used in manual assertion
A type of adoptive cell transfer evidence that is used in a manual assertion.
adoptive cell transfer evidence used in manual assertion
A type of alamarBlue assay evidence that is used in a manual assertion.
alamarBlue assay evidence used in manual assertion
A type of allograft transplantation experiment evidence that is used in a manual assertion.
allograft transplantation experiment evidence used in manual assertion
A type of anion-exchange chromatography evidence that is used in a manual assertion.
anion-exchange chromatography evidence used in manual assertion
A type of annexin-V staining evidence that is used in a manual assertion.
annexin-V staining evidence used in manual assertion
A type of behavioral assay evidence used that is used in a manual assertion.
behavioral assay evidence used in manual assertion
A type of blocking monoclonal antibody evidence that is used in a manual assertion.
blocking monoclonal antibody evidence used in manual assertion
A type of blocking peptide evidence that is used in a manual assertion.
blocking peptide evidence used in manual assertion
A type of blocking polyclonal antibody evidence tthat is used in a manual assertion.
blocking polyclonal antibody evidence used in manual assertion
A type of blood test evidence that is used in a manual assertion.
blood test evidence used in manual assertion
A type of Boyden chamber assay evidence that is used in a manual assertion.
Boyden chamber assay evidence used in manual assertion
A type of bromodeoxyuridine incorporation assay evidence used in manual assertion.
bromodeoxyuridine incorporation assay evidence used in manual assertion
A type of caspase assay evidence that is used in a manual assertion.
caspase assay evidence used in manual assertion
A type of cell counting evidence that is used in a manual assertion.
cell counting evidence used in manual assertion
A type of cell permeability assay evidence that is used in a manual assertion.
cell permeability assay evidence used in manual assertion
A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion.
carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion
A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion.
chemiluminescence-linked immunoassay evidence used in manual assertion
A type of chimeric protein evidence that is used in a manual assertion.
chimeric protein evidence used in manual assertion
A type of co-electrophoresis evidence that is used in a manual assertion.
co-electrophoresis evidence used in manual assertion
A type of co-localization evidence that is used in a manual assertion.
co-localization evidence used in manual assertion
A type of co-sedimentation assay evidence that is used in a manual assertion.
co-sedimentation assay evidence used in manual assertion
A type of colony counting evidence that is used in a manual assertion.
colony counting evidence used in manual assertion
A type of comet assay evidence that is used in a manual assertion.
comet assay evidence used in manual assertion
A type of conditional knockin evidence that is used in a manual assertion.
conditional knockin evidence used in manual assertion
A type of conditional knockout evidence that is used in a manual assertion.
conditional knockout evidence used in manual assertion
A type of constitutively active mutant evidence that is used a in manual assertion.
constitutively active mutant evidence used in manual assertion
A type of cross-linking evidence that is used in a manual assertion.
cross-linking evidence used in manual assertion
A type of crystallography evidence that is used in a manual assertion.
crystallography evidence used in manual assertion
A type of cytochemistry evidence that is used in a manual assertion.
cytochemistry evidence used in manual assertion
A type of cytochrome C release assay evidence that is used in a manual assertion.
cytochrome C release assay evidence used in manual assertion
A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion.
4',6-diamidino-2-phenylindole staining evidence used in manual assertion
A type of deletion evidence that is used in a manual assertion.
deletion mutation evidence used in manual assertion
A type of DNA laddering assay evidence that is used in a manual assertion.
DNA laddering assay evidence used in manual assertion
A type of RNA dot blot assay evidence that is used in a manual assertion.
RNA dot blot assay evidence used in manual assertion
A type of dominant-negative mutant evidence that is used in a manual assertion.
dominant-negative mutant evidence used in manual assertion
A type of eTag assay evidence that is used in a manual assertion.
eTag assay evidence used in manual assertion
A type of filter binding assay evidence that is used in a manual assertion.
filter binding assay evidence used in manual assertion
A type of fluorescence in situ hybridization evidence that is used in a manual assertion.
fluorescence in situ hybridization evidence used in manual assertion
A type of fluorescence resonance energy transfer evidence that is used in a manual assertion.
fluorescence resonance energy transfer evidence used in manual assertion
A type of gel-filtration evidence that is used in a manual assertion.
gel-filtration evidence used in manual assertion
A type of histochemistry evidence that is used in a manual assertion.
histochemistry evidence used in manual assertion
A type of immunocytochemistry evidence that is used in a manual assertion.
immunocytochemistry evidence used in manual assertion
A type of histology evidence that is used in a manual assertion.
histology evidence used in manual assertion
A type of immunodepletion evidence that is used in a manual assertion.
immunodepletion evidence used in manual assertion
A type of immunohistochemistry evidence that is used in a manual assertion.
immunohistochemistry evidence used in manual assertion
A type of in vitro acetylation assay evidence that is used in a manual assertion.
in vitro acetylation assay evidence used in manual assertion
A type of in vitro cleavage assay evidence that is used in a manual assertion.
in vitro cleavage assay evidence used in manual assertion
A type of in vitro deacetylation assay evidence that is used in a manual assertion.
in vitro deacetylation assay evidence used in manual assertion
A type of in vitro defarnesylation assay evidence that is used in a manual assertion.
in vitro defarnesylation assay evidence used in manual assertion
A type of in vitro demethylation assay evidence that is used in a manual assertion.
in vitro demethylation assay evidence used in manual assertion
A type of in vitro desumoylation assay evidence that is used in a manual assertion.
in vitro desumoylation assay evidence used in manual assertion
A type of in vitro deubiquitination assay evidence that is used in a manual assertion.
in vitro deubiquitination assay evidence used in manual assertion
A type of in vitro farnesylation assay evidence that is used in a manual assertion.
in vitro farnesylation assay evidence used in manual assertion
A type of in vitro methylation assay evidence that is used in a manual assertion.
in vitro methylation assay evidence used in manual assertion
A type of in vitro palmitoylation assay evidence that is used in a manual assertion.
in vitro palmitoylation assay evidence used in manual assertion
A type of in vitro phosphatase assay evidence that is used in a manual assertion.
in vitro phosphatase assay evidence used in manual assertion
A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion.
in vitro polyADP-ribosylation assay evidence used in manual assertion
A type of in vitro protein kinase assay evidence that is used in a manual assertion.
in vitro protein kinase assay evidence used in manual assertion
A type of in vitro sumoylation assay evidence that is used in a manual assertion.
in vitro sumoylation assay evidence used in manual assertion
A type of in vitro transcription assay evidence that is used in a manual assertion.
in vitro transcription assay evidence used in manual assertion
A type of in vitro translation assay evidence that is used in a manual assertion.
in vitro translation assay evidence used in manual assertion
A type of in vitro ubiquitination assay evidence that is used in a manual assertion.
in vitro ubiquitination assay evidence used in manual assertion
A type of in vivo acetylation assay evidence that is used in manual assertion.
in vivo acetylation assay evidence used in manual assertion
A type of in vivo cleavage assay evidence that is used in a manual assertion.
in vivo cleavage assay evidence used in manual assertion
A type of in vivo deacetylation assay evidence that is used in a manual assertion.
in vivo deacetylation assay evidence used in manual assertion
A type of in vivo defarnesylation assay evidence that is used in a manual assertion.
in vivo defarnesylation assay evidence used in manual assertion
A type of in vivo demethylation assay evidence that is used in a manual assertion.
in vivo demethylation assay evidence used in manual assertion
A type of in vivo desumoylation assay evidence that is used in a manual assertion.
in vivo desumoylation assay evidence used in manual assertion
A type of in vivo deubiquitination assay evidence that is used in a manual assertion.
in vivo deubiquitination assay evidence used in manual assertion
A type of in vivo farnesylation assay evidence that is used in a manual assertion.
in vivo farnesylation assay evidence used in manual assertion
A type of in vivo methylation assay evidence that is used in a manual assertion.
in vivo methylation assay evidence used in manual assertion
A type of in vivo palmitoylation assay evidence that is used in a manual assertion.
in vivo palmitoylation assay evidence used in manual assertion
A type of in vivo phosphatase assay evidence that is used in a manual assertion.
in vivo phosphatase assay evidence used in manual assertion
A type of in vivo protein kinase assay evidence that is used in a manual assertion.
in vivo protein kinase assay evidence used in manual assertion
A type of in vivo sumoylation assay evidence that is used in a manual assertion.
in vivo sumoylation assay evidence used in manual assertion
A type of in vivo transcription assay evidence that is used in a manual assertion.
in vivo transcription assay evidence used in manual assertion
A type of in vivo translation assay evidence that is used in a manual assertion.
in vivo translation assay evidence used in manual assertion
A type of in vivo ubiquitination assay evidence that is used in a manual assertion.
in vivo ubiquitination assay evidence used in manual assertion
A type of induced mutation evidence that is used in a manual assertion.
induced mutation evidence used in manual assertion
A type of knockin evidence that is used in a manual assertion.
knockin evidence used in manual assertion
A type of knockout evidence that is used in a manual assertion.
knockout evidence used in manual assertion
A type of lipid binding assay evidence that is used in a manual assertion.
lipid binding assay evidence used in manual assertion
A type of LUMIER assay evidence that is used in a manual assertion.
luminescence-based mammalian interactome mapping assay evidence used in manual assertion
A type of macroscopy evidence that is used in a manual assertion.
macroscopy evidence used in manual assertion
A type of mammalian 2-hybrid assay evidence that is used in a manual assertion.
mammalian 2-hybrid assay evidence used in manual assertion
A type of mass spectrometry evidence that is used in a manual assertion.
mass spectrometry evidence used in manual assertion
A type of medical imaging evidence that is used in a manual assertion.
medical imaging evidence used in manual assertion
A type of microscopy evidence that is used in a manual assertion.
microscopy evidence used in manual assertion
A type of motility wound healing assay evidence that is used in a manual assertion.
wound healing assay evidence used in manual assertion
motility wound healing assay evidence used in manual assertion
A type of MTS assay evidence that is used in a manual assertion.
MTS assay evidence used in manual assertion
A type of MTT assay evidence that is used in a manual assertion.
MTT assay evidence used in manual assertion
A type of multiplex bead-based immunoassay evidence that is used in a manual assertion.
multiplex bead-based immunoassay evidence used in manual assertion
A type of natural variation mutant evidence that is used in a manual assertion.
natural variation mutant evidence used in manual assertion
A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion.
nuclear magnetic resonance spectroscopy evidence used in manual assertion
A type of nuclear fragmentation evidence that is used in a manual assertion.
nuclear fragmentation evidence used in manual assertion
A type of nuclease protection assay evidence that is used in a manual assertion.
nuclease protection assay evidence used in manual assertion
A type of nucleotide analog incorporation assay evidence that is used in a manual assertion.
nucleotide analog incorporation assay evidence used in manual assertion
A type of phage display evidence that is used in a manual assertion.
phage display evidence used in manual assertion
A type of phosphoamino acid analysis evidence that is used in a manual assertion.
phosphoamino acid analysis evidence used in manual assertion
A type of peptide affinity enrichment evidence that is used in a manual assertion.
peptide affinity enrichment evidence used in manual assertion
A type of peptide array evidence that is used in a manual assertion.
peptide array evidence used in manual assertion
A type of physical examination evidence that is used in a manual assertion.
physical examination evidence used in manual assertion
A type of point mutation evidence that is used in a manual assertion.
point mutation evidence used in manual assertion
A type of propidium iodide staining evidence that is used in a manual assertion.
propidium iodide staining evidence used in manual assertion
A type of protein detection by fluorescence evidence that is used in a manual assertion.
fluorescence evidence used in manual assertion
A type of protein dot blot assay evidence that is used in a manual assertion.
protein dot blot assay evidence used in manual assertion
A type of protein microarray evidence that is used in a manual assertion.
protein microarray evidence used in manual assertion
A type of protein sequencing assay evidence that is used in a manual assertion.
protein sequencing assay evidence used in manual assertion
A type of quantitative mass spectrometry evidence that is used in a manual assertion.
quantitative mass spectrometry evidence used in manual assertion
A type of radioisotope assay evidence that is used in a manual assertion.
radioisotope assay evidence used in manual assertion
A type of radioimmunoassay evidence that is used in a manual assertion.
radioimmunoassay evidence used in manual assertion
A type of imaging assay evidence that is used in a manual assertion.
imaging assay evidence used in manual assertion
A type of restriction fragment detection evidence that is used in a manual assertion.
restriction fragment detection evidence used in manual assertion
A type of spectrophotometry evidence that is used in a manual assertion.
spectrophotometry evidence used in manual assertion
A type of syngeneic transplantation experiment evidence that is used in a manual assertion.
syngeneic transplantation experiment evidence used in manual assertion
A type of xenotransplantation experiment evidence that is used in a manual assertion.
xenotransplantation experiment evidence used in manual assertion
A type of WST-1 assay evidence that is used in a manual assertion.
WST-1 assay evidence used in manual assertion
A type of urine test evidence that is used in a manual assertion.
urine test evidence used in manual assertion
A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence assay evidence that is used in a manual assertion.
TdT-mediated dUTP-biotin nick end labeling assay evidence
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion
A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion.
tryptic phosphopeptide mapping assay evidence used in manual assertion
A type of transgenic organism evidence that is used in a manual assertion.
transgenic organism evidence used in manual assertion
A type of tissue microarray evidence that is used in a manual assertion.
tissue microarray evidence used in manual assertion
A type of TACE activity assay evidence that is used in a manual assertion.
Tumor necrosis factor - alpha converting enzyme activity assay evidence
TACE activity assay evidence used in manual assertion
A type of surface plasmon resonance evidence that is used in a manual assertion.
surface plasmon resonance evidence used in manual assertion
A type of restriction landmark genome scanning evidence that is used in a manual assertion.
restriction landmark genomic scanning evidence used in manual assertion
A type of resonant mirror biosensor evidence that is used in a manual assertion.
resonant mirror biosensor evidence used in manual assertion
A type of high-performance liquid chromatography evidence that is used in a manual assertion.
high-performance liquid chromatography evidence used in manual assertion
A type of ectopic expression evidence that is used in a manual assertion.
ectopic expression evidence used in manual assertion
A type of direct assay evidence where acetylated residues are detected in a protein.
A type of direct assay evidence where the cleavage of a protein into protein fragments by a protease is detected.
A type of direct assay evidence where the removal of acetyl groups are detected in a protein.
A type of direct assay evidence where the removal of farnesyl groups from a protein is detected.
A type of direct assay evidence where the removal of methyl groups from a substrate (RNA/DNA or protein) is detected.
A type of direct assay evidence where the removal of sumo groups from a protein is detected.
A type of direct assay evidence where the removal of ubiquitin groups from a protein is detected.
A type of direct assay evidence where farnesylated residues in proteins are detected.
A type of direct assay evidence where methylated residues of a substarte (RNA/DNA or protein) are detected.
A type of direct assay evidence where palmitoylated residues in a protein are detected.
A type of direct assay evidence where the removal of phosphatase groups from a protein is detected.
A type of direct assay evidence where ADP-ribosylated residues in proteins are detected.
A type of direct assay evidence where phosphorylated residues in proteins are detected.
A type of direct assay evidence where sumoylated residues on a protein are detected.
A type of direct assay evidence where de novo protein synthesis is detected.
A type of direct assay evidence where ubiquitinated residues on a protein are detected.
A type of direct assay evidence where biological cell development, i.e. an increase in cell mass and size are measured.
A type of direct assay evidence resulting from the study of cells.
A type of protein-binding evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
A type of cell-based assay evidence in which living cells are stained with a vital stain, i.e. dye that can be used on living cells without causing cell death.
A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing.
Secreted Embryonic Alkaline Phosphatase reporter assay
Alkaline phosphatase reporter assay produces a hybrid protein with alkaline phosphatase activity following transportation across the cellular membrane.
alkaline phosphatase reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium.
The assay is often performed using a plasmid borne construction on a lacZ strain.
beta-galactosidase reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic.
The amount of acetylated chloramphenicol is directly proportional to the amount of CAT enzyme present.
chloramphenicol acetyltransferase reporter gene assay evidence
A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection.
beta-glucuronidase reporter gene assay evidence
A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence.
A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data.
chromatin immunoprecipitation- exonuclease evidence
A type of electrophoretic mobility shift that is used in a manual assertion.
electrophoretic mobility shift assay evidence used in manual assertion
A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion.
reverse transcription polymerase chain reaction evidence used in manual assertion
A type of chromatography evidence where immobilized promoter DNA is labeled and bound to a matrix through which a protein mixture is poured and then eluted to purify specific DNA binding proteins.
Biotinylation is commonly used for labeling and beads are commonly used as the matrix. Bound protein will remain attached to the beads. Results can be detected through gel electrophoresis and then sequenced by mass-spectrometry. This technique can be used to demonstrate binding of a purified protein, or to purify the binding protein from crude extract or protein mixture.
A type of nucleic acid binding evidence where proteins that have been bound to DNA protect a binding site from enzymatic cleavage with DNAse, thereby detecting protein-DNA interactions.
In DNAse footingprinting amplified DNA combined with TF and DNAse is electrophoresed for fragment comparison with a non-TF control sample. TF-bound fragments do not appear in the gel. Such fragments can be isolated, purified, and sequenced. This technique is often used to identify the binding motif of a TF resolving the protected region to 50-100 bp which can be further examined for TF-binding sites.
A type of fluorescence evidence based on rapid and quantitative analysis of diverse molecular interactions, enzyme activities, and nucleic acid hybridization which uses a fluorophore to measure the binding constants and kinetics of reactions that cause a change in the rotational time of the molecules.
The degree of polarization of a fluorophore is inversely related to its molecular rotation. When the fluorophore is bound to a small molecule, the rate at which it tumbles can decrease significantly from when it is bound tightly to a large protein. If the fluorophore is attached to the larger protein in a binding pair, the difference in polarization between bound and unbound states will be smaller and less accurate. The degree of binding is calculated by using the difference in anisotropy of the partially bound, free, and fully bound states measured by titrating the two binding partners. Fluorescence polarixation assays are homogeneous.
A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing.
The reported sequences should always be verified for presence in the genome sequence.
genomic systematic evolution of ligands by exponential amplification evidence
A type of nuclear magnetic resonance spectroscopy evidence based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum.
Chemical shifts in the spectrum indicating binding can be detected from analysis of a protein spectrum in the presence or absence of its cognate DNA binding site.
heteronuclear single quantum coherence spectroscopy evidence
A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA.
Methidiumpropyl-EDTA Fe(II) footprinting
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
A type of nucleic acid binding evidence where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts.
copper-phenanthroline footprinting evidence
A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light.
green fluorescent protein promoter fusion
green fluorescent protein reporter gene assay evidence
A type of protein binding evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions.
The recombinant protein can also be eluted following the pull-down and analyzed further with qPCR or sequencing.
glutathione S-transferase pull-down assay evidence
A type of nucleic acid binding evidence used to identify protein-binding sites on the DNA molecule where DNA that has been bound to protein is digested with hydroxyl radical produced by reduction of hydrogen peroxide with iron (II), followed by separating the cleavage products on a denaturing electrophoresis gel.
A type of transcript expression evidence used to determine expression levels of mRNA where a radiolabeled synthetic oligonucleotide primer is annealed to mRNA at the transcription start site of a gene and the mRNA is extended with reverse transcriptase producing cDNA which is electrophoresed on a polyacrylamide gel and autoradiographed, and the band size is proportional to the initial RNA.
The most commonly used radiolabel is 32P.
A type of polymerase chain reaction evidence where a mRNA primer is used for RT-PCR and terminal deoxynucleotidyl transferase (TdT) is used to add identical nucleotides to the 3' end of the cDNA after which PCR with a different primer and TdT-oligomer are performed in the other sense to obtain the full length sequence of a RNA transcript.
RACE PCR is frequently used to verify transcription start sites relevant to the function of transcription factor binding sites such as repression.
rapid amplification of cDNA ends polymerase chain reaction evidence
Use ECO:0000295 (RNA-seq evidence) in place of this term.
A type of knockout evidence based on the survival of an organism in a particular environment where a gene for an enzyme or regulator is knocked out and results are used as a natural reporter.
A type of crystallography evidence where a purified sample at high concentration is crystallised and the crystals are exposed to an x ray beam to obtain three dimensional molecular structure of proteins and biological macromolecules.
X-ray crystallography can be used for a crystal used to probe at the tridimensional structure of proteins. In some cases, it is possible to co-crystallize the protein bound to its DNA binding site, providing detail on the particular arrangement of the two components.
A type of affinity evidence used to identify DNA binding sites in eukaryotes where Escherichia coli DNA adenine methyltransferase (Dam) is fused to a transcription factor, co-factor, chromatin-associated protein, or nuclear-associated protein, followed by a methyl-dependent PCR to localize methyltransferase in the region of the binding site.
The methylation tag is detected with methylation-sensitive restriction enzymes, DpnI and DpnII.
DNA adenine methyltransferase identification evidence
A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction.
When ITC is used to study TF, the temperature of two identical cells containing a known concentration of TF is monitored. After the ligand is added to the cells in precisely measured aliquots, the temperature difference in each cell is observed to determine target binding. This value can be used to compute the energetics of the reaction and hence, binding affinity of the TF for the DNA fragment. The thermodynamic profile that is measured includes the values of binding constant (K(a)), stoichiometry (n), and the enthalpy of binding (DeltaH(b)).
isothermal titration calorimetry evidence
A type of nucleic acid binding evidence where DNA is non-specifically fragmented with ultraviolet light while protein-bound regions are protected from UV damage and strand breakage patterns are analyzed by PAGE and sequenced to detect protein-DNA contacts.
A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel.
premethylation interference footprinting evidence
A type of inference from background scientific knowledge used in manual assertion where a visual inspection of promoter region is made to identify putative binding sites.
A type of reporter gene assay evidence used to locate and isolate Fur sites where a plasmid library is created and cloned into a cell line with a ferric uptake regulator (Fur)-repressed reporter and the Fur protein is titrated away from its binding site on the reporter, after which the cell is isolated and plasmid extracted for further sequence analysis.
ferric uptake regulator titration assay evidence
A type of cell-based assay evidence resulting from analyzing the ability of cells to survive or live successfully.
A type of cell-based assay evidence resulting from the measurement of the number of cells, which is a reflection of the balance between cell division and cell loss through cell differentiation or cell death.
A type of cell proliferation assay evidence resulting from the measure of DNA synthesis in the presece of a label.
DNA synthesis cell proliferation assay evidence
A type of cell viability assay evidence resulting from the analysis of ATP concentration (by measuring light intensity) when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions and molecular oxygen.
A type of cell-based assay evidence resulting from the ability of an agent to induce cellular necrosis or apoptosis and the subsequent analysis of cell death mechanism.
Use children of ECO:0001565 (cell-based assay evidence) in place of this term.
A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image.
A type of cell-based assay evidence resulting from the evaluation of chemotactic ability (i.e. the movement, or lack of movement, in response to a chemical stimulus) of prokaryotic or eukaryotic cells.
A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA.
A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures.
A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image.
A type of cell-based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis.
A type of polyADP-ribosylation assay evidence used in an in vivo experiment.
in vivo polyADP-ribosylation assay evidence
A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion.
in vivo polyADP-ribosylation assay evidence used in manual assertion
A type of direct assay evidence derived by studying an organ, tissues, or cells taken from an organism and studied in an external environment with the minimum alteration of natural conditions.
A type of gel electrophoresis evidence that involves one dimension electrophoresis where biomolecules are electrophoresed on a low percentage polyacrylamide gel to be separated in proportion to their mass or isoelectric point, followed by high voltage electrophoresis on a higher percentage gel in the presence of ethidium bromide to alter non-linear molecular shape.
Two-dimensional polyacrylamide gel electrophoresis is commonly employed to establish a proteome for an organism and demonstrate expression changes.
two-dimensional polyacrylamide gel electrophoresis evidence
A type of experimental evidence resulting from the use of a spectrometer.
A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression.
Regular expression is a computational tool used for determining whether a given genome contains a DNA region resembling a transcription factor binding motif. For example A/T=W indicates A or T may be present in a column of the alignment. (PMID: 20708667).
regular expression motif search evidence
A type of point mutation evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another.
A type of point mutation evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon.
A type of point mutation evidence resulting from the change of a DNA nucleotide that does not cause any changes in the amino acid sequence.
A type of experimental phenotypic evidence resulting from a mutation in which there is an insertion of an additional nucleotide, or nucleotides.
A type of experimental phenotypic evidence resulting from a mutation in which inserted nucleotide(s) have a sequence identical to, or derived from, adjacent nucleotides.
A type of experimental phenotypic evidence resulting from any mutation that causes a shift in bases and therefore changes the code for the amino acids.
A type of experimental phenotypic evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated.
A type of experimental phenotypic evidence resulting from a mutation in which there is a change in nucleotides at a splice site
A type of experimental phenotypic evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome
A type of experimental evidence resulting from the detection and analysis of molecular markers.
A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins.
A type of molecule detection assay evidence resulting from the detection of specific RNAs.
A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA.
A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels.
Differences in the optical path lengths between a surface layer and a buried silica layer can be measured very precisely allowing optical height information to be converted to accumulated mass on the surface. For the purpose of TF-binding site identification, IRIS is coupled with DNA-arrays with immobilized potential binding regions exposed to the protein of interest and eluted. Protein-bound fragments exhibit changes in reflectance that can be used to gauge binding quantitatively.
interferometric reflectance imaging sensor evidence
A type of nuclease protection assay evidence where RNA is hybridized with complementary DNA probes and exposed to S1 nuclease for unbound RNA degradation after which the intact RNA is run on a gel for probe size determination and RNA identification to detect and map specific RNAs in a complex mixture of total cellular RNA.
A type of DNA detection assay evidence resulting from evaluation of the relative abundance of target sequences hybridizing to DNA samples that are immobilized on a nitrocellulose or nylon membrane.
A type of DNA dot blot assay evidence that is used in a manual assertion.
DNA dot blot assay evidence used in manual assertion
A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology.
MALDI-TOF MS is commonly used for protein identification in constructing a proteome where protein fingerprints obtained by microbial cells are compared with a database of reference spectra by means of various algorithms integrated in systems recently made commercially available.
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion.
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
A type of experimental phenotypic evidence based on target-specified mutagenesis for the characterization of various gene and protein interactions, structures, and functions where oligonucleotide primers are used to alter a nucleotide sequence.
Site-directed mutagenesis is often performed in tandem with EMSA. It is often implemented only in conserved motif positions or serially through all positions of a site.
A type of experimental phenotypic evidence where radiation or a DNA-damaging agent in vivo, or PCR with degenerate primers in vitro are used for non-targeted mutagenesis.
Random mutagenesis is not often used in TF-binding site determination; however, it is sometimes used to investigate the effect of mutations in TF binding domains in conjunction with expression assays. Random mutations can also be introduced via chemicals, error-prone PCR (EP-PCR), degenerate oligonucleotides-Pfu(DOP), UV irradiation, mutator strains, nucleotide analogs, or DNA recombination.
A type of random mutagenesis evidence that is used in a manual assertion.
random mutagenesis evidence used in manual assertion
A type of multiple sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs.
Relationship type between sequences (e.g. orthologs from multiple genomes or co-expressed genes in the same genome) is not necessarily assumed. The local multiple sequence alignment is typically ungapped. A common application of motif discovery is to infer the binding motif of a given transcription factor (TF). This can be based on the results of a whole-genome expression analysis, assuming that co-expressed genes are co-regulated by the same TF, from peaks in ChIP-seq experiments with the TF, or from the comparative genomics analysis of the promoter regions of orthologs.
A type of motif similarity evidence where the motif is represented by a consensus sequence which incorporates the most frequent nucleotide at each position acting as a generic representative for the sequences in the alignment, and is compared to the genetic sequence for a perfect or imperfect match.
This technique is used to identify transcription factor binding sites by searching a bacterial genome for DNA regions resembling a given TF-binding motif. PMID: 17085555.
A type of motif discovery evidence based on a set of algorithms that infer motifs in non-coding DNA sequences from the conservation of functional regulatory sites through evolution at a higher rate than their local surroundings for the identification of an evolutionary 'footprint'.
The name derives to experimental footprinting techniques where transcription factor (TF)-binding sites are identified by sequencing the region of DNA protected from biochemical agents by the bound TF. This technique is used to identify or verify transcription factor-binding motifs, most commonly in the Eukaryota (PMID: 11997340).
A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes.
This technique is used to predict transcription factor binding sites in gene promoter regions by identifying conserved DNA regions across multiple genomes. PMID: 22305460. Orthology is a typical comparative criterion used.
comparative genomics motif search evidence
A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences.
Machine learning algorithms include, but are not limited to artificial neural networks, random-forest, k-means clustering, hidden Markov models. This suite of methods can be used to identify or verify transcription factor-binding sites in genomic sequences (PMID: 15703297).
machine learning prediction of motif instance evidence
A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis.
This technique is used to predict transcription factor binding sites in gene promoter regions by using a position weight matrix approach. (PMID: 15604457).
position-specific scoring matrix motif search evidence
A type of reporter gene assay evidence based on the fusion of the xylE gene to a specific promoter for the expression of catechol 2,3-dioxygenase that converts the colorless catechol substrate to yellow 2-hydroxymuconic semialdehyde for identification of the expression of a particular gene.
computationally derived logical inference
computationally derived logical inference used in automatic assertion
computationally derived logical inference from automatic assertion used in automatic assertion
computationally derived logical inference from manual assertion used in automatic assertion
A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion.
Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof.
biological system reconstruction evidence by experimental evidence from single species used in manual assertion
A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion.
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. The evidence may originate from a combination of several experiments.
biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion
A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion.
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments.
biological system reconstruction evidence based on orthology evidence used in manual assertion
A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by orthology from an existing experimentally supported model to a process, pathway or complex in another species.
biological system reconstruction evidence based on orthology evidence
A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion.
biological system reconstruction evidence based on paralogy evidence used in manual assertion
A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion.
Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components.
biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion
A type of biological system reconstruction based solely on background scientific knowledge of that biological system.
The available knowledge is usually a combination of partial or weak experimental evidence where either some components are missing or no physical interaction evidence can be found but the system is inferred by similarity to related systems in taxonomically-disparate organisms with experimental evidence. Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components.
biological system reconstruction evidence based on inference from background scientific knowledge
A type of biological system reconstruction where the evidence is inferred by homology based on conservation of sequence, function, and composition from an existing experimentally supported model to a process, pathway, or complex.
Inference may be based on paralogy and/or orthology of the genome-encoded components and is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments in the same or another species.
biological system reconstruction evidence based on homology evidence
A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by paralogy from an existing experimentally supported model to a process, pathway, or complex in the same species.
biological system reconstruction evidence based on paralogy evidence
A type of biological system reconstruction evidence that uses experimental evidence as support.
biological system reconstruction evidence by experimental evidence
A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment.
biological system reconstruction evidence by experimental evidence from mixed species
A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species.
biological system reconstruction evidence by experimental evidence from single species
A type of sequence alignment evidence where two sequences are aligned to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).
A type of sequence alignment evidence where three or more biological sequences (protein or nucleic acid) of similar length are aligned to infer homology and the evolutionary relationships between the sequences studied.
A type of multiple sequence alignment evidence that is used in a manual assertion.
multiple sequence alignment evidence used in manual assertion
A type of multiple sequence alignment evidence that is used in an automatic assertion.
multiple sequence alignment evidence used in automatic assertion
A type of motif discovery evidence that is used in a manual assertion.
motif discovery evidence used in manual assertion
A type of motif discovery evidence that is used in an automatic assertion.
motif discovery evidence used in automatic assertion
A type of pairwise sequence alignment evidence that is used in a manual assertion.
pairwise sequence alignment evidence used in manual assertion
A type of pairwise sequence alignment evidence that is used in an automatic evidence.
pairwise sequence alignment evidence used in automatic assertion
A type of protein kinase assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated kinase substrate.
A type of voltage clamp recording evidence that involves recording trace of the current (pA) going through the analyzed ion channels determined from voltage clamp current recording.
A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane.
A type of electrophysiology assay evidence that involves the measurement of the current that persists after the fast and slow inactivation of the analyzed channels.
steady state inactivation curve evidence
A type of electrophysiology assay evidence in which the amount of current remaining after a series of depolarization at different frequencies described as the normalized current related to the time course.
A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell.
current clamp voltage recording evidence
current clamp voltage recording protocol
A type of voltage clamp recording evidence that involves direct measurement of ionic current across a membrane while controlling the membrane potential by maintaining the voltage.
whole-cell voltage clamp recording evidence
whole-cell voltage clamp recording protocol
A type of patch-clamp recording evidence that involves isolation of a patch of membrane electrically from the external solution and to record current flowing into the patch and this is achieved by pressing a fire-polished glass pipette, which has been filled with a suitable electrolyte solution, against the surface of a cell and applying light suction.
cell-attached patch-clamp recording evidence
cell-attached single-channel recording evidence
cell-attached single-channel recording protocol
A type of patch-clamp recording evidence that involves study of individual ion channels by gently pulling the patch of membrane away from the cell, and the patch remains attached to the pipette with its cytoplasmic surface exposed to the bathing solution.
cell-detached inside-out patch-clamp recording evidence
cell-detached inside-out single-channel recording evidence
cell-detached inside-out single-channel recording protocol
A type of patch-clamp reocrding evidence that involves ion channel analysis by incorporating the ion channels into liposomes suitable for patch-clamping which allows isolation and study of a specific population of channels into that bilayer membrane.
reconstituted bilayer single-channel patch recording evidence
reconstituted bilayer single-channel patch recording protocol
A type of electrophysiology assay evidence that involves recording membrane potential by controlling the membrane voltage and measuring the transmembrane current required to maintain that voltage.
voltage clamp current recording evidence
voltage clamp current recording protocol
A type of electrophysiology assay evidence that involves recording the electrical activity of the brain by means of electrodes placed on the surface of the head.
electroencephalography recording evidence
electroencephalography recording protocol
A type of microscopy evidence where the images are taken with a higher resolution than the diffraction limit that help in studying nanoscopic sub-cellular structures.
A type of immunogold labelling evidence that is used in a manual assertion.
immunogold labelling evidence used in manual assertion
A type of flow cytometry evidence that is used in a manual assertion.
flow cytometry evidence used in manual assertion
A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion.
ELISA evidence|enzyme-linked immunosorbent assay evidence
enzyme-linked immunoabsorbent assay evidence used in manual assertion
A type of patch-clamp recording evidence where a part of cellular membrane is detached from the cell and whose external face is exposed to the extracellular medium which allows isolating and studying a single or at least a small number of channels into that fragment (patch).
cell-detached outside-out patch-clamp evidence
cell-detached outside-out single-channel recording evidence
A type of voltage clamp recording evidence that involves inserting the oocyte in a chamber that separates the surface into 3 regions where the top portion of the oocyte membrane is the region that is clamped from which currents are actually recorded while the bottom portion is the region of the oocyte that is cut-open, making it possible to inject current intracellularly through a low resistance pathway.
cut-open oocyte voltage clamp recording evidence
A type of voltage clamp recording evidence where recording is done on a fragment of the cell membrane (attached to or detached from the cell) using a large tip diameter pipette that allows isolating and studying a small number of channels into that fragment (patch).
macropatch voltage clamp recording evidence
A type of mass spectrometry evidence where mass-to-charge ratio (m/z) of gas-phase ions is measured which is used to identify and quantify molecules in complex solutions within the framework of high throughput studies.
There are significant differences in data analysis and data evaluation if to compare a HTP mass-spec and a regular mass-spec. The regular mass spec method is quite a reliable technique for identifying a protein molecular weight and analysing its post-modifications, other mass-spec applications might require the additional quality controls and more stringent data evaluation. More complex sample mixture is processed, more quality questions should be addressed, such as a sample contamination and sensitivity of the mass spectrometer while using HTP mass-spec. For HTP mass-spec, the analysis of the small data sets allows to manually assign the spectra to proteins or peptides, but for large data sets only the statistical tools can be used instead.
high throughput mass spectrometry evidence
A type of high throughput mass spectrometry evidence that is used in a manual assertion.
high throughput mass spectrometry evidence used in manual assertion
A type of microscopy evidence where sharp images are taken by excluding most of the light from the specimen that is not from the microscope's focal plane, thus allowing better contrast and less haze, which makes it possible to build three-dimensional reconstructions of a volume of the specimen by assembling a series of thin slices taken along the vertical axis.
A type of microscopy evidence where imaging of a thin cell or a tissue specimen is performed by full aperture emission of light gathered by the microscope's objective, which maximizes the recorded signal and simultaneously minimizes the required exposure times.
A type confocal microscopy evidence that is used in a manual assertion.
confocal microscopy evidence used in manual assertion
A type of wide-field microscopy evidence that is used in a manual assertion.
wide-field microscopy evidence used in manual assertion
A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles.
immunogold labelling electron microscopy assay evidence
A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion.
immunogold labelling electron microscopy assay evidence used in manual assertion
A type of direct assay evidence that involves the use of antibodies to detect biomolecules.
A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody.
immunoperoxidase immunolocalization evidence
A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion.
immunoperoxidase immunolocalization evidence used in manual assertion
A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody.
Immunoperoxidase labelling electron microscopy
immunoperoxidase immunolocalization electron microscopy evidence
A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion.
immunoperoxidase labelling electron microscopy evidence
immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion
A type of wide-field microscopy evidence where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter.
The optical filter is used to select the wavelength of excitation light. The detection camera is typically a CCD camera. Both topographical and dynamic information of a sample are obtained.
wide-field fluorescence microscopy evidence
A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
immunofluorescence wide-field microscopy evidence
A type of confocal microscopy evidence where light passes through immunofluorescent-stained tissue sections or cells and then the emitted light passes through the dichroic mirror and is focused onto the pinhole for subsequent detection.
This allows visualization of sub cellular distribution of biomolecules of interest.
immunofluorescence confocal microscopy evidence
A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion.
immunofluorescence confocal microscopy evidence used in manual assertion
A type of protein expression level evidence where the level of expression of a protein is determined in a cell or tissue extract by western blot technique.
protein expression level evidence based on western blot
A type of mass spectrometry evidence where one or more protein analyses are performed.
A type of cell proliferation assay evidence where the investigated organism or a potential antagonist is inoculated so as to grow along the diameter line of the agar medium in a Petri dish, then, potentially susceptible microbes (usually bacteria) are streaked perpendicularly to the growth line and inhibition of growth of a test microbe in the vicinity of that line suggests that the antagonist secretes one or more diffusible antibiotics.
A type of zone of inhibition evidence where sensitivity/resistance to an antimicrobial agent is tested by impregnating small filter disks with a known concentration of antimicrobial agent which is then placed on a Mueller-Hinton agar plate inoculated with the test organism.
A type of experimental evidence where a foreign genetic material is introduced into the cell for study of gene function and regulation and protein function.
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by observing the rotational behavior of the cells tethered to a coverslip by their flagella.
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by measuring chemotaxis in response to sudden concentration changes from one uniform spatial environment to another.
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the rate of accumulation of the cells into a capillary.
To determine the presence of negative chemotaxis, a repellent is added to the organismal suspension (but not in the capillary) and the organisms that fled into the capillary are measured.
To determine the presence of positive chemotaxis, an attractant is placed in the capillary and the presence of positive chemotaxis is determined based on the amount of organism that accumulated in the capillary.
A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion.
biological system reconstruction evidence based on homology evidence used in manual assertion
A type of direct assay evidence used in manual assertion where phenotype or disease association is made with the gene because of involvement in the molecular mechanism of disease or involvement in a pathway known to contribute to a disease.
inference from experimental data evidence
A type of mutant phenotype evidence used in manual assertion where variations or changes, such as mutations or abnormal levels of the product(s) of a single gene of interest, including non-mutational changes such as inhibition with antibodies or other inhibitors are determined.
Changes can include any gene mutation/knockout, over-expression or ectopic expression of wild-type or mutant genes, anti-sense experiments, RNAi experiments, specific protein inhibitors.
inference from phenotype manipulation evidence
A type of natural variation mutant evidence used in manual assertion where alleles are directly linked to phenotype and Mendelian diseases as a result of various experiments.
inferred by association of genotype from phenotype
Used for 1) polymorphism or segregation of genetic markers (SNPs, mutations, RFLPs, microsatellites); 2) polymorphism or segregation of physical markers (FISH, centromeric or heterochromatic regions, chromosomal banding patterns); 3) detection of polymorphisms in inbred stock.
inference by association of genotype from phenotype
A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion.
two-dimensional polyacrylamide gel electrophoresis evidence used in manual assertion
A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion.
alkaline phosphatase reporter gene assay evidence used in manual assertion
A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion.
beta-galactosidase reporter gene assay evidence used in manual assertion
A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion.
chloramphenicol acetyltransferase reporter gene assay evidence used in manual assertion
A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion.
chromatin immunoprecipitation-chip evidence used in automatic assertion
A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion.
chromatin immunoprecipitation- exonuclease evidence used in automatic assertion
A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion.
chromatin immunoprecipitation-PCR evidence used in manual assertion
A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion.
chromatin immunoprecipitation-seq evidence used in automatic assertion
A type of comparative genomics motif search evidence that is used in a manual assertion.
comparative genomics motif search evidence used in manual assertion
A type of comparative genomics motif search evidence that is used in an automatic assertion.
comparative genomics motif search evidence used in automatic assertion
A type of consensus search evidence that is used in a manual assertion.
consensus search evidence used in manual assertion
A type of consensus search evidence that is used in an automatic assertion.
consensus search evidence used in automatic assertion
A type of copper-phenanthroline footprinting evidence that is used in a manual assertion.
1,10-phenanthroline-copper footprinting evidence
copper-phenanthroline footprinting evidence used in manual assertion
A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion.
DNA adenine methyltransferase identification evidence used in manual assertion
A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion.
DNA adenine methyltransferase identification evidence used in automatic assertion
A type of DNA affinity chromatography evidence that is used in a manual assertion.
DNA affinity chromatography evidence used in manual assertion
A type of cDNA to DNA expression microarray evidence that is used in an automatic assertion.
cDNA to DNA expression microarray evidence used in automatic assertion
A type of DNAse footprinting evidence that is used in a manual assertion.
DNAse footprinting evidence used in manual assertion
A type of fluorescence anisotropy evidence that is used in a manual assertion.
fluorescence anisotropy evidence used in manual assertion
A type of ferric uptake regulator titration assay evidence that is used in a manual assertion.
ferric uptake regulator titration assay evidence used in manual assertion
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion.
genomic systematic evolution of ligands by exponential amplification evidence used in manual assertion
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion.
genomic systematic evolution of ligands by exponential amplification evidence used in automatic assertion
A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion.
green fluorescent protein reporter gene assay evidence used in manual assertion
A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion.
green fluorescent protein reporter gene assay evidence used in automatic assertion
A type of cell growth regulation assay evidence that is used in a manual assertion.
cell growth regulation assay evidence used in manual assertion
A type of cell growth regulation assay evidence that is used in an automatic assertion.
cell growth regulation assay evidence used in automatic assertion
A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion.
glutathione S-transferase pull-down assay evidence used in manual assertion
A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion.
beta-glucuronidase reporter gene assay evidence used in manual assertion
A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion.
heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
A type of hydroxyl-radical footprinting evidence that is used in a manual assertion.
hydroxyl-radical footprinting evidence used in manual assertion
A type of immunoprecipitation evidence that is used in a manual assertion.
immunoprecipitation evidence used in manual assertion
A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion.
spectral reflectance imaging biosensor evidence
interferometric reflectance imaging sensor evidence used in manual assertion
A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion.
interferometric reflectance imaging sensor evidence used in automatic assertion
A type of isothermal titration calorimetry evidence that is used in a manual assertion.
isothermal titration calorimetry evidence used in manual assertion
A type of luciferase reporter gene assay evidence that is used in a manual assertion.
luciferase reporter gene assay evidence used in manual assertion
A type of machine learning prediction of motif instance evidence that is used in a manual assertion.
machine learning prediction of motif instance evidence used in manual assertion
A type of machine learning prediction of motif instance evidence that is used in an automatic assertion.
machine learning prediction of motif instance evidence used in automatic assertion
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion.
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in automatic assertion
A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion.
Methidiumpropyl-EDTA Fe(II) footprinting evidence
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in manual assertion
A type of northern assay evidence that is used in a manual assertion.
northern assay evidence used in manual assertion
A type of phylogenetic footprinting evidence that is used in a manual assertion.
phylogenetic footprinting evidence used in manual assertion
A type of phylogenetic footprinting evidence that is used in an automatic assertion.
phylogenetic footprinting evidence used in automatic assertion
A type of premethylation interference footprinting evidence that is used in a manual assertion.
premethylation interference footprinting evidence used in manual assertion
A type of primer extension assay evidence that is used in a manual assertion.
primer extension assay evidence used in manual assertion
A type of position-specific scoring matrix motif search evidence that is used in a manual assertion.
position-specific scoring matrix motif search evidence used in manual assertion
A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion.
position-specific scoring matrix motif search evidence used in automatic assertion
A type of quantitative polymerase chain reaction evidence that is used in a manual assertion.
quantitative polymerase chain reaction evidence used in manual assertion
A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion.
rapid amplification of cDNA ends polymerase chain reaction evidence used in manual assertion
A type of regular expression motif search evidence that is used in a manual assertion.
regular expression motif search evidence used in manual assertion
A type of regular expression motif search evidence that is used in an automatic assertion.
regular expression motif search evidence used in automatic assertion
Use ECO:0006068 (RNA-seq evidence used in manual assertion) in place of this term.
RNA sequencing assay evidence used in manual assertion
Use ECO:0006069 (RNA-seq evidence used in automatic assertion) in place of this term.
RNA sequencing assay evidence used in automatic assertion
A type of S1 nuclease protection assay evidence that is used in a manual assertion.
S1 nuclease protection assay evidence used in manual assertion
A type of site-directed mutagenesis evidence that is used in a manual assertion.
site-directed mutagenesis evidence used in manual assertion
A type of survival rate analysis evidence that is used in a manual assertion.
survival rate analysis evidence used in manual assertion
A type of ultraviolet light footprinting evidence that is used in a manual assertion.
ultraviolet light footprinting evidence used in manual assertion
A type of x-ray crystallography evidence that is used in a manual assertion.
x-ray crystallography evidence used in manual assertion
A type of x-ray crystallography evidence that is used in an automatic assertion.
x-ray crystallography evidence used in automatic assertion
A type of xylE reporter gene assay evidence that is used in a manual assertion.
xylE reporter gene assay evidence used in manual assertion
A type of experimental phenotypic evidence where a non-standard trait (e.g. natural competence) is assessed qualitatively (e.g. presence/absence) and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor.
ad-hoc qualitative phenotype observation evidence
A type of ad-hoc qualitative phenotype observation that is used in a manual assertion.
ad-hoc qualitative phenotype observation evidence used in manual assertion
A type of experimental phenotypic evidence where a quantifiable phenotypic trait (e.g. glucose intake) is assessed in a quantitative manner after induction of the regulatory mechanism and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor.
ad-hoc quantitative phenotype observation evidence
A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion.
ad-hoc quantitative phenotype observation evidence used in manual assertion
A direct assay evidence where the activity of a solution is determined by exposing an indicator culture or organism to a series of dilutions and determining the lowest concentration that elicits a biological response.
For chemicals, bacteriocins, or phage, the indicator culture is typically present in a soft-agar layer on top of nutrient agar and a small quantity of each dilution is spotted onto the soft agar overlay.
dilution assay evidence
A type of enzyme assay evidence that is used in a manual assertion.
enzyme assay evidence used in manual assertion
A type of cell transfection experiment evidence that is used in a manual assertion.
cell transfection experiment evidence used in manual assertion
A type of direct assay evidence where the motility of a cell or cells is determined.
A type of immunofluorescence evidence that is used in a manual assertion.
immunofluorescence evidence used in manual assertion
A type of yeast 2-hybrid evidence that is used in a manual assertion.
yeast 2-hybrid evidence used in manual assertion
A type of evidence derived from exploiting the CyaA (calmodulin-activated adenylate cyclase toxin) secreted by Bordatella pertussis to synthesize cAMP and alter cellular physiology in a host cell for various biological applications.
A type of Cya fusion reporter assay evidence that is used in a manual assertion.
Cya fusion reporter assay evidence used in manual assertion
A type of electron microscopy evidence that is used in a manual assertion.
electron microscopy evidence used in manual assertion
A type of super-resolution microscopy evidence that is used in a manual assertion.
super-resolution microscopy evidence used in manual assertion
A type of fractionation evidence that is used in a manual assertion.
fractionation evidence used in manual assertion
A type of electrophysiology assay evidence that is used in a manual assertion.
electrophysiology assay evidence used in manual assertion
A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion.
chromatin immunoprecipitation-chip evidence used in manual assertion
A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion.
chromatin immunoprecipitation- exonuclease evidence used in manual assertion
A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion.
chromatin immunoprecipitation-seq evidence used in manual assertion
A type of nucleic acid binding evidence in which RNA-binding proteins are identified through cross-linking RNA and proteins by UV light, capturing RNA-protein complexes on oligo(dT) beads, and finally identifying by mass spectrometry.
ultraviolet light cross-linking RNA binding evidence
A type of mRNA interactome capture evidence that is used in a manual assertion.
mRNA interactome capture evidence used in manual assertion
A type of electrophysiology assay evidence in which a glass micropipette is sealed to the surface of a cell membrane (patch) to study ion channels.
A type of patch-clamp recording evidence that is used in a manual assertion.
patch-clamp recording evidence used in manual assertion
A type of patch-clamp recording evidence in which a glass micropipette filled with a prepared solution is used to form a seal with the cell membrane followed by rupture of membrane to provide accurate and high resolution electrical property measurements of the whole cell.
whole-cell patch-clamp recording evidence
A type of whole-cell patch-clamp recording evidence that is used in a manual assertion.
whole-cell patch-clamp recording evidence used in manual assertion
A type of traceable author statement that is based on a publication about a clinical study.
traceable author statement from published clinical study
A type of traceable author statement from published clinical study that is used in a manual assertion.
Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used when evidence for an HPO annotation is information extracted from articles in the medical literature.
traceable author statement from published clinical study used in manual assertion
A type of curator inference that is based on the individual clinical experience of a clinician
inference based on individual clinical experience
A type of inference based on individual clinical experience that is used in a manual assertion.
Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used for annotating disorders with a limited amount of published data, and is accompanied by a reference to the individual or center performing the annotation.
inference based on individual clinical experience used in manual assertion
A type of cell proliferation assay evidence in which biofilm growth is monitored and detected from attachment to development.
A type of biofilm formation assay evidence that is used in a manual assertion.
biofilm formation assay evidence used in manual assertion
A type of biofilm formation assay evidence in which microtiter dishes or tubes are inoculated and incubated to promote biofilm formation, and then biofilms are detected by staining with crystal violet or safranin to observe phenotypes.
A type of microtiter plate biofilm assay evidence that is used in a manual assertion.
microtiter plate biofilm assay evidence used in manual assertion
A type of biofilm formation assay evidence in which biofilm formation is analyzed, without staining, over 4 to 48 hours by growth on a tilted multiwell plate.
Tilting of the plate positions the air-liquid interface on a clear portion to improve visability.
A type of air-liquid interface assay evidence that is used in a manual assertion.
air-liquid interface assay evidence used in manual assertion
A type of biofilm formation assay evidence in which a colony is grown on a semipermeable membrane on an agar plate. The plate serves to supply nutrients and the semipermeable membrane can be relocated to fresh plates.
The plates commonly contain different carbon sources or antibiotic treatments to observe properties of the cells.
A type of colony biofilm assay evidence that is used in a manual assertion.
colony biofilm assay evidence used in manual assertion
A type of biofilm formation assay evidence in which mature bacterial biofilms are grown in a multiwell plate that has a growth medium continually pumped through the wells while waste is continually pumped out.
A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion.
Kadouri drip-fed biofilm assay evidence used in manual assertion
A type of co-immunoprecipitation evidence that is used in a manual assertion.
co-immunoprecipitation evidence used in manual assertion
A type of immunolocalization evidence that is used in a manual assertion.
immunolocalization evidence used in manual assertion
A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators.
A type of optogenetic evidence that is used in a manual assertion.
optogenetic evidence used in manual assertion
A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor.
Examples include sensors for ion concentration and potential difference across a membrane.
A type of fluorescent sensor evidence that is used in a manual assertion.
fluorescent sensor evidence used in manual assertion
A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor.
genetically encoded fluorescent sensor evidence
A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion.
genetically encoded fluorescent sensor evidence used in manual assertion
A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors.
electrophysiology - optical assay evidence
Examples include genetically encoded sensors that detect potential difference across plasma membrane.
genetically encoded fluorescent electrophysiology assay evidence
A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion.
genetically encoded fluorescent electrophysiology assay evidence used in manual assertion
A type of genetically encoded fluorescent electrophysiology assay evidence that is based on direct, quantitative measurement of ion concentration using a genetically encoded fluorescent sensor.
Examples include the genetically encoded calcium indicator GCaMP.
genetically encoded fluorescent ion concentration sensor assay evidence
A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion.
genetically encoded fluorescent ion concentration sensor assay evidence used in manual assertion
A type of cell fractionation evidence that is used in a manual assertion.
cell fractionation evidence used in manual assertion
A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons.
A type of extracellular recording evidence that is used in a manual assertion.
extracellular recording evidence used in manual assertion
A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron.
single-unit extracellular recording evidence
A type of single-unit extracellular recording evidence that is used in a manual assertion.
single-unit extracellular recording evidence used in manual assertion
A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes.
local field potential recording evidence
A type of field potential recording evidence that is used in a manual assertion.
field potential recording evidence used in manual assertion
A type of genetic transformation evidence that is used in a manual assertion
genetic transformation evidence used in manual assertion
A type of anti-sense experiment evidence that is used in a manual assertion.
anti-sense experiment evidence used in manual assertion
A type of morpholino experiment evidence that is used in a manual assertion.
morpholino experiment evidence used in manual assertion
A type of RNAi evidence that is used in a manual assertion.
A type of experimental phenotypic evidence that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist.
A type of experimental phenotypic evidence used in a manual assertion that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist.
pharmacological assay evidence used in manual assertion
A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
Some relevant articles include: PMID: 23340846, doi:10.1038/nmeth0607-523
A type of evidence that is used in a manual assertion where data generation is automated with equipment to allow for assaying large numbers of samples or molecules in parallel.
inferred from high throughput experiment
high throughput evidence used in manual assertion
A type of evidence that is used in an automatic assertion where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
high throughput evidence used in automatic assertion
A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
HT methodologies may incorporate techniques from optics, chemistry, biology or image analysis (https://en.wikipedia.org/wiki/High_throughput_biology)
A type of high throughput evidence used in a manual assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
high throughput cell biology evidence used in manual assertion
A type of high throughput evidence used in an automatic assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
high throughput cell biology evidence used in automatic assertion
A type of wide-field fluorescence microscopy evidence used in a manual assertion where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
wide-field epifluorescence microscopy evidence
immunofluorescence wide-field microscopy evidence used in manual assertion
A type of wide-field microscopy evidence that is used in a manual assertion where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter.
wide-field fluorescence microscopy evidence used in manual assertion
A type of experimental phenotypic evidence that is used in a manual assertion where a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product.
over expression analysis evidence used in manual assertion
A type of cell-free assay evidence that is used in a manual assertion.
cell-free assay evidence used in manual assertion
in vitro cell based assay evidence used in manual assertion
A type of fluorescence evidence where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse.
FRAP is a fluorescence microscopy-based technique.
fluorescence recovery after photobleaching evidence
A type of fluorescence evidence that is used in a manual assertion where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse.
fluorescence recovery after photobleaching evidence used in manual assertion
A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
RNA sequencing|differential gene expression evidence from RNA-seq experiment
RNA-seq evidence used in manual assertion
A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
RNA-seq evidence used in automatic assertion
A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
immunolabelling electron microscopy evidence
immuno-labelling electron microscopy evidence
A type of electron microscopy evidence used in a manual assertion resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
immuno-labelling electron microscopy evidence used in manual assertion
A type of super-resolution microscopy evidence resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue.
immunofluorescence super resolution microscopy evidence
A type of super-resolution microscopy evidence used in a manual assertion resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue.
immunofluorescence super resolution microscopy evidence used in manual assertion
A type of physical interaction evidence that is used in manual assertion where a cellular component subunit is isolated as part of purification of its larger complex.
co-purification evidence used in manual assertion
A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities.
affinity evidence used in manual assertion
A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex.
protein binding evidence used in manual assertion
A type of affinity evidence that is used in manual assertion where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein.
hybrid interaction evidence used in manual assertion
A type of affinity evidence that is used in manual assertion resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
immunological assay evidence used in manual assertion
A type of hybrid interaction evidence that is used in manual assertion that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
yeast one-hybrid evidence used in manual assertion
A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein.
split-ubiquitin assay evidence used in manual assertion
A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes.
far-Western blotting evidence used in manual assertion
A type of affinity evidence that is used in a manual assertion that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound.
affinity chromatography evidence used in manual assertion
A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid.
nucleic acid binding evidence used in manual assertion
A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer.
ribohomopolymer binding assay evidence used in manual assertion
A type of protein binding evidence that is used in a manual assertion resulting from a metal ion binding to a protein at a specific binding site.
protein:ion binding evidence used in manual assertion
A type of nucleic acid binding evidence that is used in a manual assertion in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
Southwestern blot evidence used in manual assertion
A type of nucleic acid binding evidence that is used in a manual assertion in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
Northwestern blot evidence used in manual assertion
A type of evidence that is used in a manual assertion arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
systematic evolution of ligands by exponential amplification evidence used in manual assertion
A type of hybrid interaction evidence that is used in a manual assertion that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
bacterial one-hybrid evidence used in manual assertion
A type of oligonucleotide microarray evidence that is used in a manual assertion that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
protein-binding microarray evidence used in manual assertion
A type of genetic interaction evidence that is used in a manual assertion where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background.
functional complementation evidence used in manual assertion
A type of functional complementation evidence that is used in a manual assertion that is used in manual assertion resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
transgenic rescue experiment evidence used in manual assertion
A type of transient rescue experiment evidence that is used in a manual assertion.
transient rescue experiment evidence used in manual assertion
A type of genetic interaction evidence that is used in a manual assertion resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
suppressor/enhancer interaction evidence used in manual assertion
A type of genetic interaction evidence that is used in a manual assertion that is based on the phenotypic outcome of two mutations in unrelated genetic loci.
double mutant phenotype evidence used in manual assertion
A type of genetic interaction evidence that is used in a manual assertion that is based on the suppression of one allelic effect by an allele at another genetic locus.
epistatic interaction evidence used in manual assertion
A type of functional complementation evidence that is used in a manual assertion that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene.
functional complementation in heterologous system evidence used in manual assertion
A type of mutant phenotype evidence based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures.
temperature-sensitive mutant phenotype evidence
A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures.
temperature-sensitive mutant phenotype evidence used in manual assertion
A type of mutant phenotype evidence based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself.
A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself.
recessive mutant phenotype evidence used in manual assertion
A type of high throughput evidence derived from high throughput analysis of differences in alleles of a corresponding gene.
high throughput mutant phenotype evidence
A type of high throughput evidence that is used in a manual assertion derived from high throughput analysis of differences in alleles of a corresponding gene.
inferred from high throughput mutant phenotype
When using the HMP evidence code, the guidelines for IMP should be adhered to (http://geneontology.org/page/imp-inferred-mutant-phenotype)
high throughput mutant phenotype evidence used in manual assertion
A type of high throughput evidence derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products.
high throughput genetic interaction evidence
A type of high throughput evidence that is used in a manual assertion derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products.
inferred from high throughput genetic interaction
When using the HGI evidence code, the guidelines for IGI should be adhered to (http://geneontology.org/page/igi-inferred-genetic-interaction)
high throughput genetic interaction evidence used in manual assertion
A type of high throughput evidence derived from the high throughput direct measurement of some aspect of a biological feature.
A type of high throughput evidence that is used in a manual assertion derived from the high throughput direct measurement of some aspect of a biological feature.
inferred from high throughput direct assay
When using the HDA evidence code, the guidelines for IDA should be adhered to (http://geneontology.org/page/ida-inferred-direct-assay)
high throughput direct assay evidence used in manual assertion
A type of high throughput evidence derived from the high throughput characterization of gene expression.
high throughput expression pattern evidence
A type of high throughput evidence that is used in a manual assertion derived from the high throughput characterization of gene expression.
inferred from high throughput expression pattern
When using the HEP evidence code, the guidelines for EXP should be adhered to (http://geneontology.org/page/iep-inferred-expression-pattern)
high throughput expression pattern evidence used in manual assertion
A type of protein binding evidence in which radioactive ligands are used to measure receptor-ligand interactions, such as in determining selectivity for a particular ligand.
radioactive ligand binding assay evidence
radiometric ligand-binding assay evidence
A type of radioligand binding assay evidence that is used in a manual assertion.
radioligand binding assay evidence used in manual assertion
A type of inferential evidence resulting from a conclusion drawn by the author of the publication.
A type of combinatorial evidence in which the author draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments.
combinatorial evidence from author knowledge and experimental evidence
A type of combinatorial evidence in which the curator draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments.
combinatorial evidence from curator knowledge and experimental evidence
A type of combinatorial evidence from author knowledge and experimental evidence that is used in a manual assertion.
combinatorial evidence from author knowledge and experimental evidence used in manual assertion
A type of combinatorial evidence from curator knowledge and experimental evidence that is used in a manual assertion.
combinatorial evidence from curator knowledge and experimental evidence used in manual assertion
A type of substance quantification evidence where an electrical gradient potential is applied to analyze an analyte of interest, resulting in a measurement amount of electrical current across the potential range applied.
A type of voltammetry evidence that is used in a manual assertion.
voltammetry evidence used in manual assertion
A type of fluorescence evidence where a molecule tagged with a fluorescent protein is exposed to ultraviolet or blue light to shift the spectral emission properties for visualization.
A type of photoconversion evidence that is used in a manual assertion.
photoconversion evidence used in manual assertion
A type of immunological assay evidence that involves observation of visible clumping of antibody and antigen into a complex.
A type of agglutination test evidence that is used in a manual assertion.
agglutination test evidence used in manual assertion
A type of agglutination test evidence that involves observaiton of visible clumping of antibody and antigen into a complex on a slide.
A type of slide agglutination test evidence that is used in a manual assertion.
slide agglutination test evidence used in manual assertion
A type of agglutination test evidence that results in detection of nonagglutinating antibodies or complement proteins on red blood cells in vivo.
direct Coombs test evidence that is used in a manual assertion.
direct Coombs test evidence used in manual assertion
A type of agglutination test evidence that results in screening of antibodies against red blood cell antigens (other than the A and B antigens) that are unbound in a patient's serum in vitro.
A type of indirect Coombs test evidence that is used in a manual assertion.
indirect Coombs test evidence used in manual assertion
A type of agglutination test evidence where some bacteria and viruses cross-link red blood cells and clump together.
A type of direct hemagglutination assay evidence that is used in a manual assertion.
direct hemagglutination assay evidence used in manual assertion
A type of agglutination test evidence where antiviral antibodies in a patient's serum or in a lab-produced antiserum neutralize the virus and block it from agglutinating the red blood cells.
viral hemagglutination inhibition assay evidence
A type of viral hemagglutination inhibition assay evidence that is used in a manual assertion.
viral hemagglutination inhibition assay evidence used in manual assertion
A type of immunological assay evidence that results in the detection of presence of specific antibodies in the patient's serum based on the use of complement, a biologically labile serum factor.
A type of compement fixation assay evidence that is used in a manual assertion.
compement fixation assay evidence used in manual assertion
A type of immunogical assay evidence that results in detection of specific neutralizing antibodies in a sample.
A type of neutralization test assay evidence that is used in a manual assertion.
neutralization test assay evidence used in manual assertion
A type of transport assay evidence where the rate of copper transport is estimated.
A type of copper transport assay evidence that is used in a manual assertion.
copper transport assay evidence used in manual assertion
A type of staining evidence that involves the use of the redox dye 5-cyano-2,3-ditolyl tetrazolium chloride to evaluate the respiratory activity of cells.
5-cyano-2,3-ditolyl tetrazolium chloride staining evidence
A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in a manual assertion.
5-cyano-2,3-ditolyl tetrazolium chloride staining evidence used in manual assertion
A type of cell growth assay evidence resulting in direct quantification of infectious virons and antiviral substances through the counting of discrete plaques (infectious units and cellular dead zones) in cell culture.
A type of plaque assay evidence that is used in a manual assertion.
plaque assay evidence used in manual assertion
A type of microscopy evidence where the light source is mounted above the specimen and the excitation light passes through the microscope objective lens on its way toward the specimen.
A type of epifluorescence microscopy evidence that is used in a manual assertion.
epifluorescence microscopy evidence used in manual assertion
A type of electron microscopy evidence where a beam of electrons are transmitted through an ultra thin specimen forming an image which is magnified and focused onto an imaging device, such as a fluorescent screen, on a layer of photographic film, or to be detected by a sensor such as a CCD camera.
conventional transmission electron microscopy(CTEM)
transmission electron microscopy evidence
A type of transmission electron microscopy evidence that is used in a manual assertion.
transmission electron microscopy evidence used in manual assertion
A type of electron microscopy evidence where a focused beam of high-energy electrons is used to generate a variety of signals at the surface of solid specimens.
A type of scanning electron microscopy evidence that is used in a manual assertion.
scanning electron microscopy evidence used in manual assertion
A type of microscopy evidence where a serial images are taken at regular time points to capture the dynamics of what is being observed.
A type of time-lapsed microscopy evidence that is used in a manual assertion.
time-lapsed microscopy evidence used in manual assertion
A type of microscopy evidence where a transparent specimen is illuminated with visible light and small phase shifts in the light passing through the specimen are used to produce an image.
A type of phase contrast microscopy evidence that is used in a manual assertion.
phase contrast microscopy evidence used in manual assertion
A type of microscopy evidence where a sample is illuminated with transmitted white light from below and observed from above.
transmitted light brightfied mircoscopy evidence
A type of transmitted light brightfied mircoscopy evidence that is used in a manual assertion.
transmitted light brightfied mircoscopy evidence used in manual assertion
A type of microscopy evidence that results in a bright image without glare and minimum heating of the specimen by employing both field and an aperture iris diaphragm for illumination.
koehler illumination microscopy evidence
A type of koehler illumination microscopy evidence that is used in a manual assertion.
koehler illumination microscopy evidence used in manual assertion
A type of microscopy evidence that results in visualization of living cells and transparent specimens by taking advantage of differences in the light refraction of different parts of the specimen.
Nomarski interference contrast microscopy
differential interference contrast microscopy evidence
A type of differential interference contrast microscopy evidence that is used in a manual assertion.
differential interference contrast microscopy evidence used in manual assertion
A type of confocal microscopy evidence that results in creation of a continuous confocal multi-colour mosaic from thousands of individually captured images.
extended field laser confocal microscopy evidence
A type of extended field laser confocal microscopy evidence that is used in a manual assertion.
extended field laser confocal microscopy evidence used in manual assertion
A type of confocal microscopy evidence that results in an image that is built up pixel-by-pixel by collecting the emitted photons from the fluorophores in the sample by passing a laser beam through a light source aperture which is then focused by an objective lens into a small area on the surface of the sample.
confocal laser scanning fluorescence microscopy
fluorescence confocal scanning laser microscopy
scanning confocal fluorescence microscopy
confocal laser scanning microscopy evidence
A type of confocal laser scanning microscopy evidence that is used in a manual assertion.
confocal laser scanning microscopy evidence used in manual assertion
A type of direct assay evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight, diffusion and interaction strength by illuminating the sample with a laser beam and the scattered intensity is probed at a certain angle by a detector.
A type of light scattering assay evidence that is used in a manual assertion.
light scattering assay evidence used in manual assertion
A type of light scattering assay evidence derived by analyzing the fluctuations in the internsity of the scattered light by the particles in motion.
A type of dynamic light scattering assay evidence that is used in a manual assertion.
dynamic light scattering assay evidence used in manual assertion
A type of light scattering assay evidence derived by measuring the average intensity of scattered light by the particles at multiple angles.
A type of static light scattering assay evidence that is used in a manual assertion.
static light scattering assay evidence used in manual assertion
A type of mutant phenotype evidence derived from formation of papillae that protrude outwards from the main colony by mutant cells.
A type of colony papillation assay evidence that is used in a manual assertion.
colony papillation assay evidence used in manual assertion
A type of staining evidence that is derived from the use of gentian violet as a general biological stain and an acid-base indicator.
A type of crystal violet staining evidence that is used in a manual assertion.
crystal violet staining evidence used in manual assertion
A type of biofilm formation assay evidence derived from in vitro cultivation and evaluation of bacterial biofilms under hydrodynamic conditions of flow.
A type of flow cell biofilm assay evidence that is used in a manual assertion.
flow cell biofilm assay evidence used in manual assertion
A type of hybrid interaction evidence that involves the detection of protein-protein interaction by fusing the protein target (the "bait") to RNA polymerase and fusing protein or peptide library to be analyzed (the "prey") to DNA-binding domain.
A type of bacterial 2-hybrid assay evidence that is used in a manual assertion.
bacterial 2-hybrid assay evidence used in manual assertion
A type of experimental phenotypic evidence that results from the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors.
A type of phenomic profiling assay evidence that is used in a manual assertion.
phenomic profiling assay evidence used in manual assertion
A type of experimental phenotypic evidence that results from studying the physical characteristics of an assemblage of microorganisms growing on a solid surface such as the surface of an agar culture medium.
A type of colony morphology evidence that is used in a manual assertion.
colony morphology evidence used in manual assertion
A type of colony morphology evidence that results from studying the colony pigmentation.
A type of colony color evidence that is used in a manual assertion.
colony color evidence used in manual assertion
A type of colony morphology evidence that results from studying the size of the colony.
A type of colony size evidence that is used in a manual assertion.
colony size evidence used in manual assertion
A type of cell growth assay evidence resulting from assessing the sensitivity or resistance of bacteria or fungi to an antimicrobial agent or chemical by measuring the size of the zone of inhibition that results when the test organism is grown on a solid surface in the presence of the antimicrobial agent or chemical.
A type of zone of inhibition evidence that is used in a manual assertion.
zone of inhibition evidence used in manual assertion
A type of zone of inhibition evidence resulting from testing the antimicrobial susceptibility by using predefined, continuous, and exponential gradient of antibiotic concentrations immobilized along a rectangular plastic test strip.
A type of Etest evidence that is used in a manual assertion.
A type of expression pattern evidence in which translation is measured by the positions of ribosomes active in a cell, identified through deep sequencing of ribosome-protected mRNA fragments.
A type of ribosome profiling evidence that is used in a manual assertion.
ribosome profiling evidence used in manual assertion
The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides.
Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
The part of a cell, extracellular environment or virus 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.
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
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.
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
nucleobase, nucleoside and nucleotide metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
nucleobase-containing compound metabolic process
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
DNA fragmentation involved in apoptotic nuclear change
endonucleolytic DNA catabolic process involved in apoptosis
DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases. In human, these include DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in PMID:15723341). Caution is needed when apoptotic DNA laddering assays show presence of fragmented DNA. A positive assay may simply reflect the end point of a whole apoptotic process. Unless clear experimental evidence is available to show that a gene product is directly involved in fragmenting DNA, please do not annotate to GO:0006309 'apoptotic DNA fragmentation' and consider annotating instead to a more upstream process such as, e.g., GO:0042981 'regulation of apoptotic process', GO:0006915 'apoptotic process', GO:0097190 'apoptotic signaling pathway'. Also, note that gene products involved in compartmentalization of apoptotic nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341).
Apoptosis induced DNA fragmentation, Bos taurus
Apoptosis induced DNA fragmentation, Sus scrofa
Apoptosis induced DNA fragmentation, Xenopus tropicalis
Apoptosis induced DNA fragmentation, Plasmodium falciparum
Apoptosis induced DNA fragmentation, Homo sapiens
Apoptosis induced DNA fragmentation, Rattus norvegicus
Apoptosis induced DNA fragmentation, Mus musculus
Apoptosis induced DNA fragmentation, Drosophila melanogaster
Apoptosis induced DNA fragmentation, Taeniopygia guttata
Apoptosis induced DNA fragmentation, Canis familiaris
Apoptosis induced DNA fragmentation, Gallus gallus
Apoptosis induced DNA fragmentation, Danio rerio
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.
cellular aromatic compound metabolic process
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Transport of inorganic cations/anions and amino acids/oligopeptides, Xenopus tropicalis
Transport of inorganic cations/anions and amino acids/oligopeptides, Staphylococcus aureus N315
Transport of inorganic cations/anions and amino acids/oligopeptides, Sus scrofa
Transport of inorganic cations/anions and amino acids/oligopeptides, Saccharomyces cerevisiae
Transport of inorganic cations/anions and amino acids/oligopeptides, Arabidopsis thaliana
Transport of inorganic cations/anions and amino acids/oligopeptides, Homo sapiens
Transport of inorganic cations/anions and amino acids/oligopeptides, Oryza sativa
Transport of inorganic cations/anions and amino acids/oligopeptides, Mus musculus
Transport of inorganic cations/anions and amino acids/oligopeptides, Danio rerio
Transport of inorganic cations/anions and amino acids/oligopeptides, Gallus gallus
Transport of inorganic cations/anions and amino acids/oligopeptides, Caenorhabditis elegans
Transport of inorganic cations/anions and amino acids/oligopeptides, Escherichia coli
Transport of inorganic cations/anions and amino acids/oligopeptides, Bos taurus
Transport of inorganic cations/anions and amino acids/oligopeptides, Dictyostelium discoideum
Transport of inorganic cations/anions and amino acids/oligopeptides, Drosophila melanogaster
Transport of inorganic cations/anions and amino acids/oligopeptides, Mycobacterium tuberculosis
Transport of inorganic cations/anions and amino acids/oligopeptides, Canis familiaris
Transport of inorganic cations/anions and amino acids/oligopeptides, Rattus norvegicus
Transport of inorganic cations/anions and amino acids/oligopeptides, Plasmodium falciparum
Transport of inorganic cations/anions and amino acids/oligopeptides, Taeniopygia guttata
Transport of inorganic cations/anions and amino acids/oligopeptides, Schizosaccharomyces pombe
The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
NRIF signals cell death from the nucleus, Danio rerio
NRAGE signals death through JNK, Taeniopygia guttata
NADE modulates death signalling, Rattus norvegicus
NRAGE signals death through JNK, Xenopus tropicalis
NADE modulates death signalling, Sus scrofa
NRIF signals cell death from the nucleus, Xenopus tropicalis
NRAGE signals death through JNK, Mus musculus
NRAGE signals death through JNK, Arabidopsis thaliana
NRAGE signals death through JNK, Schizosaccharomyces pombe
NRAGE signals death through JNK, Dictyostelium discoideum
NADE modulates death signalling, Homo sapiens
NRAGE signals death through JNK, Homo sapiens
NRIF signals cell death from the nucleus, Homo sapiens
NRAGE signals death through JNK, Saccharomyces cerevisiae
NRAGE signals death through JNK, Caenorhabditis elegans
NRAGE signals death through JNK, Oryza sativa
NRAGE signals death through JNK, Canis familiaris
NRAGE signals death through JNK, Gallus gallus
NRAGE signals death through JNK, Drosophila melanogaster
NADE modulates death signalling, Bos taurus
NRIF signals cell death from the nucleus, Canis familiaris
NADE modulates death signalling, Canis familiaris
NRAGE signals death through JNK, Rattus norvegicus
NRIF signals cell death from the nucleus, Gallus gallus
NRIF signals cell death from the nucleus, Rattus norvegicus
NRIF signals cell death from the nucleus, Sus scrofa
NRIF signals cell death from the nucleus, Mus musculus
NRIF signals cell death from the nucleus, Taeniopygia guttata
NADE modulates death signalling, Mus musculus
NRAGE signals death through JNK, Danio rerio
NRIF signals cell death from the nucleus, Bos taurus
NRAGE signals death through JNK, Bos taurus
NRAGE signals death through JNK, Sus scrofa
The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
Note that in GO cellular components include whole cells (cell is_a cellular component).
movement of cell or subcellular component
The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus.
The cell aging process that results in the nucleolus breaking down into fragments.
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.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
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.
metabolic process resulting in cell growth
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term.
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.
The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
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 biotic stimulus, a stimulus caused or produced by a living organism.
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 indicating damage to the organism.
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 toxic stimulus.
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.
The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
Gene Expression, Drosophila melanogaster
Gene Expression, Staphylococcus aureus N315
Gene Expression, Mycobacterium tuberculosis
Gene Expression, Dictyostelium discoideum
Gene Expression, Schizosaccharomyces pombe
Gene Expression, Saccharomyces cerevisiae
A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children, which are descendants of GO:0034050 'host programmed cell death induced by symbiont'.
The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage.
The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Fatty acids are aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
The directed movement of long-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
non-developmental growth of a unicellular organism
The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
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).
The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
aromatic hydrocarbon biosynthetic process
The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
The controlled release of icosanoids, any of a group of C20 polyunsaturated fatty acids from a cell or a tissue.
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular nitrogen compound metabolic process
Metabolism of amino acids and derivatives, Mycobacterium tuberculosis
Metabolism of amino acids and derivatives, Escherichia coli
Metabolism of amino acids and derivatives, Arabidopsis thaliana
Metabolism of amino acids and derivatives, Xenopus tropicalis
Metabolism of amino acids and derivatives, Sus scrofa
Metabolism of amino acids and derivatives, Homo sapiens
Metabolism of amino acids and derivatives, Saccharomyces cerevisiae
Metabolism of amino acids and derivatives, Caenorhabditis elegans
Metabolism of amino acids and derivatives, Rattus norvegicus
Metabolism of amino acids and derivatives, Mus musculus
Metabolism of amino acids and derivatives, Staphylococcus aureus N315
Metabolism of amino acids and derivatives, Gallus gallus
Metabolism of amino acids and derivatives, Taeniopygia guttata
Metabolism of amino acids and derivatives, Bos taurus
Metabolism of amino acids and derivatives, Drosophila melanogaster
Metabolism of amino acids and derivatives, Oryza sativa
Metabolism of amino acids and derivatives, Plasmodium falciparum
Metabolism of amino acids and derivatives, Danio rerio
Metabolism of amino acids and derivatives, Canis familiaris
Metabolism of amino acids and derivatives, Dictyostelium discoideum
Metabolism of amino acids and derivatives, Schizosaccharomyces pombe
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 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, nucleoside, nucleotide and nucleic acid synthesis
nucleobase-containing compound biosynthetic 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
nucleobase, nucleoside, nucleotide and nucleic acid catabolic process
nucleobase-containing compound catabolic process
The increase in size or mass of an entire organism, a part of an organism or a cell.
See also the biological process term 'cell growth ; GO:0016049'.
Self-propelled movement of a cell or organism from one location to another.
The series of events that restore integrity to a damaged tissue, following an injury.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
The directed movement of a motile cell or organism in response to an external stimulus.
directed movement in response to stimulus
A process in which planktonically growing microorganisms grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
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.
The chemical reactions and pathways by which individual cells transform chemical substances.
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
cellular macromolecule metabolic 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 macromolecule catabolic process
The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds.
cellular nitrogen compound catabolic process
The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.
cellular nitrogen compound biosynthetic process
Any process that is carried out at the cellular level which involves another organism of the same or different species.
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).
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 antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
The controlled release of acid by a cell or a tissue.
The controlled release of a substance by a cell or a tissue.
The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-).
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
The controlled release of arachidonic acid from a cell or a tissue.
This term should be used to annotate release of arachidonic acid from the cell. For the hydrolytic release of arachidonic acid from a phospholipid, consider instead annotating to 'phospholipase A2 activity ; GO:0004623'.
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.
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
establishment and maintenance of localization
establishment and maintenance of position
establishment and maintenance of cellular component location
establishment and maintenance of substance location
establishment and maintenance of substrate location
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
A biological process which involves another organism of the same or different species.
physiological interaction between organisms
physiological interaction with other organism
The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon.
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
organic molecular entity metabolic process
The directed movement of icosanoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Icosanoids are unsaturated C20 fatty acids and skeletally related compounds.
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
cellular component organization or biogenesis
The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
Any cellular metabolic process involving nucleic acids.
The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
nucleic acid phosphodiester bond hydrolysis
Synthesis of DNA that is a part of the process of duplicating one or more molecules of DNA.
DNA synthesis involved in DNA replication
The chemical reactions and pathways involving organic cyclic compound.
organic cyclic compound metabolic process
The chemical reactions and pathways resulting in the breakdown of organic cyclic compound.
organic cyclic compound catabolic process
The chemical reactions and pathways resulting in the formation of organic cyclic compound.
organic cyclic compound biosynthetic process
The directed movement of a fatty acid derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon.
organic molecular entity catabolic process
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
organic molecular entity biosynthetic process
The directed movement of an arachidonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
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).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
PERSON: Chris Stoeckert
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
OBI Plan and Planned Process branch
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
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.
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
PlanAndPlannedProcess Branch
measuring
scientific observation
OBI branch derived
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
intervention design
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
Philppe Rocca-Serra
cell co-culturing
Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay
A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
cDNA library
PMID:6110205. collection of cDNA derived from mouse splenocytes.
Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
PERSON: Luisa Montecchi
PERSON: Philippe Rocca-Serra
GROUP: PSI
PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction
microtiter plate
A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
A microtiter_plate is a flat plate with multiple wells used as small test tubes.
Melanie Courtot
microplate
artificially induced nucleic acid hybridization
www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf
Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules.
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
adding a material entity into a target
Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019
metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism
metabolite profiling
extract
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
an extract is a material entity which results from an extraction process
extracted material
Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot
gene expression profiling
transcription profiling assay
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration'))
PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch
analyte assay
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity.
A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating.
Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time
Need to point out more specifically that survival / death is measured.
A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.
The presentation of a flashing light to a monkey during reward training
a planned process in which an organism is exposed to some stimulus with the intent to invoke an action
Helen Parkinson, Jessica Turner, Dirk Derom
PMID: 18428227. Analysis of RNA by northern blot hybridization. Brown T, Mackey K. Curr Protoc Hum Genet. 2001 Nov;Appendix 3:Appendix 3K.
a northern blot analysis is an assay allowing monitoring presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing agarose gel, transfered by blotting procedure to a nitrocellulose or nylon membrane and immobilized by cross linking or baking to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager
2010-01-31: Philippe Rocca-Serra: Need to add a restriction taking into account probe and transcript information
single-nucleotide-resolution nucleic acid structure mapping assay
is an assay which aims to provide information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity.
2010-01-31: Philippe Rocca-Serra: OBI needs to review 'structure assay' as currently defined. Need to get feedback from Kevin Clancy.
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
A cytometry assay that monitors a cell population to track how many are killed by other cells.
secondary structure of sequence macromolecule
A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford.
2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO
Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation.
A cytometry assay which measures the degreee to which input cells are replicating.
PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. Li C, Weber G, Ekman P, Lagercrantz J, Norlen BJ, Akerström G, Nordenskjöld M, Bergerheim US. Hum Mutat. 1998;Suppl 1:S31-3.
Southern blot analysis is a an assay used in molecular biology to assert the presence/absence status of a specific DNA sequence in DNA samples. DNA samples to be assayed are first digested by restriction enzymes, fragments are then resolved by gel electrophoresis following by a blotting ensuring transfer to nitrocellulose or nylon membrane. Immobilization of DNA fragments to the membrane is achieved by UV crosslinking and/or baking. Probes raised against the specific sequences are then hybridized to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager.
2010-01-31: Philippe Rocca-Serra: need extra work on 'labeled probe'
2010-01-31: Philippe Rocca-Serra: departure from naming convention as the assay is named after Edwin Southern.
real time polymerase chain reaction assay
A laboratory technique based on the PCR, which is used to amplify and simultaneously quantify a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.
quantitative real time polymerase chain reaction
WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE. J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23.
a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation,
Extraction of total RNA from cells with Qiagen mini RNeasy kit.
A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA.
PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28.
is a single-nucleotide-resolution nucleic acid structure mapping assay which uses DEPC as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture.
A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
An assay in which a measurement is made by observing entities located in a live cell.
Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells.
An assay in which a measurement is made by observing entities located in an organism.
A device that can be used to restrict the location of material entities over time
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
an assay in which a measurement is made by observing entities located in a container.
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
a single-nucleotide-resolution nucleic acid structure mapping assay which relies on small chemical compounds acting as chemical probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study.
cell culture expansion
a processual entity that results in the increase of cell numbers
including grow of yeast and bacteria
PERSON: Chris Stoeckert, Jie Zheng
MO_758 grow
BP: add it as subclass of 'cell culturing' JZ: No 'cell culturing' in OBI Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process.
induced mutation
a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation.
MO_564 induced_mutation
in vivo design
A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
MO_454 in_vivo_design
transcription profiling by high thoughput sequencing design
A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance
Group: ArrayExpress production team
transcription profiling by high throughput sequencing design
RNA-seq assay
An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance
PERSON: James Malone
transcription profiling by high throughput sequencing
EFO_0002770 transcription profiling by high throughput sequencing
JZ: should be inferred as 'DNA sequencing'. Will check in the future.
an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. WEB: http://en.wikipedia.org/wiki/RNA-Seq
in vitro design
A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
MO_347 in_vitro_design
transcription profiling by array design
A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
transcription profiling by RT-PCR design
A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR).
transcription profiling by RT-PCR assay
An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR)
Person: Anna Farne
EFO_0002943: transcription profiling by RT-PCR
cellular process design
A study design that aims to study the processes 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.
MO_810 cellular_process_design
stimulus or stress design
A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
MO_568 stimulus_or_stress_design
transcription profiling design
A study design that identifies forms and abundance of transcripts in the genome.
transcription profiling by array assay
An assay in which the transcriptome of a biological sample is analysed using array technology.
JZ: add alternative term: 'RNA profiling by array assay' requested by ENCODE developer. See tracker: https://sourceforge.net/p/obi/obi-terms/757/
EFO_0002768: transcription profiling by array
nano-cap analysis of gene expression
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. PMID:20543846
nano-CAGE is a type of CAGE developed to work from very low amount (nanogram scale) of mRNA samples
PERSON:Philippe Rocca-Serra; Marcus Chibucos
nano-CAGE
PMID: 20543846
cap analysis of gene expression
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Takahashi H, Lassmann T, Murata M, Carninci P. Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005. PMID: 22362160
An assay which aims at monitoring RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome
CAGE
An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells.
An assay that measures properties of cells.
An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen.
An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library.
An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes.
organism
animal
fungus
plant
virus
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.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
GROUP: OBI Biomaterial Branch
differential expression analysis objective
Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
James Malone
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
staining
Biofilm Flow Cell
Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.
Person:John Quinn
flow cell
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
adding substance to cell culture
adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient
is process in which a material substance is added to a cell culture
renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms
Bjoern Peters
IEDB
genetic transformation
The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35
the introduction. alteration or integration of genetic material into a cell or organism
PERSON:Kevin Clancy
genetic modification
sequencing assay
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
the use of a chemical or biochemical means to infer the sequence of a biomaterial
has_output should be sequence of input; we don't have sequence well defined yet
is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture
experimental infection of cell culture
Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1. After a 4-h incubation of the effector cells with the target cells, supernatants were collected following brief centrifugation and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac). Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died.
quality of a single physical entity
A physical object quality which inheres in a single-bearer.