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.
eco
OBO-Edit 2.3.1
04:06:2018 22:02
rctauber
1.2
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
Person:Alan Ruttenberg
Really of interest to developers only
BFO CLIF specification label
editor preferred label
editor preferred label
editor preferred term
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
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
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.
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
IAO
example of usage
example of usage
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
OBI_0000281
has curation status
definition
definition
definition
textual definition
textual 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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
IAO
definition
definition
definition
textual definition
textual definition
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
editor note
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
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
IAO
term editor
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
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
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
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
IAO
definition source
definition source
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
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.
IAO
ontology term requester
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
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
elucidation
has associated axiom(nl)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(nl)
has associated axiom(fol)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom expressed in first order logic using CLIF syntax
has associated axiom(fol)
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
Person: Alejandra Gonzalez-Beltran
Person: Philippe Rocca-Serra
ISA tools project (http://isa-tools.org)
ISA alternative term
IEDB alternative term
An alternative term used by the IEDB.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB
IEDB alternative term
Grouping classes used by GO
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
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
Source
A legal document giving official permission to do something with the resource.
DC
license
subset_property
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
in_subset
shorthand
label
label
A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence.
mchibucos
2010-12-09T05:00:20Z
ECO:9000000
eco
used_in
used_in
In the future we may use a more generic relation with weaker domain and range constraints taken from IAO, RO or OBI.
used_in
A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence.
GOC:cjm
ECO:9000001
eco
uses
uses
uses
has_specified_input
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
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
is_specified_output_of
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
PERSON:Bjoern Peters
is_specified_output_of
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
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
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
entity
Entity
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
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
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
(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 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]
occurrent
Occurrent
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
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.
per discussion with Barry Smith
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]
ic
IndependentContinuant
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
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]
process
Process
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
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
quality
Quality
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
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]
sdc
SpecificallyDependentContinuant
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
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.
per discussion with Barry Smith
(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]
gdc
GenericallyDependentContinuant
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
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]
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
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 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]
A type of information that is used to support an assertion.
eco
evidence code
evidence_code
ECO:0000000
evidence
A type of information that is used to support an assertion.
ECO:MCC
A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator.
eco
ECO:0000001
inference from background scientific knowledge
A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator.
ECO:SN
A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature.
ECO:0005006
eco
ECO:0000002
direct assay evidence
A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature.
ECO:SN
A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
eco
ECO:0000003
reconstitution assay evidence
A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
ECO:KAV
PMID:26029343
A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
eco
IDA: cell fractionation
ECO:0000004
If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology.
cell fractionation evidence
A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
ECO:KIM
TAIR:TED
A type of protein assay evidence where the catalytic activity of an enzyme is determined.
ECO:0005001
MI:0415
eco
IDA: enzyme assays
ECO:0000005
enzyme assay evidence
A type of protein assay evidence where the catalytic activity of an enzyme is determined.
url:http://www.sciencedirect.com/science/article/pii/S2213020914000068
MI:0415
enzymatic study
A type of evidence resulting from manipulation of variables in order to discover cause and effect.
ECO:0005023
eco
ECO:0000006
experimental evidence
A type of evidence resulting from manipulation of variables in order to discover cause and effect.
url:http://holah.co.uk/page/experimental/
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.
eco
IDA: immunofluorescence
ECO:0000007
immunofluorescence evidence
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.
ECO:MCC
TAIR:TED
A type of experimental evidence that is based on characterization of gene expression.
eco
ECO:0000008
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.
expression pattern evidence
A type of experimental evidence that is based on characterization of gene expression.
ECO:MCC
GO:IEP
A type of expression pattern evidence where abundance of a transcript is analyzed.
ECO:0000048
transcript expression level evidence
eco
ECO:0000009
transcript expression evidence
A type of expression pattern evidence where abundance of a transcript is analyzed.
ECO:RCT
A type of expression pattern evidence resulting from protein abundance quantification techniques.
eco
ECO:0000010
protein expression evidence
A type of expression pattern evidence resulting from protein abundance quantification techniques.
PMC:4029002
url:https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-protein-expression-systems.html
A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products.
TAIR:TED
eco
ECO:0000011
genetic interaction evidence
A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products.
ECO:RCT
PMID:11822023
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.
eco
IGI: functional complementation
ECO:0000012
functional complementation evidence
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.
PMID:27403640
A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
eco
ECO:0000013
transgenic rescue experiment evidence
A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
url:http://www.mdpi.com/1420-3049/19/9/13932/pdf
url:http://www.nature.com/gt/journal/v11/n15/full/3302282a.html
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.
eco
ECO:0000015
mutant phenotype evidence
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.
GO:IMP
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.
eco
ECO:0000016
loss-of-function mutant phenotype evidence
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.
SO:0002054
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.
eco
IMP: analysis of overexpression/ectopic expression phenotype
ECO:0000017
ectopic expression 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.
PMID:10948520
PMID:19301619
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.
eco
IMP: anti-sense experiments
ECO:0000018
anti-sense experiment evidence
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.
ECO:SN
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.
eco
IMP: RNAi experiment
ECO:0000019
RNAi evidence
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.
ECO:MCC
A type of protein assay evidence based on the inhibition of the molecular function of a protein.
eco
ECO:0000020
specific protein inhibition evidence
A type of protein assay evidence based on the inhibition of the molecular function of a protein.
ECO:MCC
A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
ECO:0005025
MI:0045
eco
ECO:0000021
Molecules interacted with might include protein, nucleic acid, ion, or complex.
physical interaction evidence
A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
ECO:SN
MI:0045
experimental interaction detection
A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
MI:0025
eco
IPI: co-purification
ECO:0000022
co-purification evidence
A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
TAIR:TED
MI:0025
copurification
A type of physical interaction evidence that depends on the strength of the interaction between two entities.
MI:0400
ligand binding evidence
eco
ECO:0000023
affinity evidence
A type of physical interaction evidence that depends on the strength of the interaction between two entities.
ECO:MCC
PSI-MI:MI:0400
MI:0400
affinity technology
A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex.
eco
ECO:0000024
protein binding evidence
A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex.
GO:0005515
url:https://en.wikipedia.org/wiki/Mutation
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.
MI:0090
eco
ECO:0000025
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.
hybrid interaction evidence
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.
ECO:MCC
PSI-MI:MI:0090
MI:0090
protein complementation assay
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.
eco
ECO:0000026
nucleic acid hybridization evidence
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.
OBI:0302903
A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
eco
ECO:0000027
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.
structural similarity evidence
A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
ECO:MCC
TAIR:TED
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.
eco
ISS: recognized domains
ECO:0000028
motif similarity evidence
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.
ECO:SN
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.
eco
ECO:0000029
match to InterPro member signature evidence
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.
PMC:2686546
url:http://www.ncbi.nlm.nih.gov/mesh?term=Nucleic+Acid+Hybridization
A type of BLAST evidence that is used in a manual assertion.
eco
curated BLAST analysis
ECO:0000030
BLAST evidence used in manual assertion
true
true
A type of BLAST evidence that is used in a manual assertion.
ECO:MCC
A type of protein BLAST evidence that is used in a manual assertion.
GO_REF:0000012
GO_REF:0000027
eco
curated protein BLAST analysis
ECO:0000031
protein BLAST evidence used in manual assertion
true
true
A type of protein BLAST evidence that is used in a manual assertion.
ECO:SN
GO_REF:0000012
Pairwise alignment (TIGR)
GO_REF:0000027
BLAST search criteria for ISS assignment in PAMGO_GAT
A type of nucleotide BLAST evidence that is used in a manual assertion.
eco
curated nucleic acid BLAST analysis
ECO:0000032
nucleotide BLAST evidence used in manual assertion
true
true
A type of nucleotide BLAST evidence that is used in a manual assertion.
ECO:SN
A type of author statement that is based on a cited reference.
eco
ECO:0000033
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.
traceable author statement
A type of author statement that is based on a cited reference.
ECO:MCC
GO:TAS
A type of author statement that is not associated with results presented or a cited reference.
eco
ECO:0000034
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.
non-traceable author statement
A type of author statement that is not associated with results presented or a cited reference.
ECO:SN
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.
eco
ECO:0000035
An assertion of "no biological data found" carries the assumption that a more-or-less exhaustive search has been conducted.
no biological data found
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.
ECO:SN
eco
ECO:0000037
The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations.
not_recorded
true
eco
ECO:0000038
transient rescue experiment evidence
A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins.
ECO:0005022
eco
ECO:0000039
protein assay evidence
A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins.
PMID:18429326
A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
ECO:0005018
eco
ECO:0000040
immunological assay evidence
A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
ERO:0001362
url:http://www.ncbi.nlm.nih.gov/books/NBK21589/,http://cores.ucsf.edu/protein-assay.html
A type of evidence resulting from comparing likeness of distinct biological entities.
IS
eco
inferred from similarity
ECO:0000041
similarity evidence
A type of evidence resulting from comparing likeness of distinct biological entities.
ECO:SN
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.
eco
ECO:0000042
gain-of-function mutant phenotype evidence
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.
SO:0002053
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614608/
A type of similarity based on biomolecular sequence.
eco
ECO:0000044
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.
sequence similarity evidence
A type of similarity based on biomolecular sequence.
ECO:MCC
TAIR:TED
eco
ECO:0000045
spatial pattern of protein expression evidence
A type of protein expression evidence resulting from the quantification of protein production in a sample.
eco
ECO:0000046
protein expression level evidence
A type of protein expression evidence resulting from the quantification of protein production in a sample.
NBK:22011
url:http://www.informatics.jax.org/glossary/gain-of-function
eco
ECO:0000047
spatial pattern of transcript expression evidence
A type of experimental phenotypic evidence that is based on the expression pattern of a reporter gene.
eco
IEP: expression of a reporter gene
ECO:0000049
reporter gene assay evidence
A type of experimental phenotypic evidence that is based on the expression pattern of a reporter gene.
TAIR:TED
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.
IVS
eco
ECO:0000050
voucher specimen analysis evidence
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.
TAIR:TED
A type of similarity based on genotype without respect to expression.
IGTS
eco
inferred from genetic similarity
ECO:0000051
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.
genetic similarity evidence
A type of similarity based on genotype without respect to expression.
ECO:MCC
PhenoScape:IGTS
A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
TAIR:TED
eco
IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)
ECO:0000052
suppressor/enhancer interaction evidence
A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
url:http://biorxiv.org/content/early/2015/10/03/021592
url:http://www.wormbook.org/chapters/www:geneticsuppression/geneticsuppression.html
A type of combinatorial analysis where data are combined and evaluated by an algorithm.
TAIR:TED
eco
ECO:0000053
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.
computational combinatorial evidence
A type of combinatorial analysis where data are combined and evaluated by an algorithm.
ECO:MCC
ECO:go
A type of genetic interaction evidence that is based on the phenotypic outcome of two mutations in unrelated genetic loci.
eco
IGI: double mutant analysis
ECO:0000054
double mutant phenotype evidence
A type of genetic interaction evidence that is based on the phenotypic outcome of two mutations in unrelated genetic loci.
ECO:RCT
eco
ECO:0000055
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.)
array experiment evidence
true
A type of genetic interaction evidence that is based on the suppression of one allelic effect by an allele at another genetic locus.
eco
IGI: epistatic interactions
ECO:0000056
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.
epistatic interaction evidence
A type of genetic interaction evidence that is based on the suppression of one allelic effect by an allele at another genetic locus.
PMID:18852697
A type of similarity based on the expression of a genotype in an environment.
IPTS
phenotype similarity evidence
eco
inferred from phenotypic similarity
ECO:0000057
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.
phenotypic similarity evidence
A type of similarity based on the expression of a genotype in an environment.
ECO:MCC
PhenoScape:IPTS
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.
ECO:0000356
differential gene expression evidence from microarray experiment
eco
ECO:0000058
expression microarray evidence
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.
url:http://www.illumina.com/techniques/microarrays/gene-expression-arrays.html
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435252/
A type of experimental evidence that is based on the expression of a genotype in an environment.
ECO:0000014
ECO:0005017
eco
inferred from phenotype
ECO:0000059
experimental phenotypic evidence
A type of experimental evidence that is based on the expression of a genotype in an environment.
ECO:SN
A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements.
IPS
eco
ECO:0000060
positional similarity evidence
A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements.
TAIR:TED
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.
QTL analysis evidence
eco
IGI: quantitative trait analysis
ECO:0000061
quantitative trait analysis evidence
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.
TAIR:TED
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.
genomic microarray evidence
eco
ECO:0000062
cRNA to DNA expression microarray evidence
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.
url:https://link.springer.com/chapter/10.1007/978-94-017-9716-0_30
A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures.
ICS
eco
ECO:0000063
compositional similarity evidence
A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures.
TAIR:TED
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.
eco
IGI: functional complementation in heterologous system
ECO:0000064
functional complementation in heterologous system evidence
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.
TAIR:TED
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.
MI:0432
eco
IPI: yeast one-hybrid assay
ECO:0000066
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).
yeast one-hybrid 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.
ECO:MCC
PSI-MI:MI:0432
TAIR:TED
MI:0432
one hybrid
A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures.
IDS
eco
ECO:0000067
developmental similarity evidence
A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures.
TAIR:TED
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.
eco
IPI: yeast two-hybrid assay
ECO:0000068
yeast 2-hybrid evidence
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.
PMID:12734586
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.
ECO:0000065
CpG island microarray evidence
eco
ECO:0000069
differential methylation hybridization evidence
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.
PMID:18987809
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.
MI:0019
eco
IPI: co-immunoprecipitation
ECO:0000070
If performing GO annotation, the interacting protein is referenced in the evidence_with column.
co-immunoprecipitation 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.
ECO:MCC
MI:0019
coimmunoprecipitation
A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures.
IMS
eco
ECO:0000071
morphological similarity evidence
A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures.
TAIR:TED
eco
ECO:0000072
Sos-recruitment assay evidence
true
A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product.
inferred from genomic analysis
eco
ECO:0000073
experimental genomic evidence
A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product.
ECO:MCC
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.
MI:0112
eco
IPI: split-ubiquitin assay
ECO:0000074
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
split-ubiquitin assay evidence
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.
PMID:15064465
MI:0112
ubiquitin reconstruction
A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles.
IGES
eco
ECO:0000075
gene expression similarity evidence
A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles.
PMID:19958477
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.
MI:0047
eco
IPI: far-Western analysis
ECO:0000076
The interacting protein is referenced in the evidence_with column.
far-Western blotting evidence
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.
PMID:18079728
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 PCR evidence
eco
ECO:0000077
methylation-specific polymerase chain reaction evidence
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.
PMC:38513
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.
Southern blot
eco
ISS: Southern blotting
ECO:0000078
The DNA fragments are prepared through gel electrophoresis then transferred to a filter membrane.
southern hybridization 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.
PMID:18432697
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.
MI:0004
eco
IDA: affinity chromatography
ECO:0000079
"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.
affinity chromatography evidence
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.
ECO:MCC
TAIR:TED
MI:0004
affinity chromatography technology
A type of similarity that indicates common ancestry.
IP
eco
ECO:0000080
phylogenetic evidence
A type of similarity that indicates common ancestry.
ECO:MCC
PhenoScape:IP
IP
PhenoScape:IP
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.
eco
ISS: targeting sequence prediction
ECO:0000081
targeting sequence prediction evidence
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.
ECO:RCT
TAIR:TED
A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand.
PCR evidence
eco
ECO:0000082
polymerase chain reaction evidence
A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand.
OBI:0000415
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.
eco
ISS: transmembrane domain prediction
ECO:0000083
transmembrane domain prediction evidence
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.
ECO:RCT
TAIR:TED
A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes.
mgiglio
2009-03-20T11:55:18Z
GO_REF:0000025
inferred from genome cluster
eco
ICL
ECO:0000084
Genomic cluster analyses include synteny and operon structure.
gene neighbors 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.
ECO:MCC
GOC:MG
GO_REF:0000025
Operon structure as IGC evidence
A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
CollecTF
eco
IDA: immunoprecipitation
ECO:0000085
Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding.
immunoprecipitation evidence
A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
ECO:MCC
ECO:SW
TAIR:TED
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.
eco
ECO:0000086
intermethylated site amplification evidence
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.
PMID:18987810
url:https://www.ncbi.nlm.nih.gov/probe/docs/techpcr/
A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues.
eco
IDA: immunolocalization
ECO:0000087
immunolocalization evidence
A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues.
ECO:MCC
ECO:SN
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.
mgiglio
2009-03-20T12:00:17Z
eco
ISR
inferred from system reconstruction
ECO:0000088
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 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.
ECO:MCC
GOC:mg
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.
SIB:PG
ECO:0001125
RLGS evidence
restriction landmark genome scanning evidence
eco
ECO:0000089
restriction landmark genomic scanning 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.
PMID:8388788
A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy.
eco
IDA: immunogold labelling
ECO:0000090
immunogold labelling evidence
A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy.
ECO:MCC
A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies.
eco
IDA: immunolocalization of epitope-tagged protein
ECO:0000092
epitope-tagged protein immunolocalization evidence
A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies.
TAIR:TED
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.
DNA microarray
oligonucleotide microarray evidence
SNP array evidence
single nucleotide polymorphism array evidence
eco
ECO:0000093
array-based sequence capture 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.
PMID:21049075
eco
ECO:0000094
The children of 'biological assay evidence' have been moved under 'direct assay evidence', and this term has been deprecated with no children left.
biological assay evidence
true
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.
mchibucos
2014-10-15T00:58:50Z
eco
growth curve analysis
ECO:0000095
Cell growth aspects can include growth rate and extent of growth. A cell growth curve acts as a natural reporter.
cell growth regulation assay evidence
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.
ECO:SW
PomBase:MAH
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.
CollecTF
MI:0413
EMSA: electrophoretic mobility shift assay
eco
Gel retardation assay
IDA: electrophoretic mobility shift assay
ECO:0000096
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 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.
ECO:KIM
ECO:SW
PMID:17703195
TAIR:TED
MI:0413
electrophoretic mobility shift assay
Gel retardation assay
PMID:17703195
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.
CollecTF
ECO:0001041
ECO:0005524
eco
DNA microarray
RNA microarray
ECO:0000097
cDNA to DNA expression microarray 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.
ECO:RCT
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.
eco
IDA: in situ hybridization
ECO:0000098
in situ hybridization 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.
url:https://www.ncbi.nlm.nih.gov/probe/docs/techish/
A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions.
eco
ECO:0000100
fractionation evidence
A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions.
NBK:26936
url:https://www.ncbi.nlm.nih.gov/books/NBK26936/
A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information.
Affymetrix array experiment evidence
eco
ECO:0000101
Affymetrix GeneChip evidence
A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information.
ERO:0001265
A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules.
eco
IDA: co-fractionation
ECO:0000102
co-fractionation evidence
A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules.
TAIR:TED
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.
REM evidence
RNA expression microarray evidence
microarray RNA expression level evidence
eco
IEP: transcript levels (e.g. microarray data)
ECO:0000104
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 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.
ECO:RCT
PMID:15329382
REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that.
PMID:15329382
A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels.
eco
ECO:0000105
Nimblegen array evidence
A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels.
PMID:15607417
url:https://roche-biochem.jp/pdf/products/microarray/user_guide/SeqCap/SeqCap_UserGuide_Delivery_ver3.0.pdf
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.
CollecTF
RNA blot evidence
northern assay evidence
eco
IEP: transcript levels (e.g. Northerns)
ECO:0000106
northern blot evidence
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.
ECO:SW
TAIR:TED
A type of transcript expression evidence in which expression levels are determined through RT-PCR (quantitative or otherwise).
RT-PCR transcription evidence
eco
IEP: transcript levels (e.g. RT-PCR)
ECO:0000108
reverse transcription polymerase chain reaction transcription evidence
A type of transcript expression evidence in which expression levels are determined through RT-PCR (quantitative or otherwise).
TAIR:TED
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.
CollecTF
RT-PCR evidence
qRT-PCR
eco
ECO:0000109
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 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.
ECO:SW
PMID:11013345
PMID:12901609
qRT-PCR
PMID:12901609
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.
CollecTF
ribonuclease protection assay
RPA
eco
IEP: RNA protection assay
RNAse protection assay
ECO:0000110
RNA protection assay 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.
ECO:SW
PMID:23457339
TAIR:TED
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.
CollecTF
eco
IEP: protein levels (e.g. Western blots)
Western blot expression analysis
protein immunoblot
ECO:0000112
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.
western blot evidence
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.
ECO:SW
PMID:23050259
TAIR:TED
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.
eco
IEP: expression library screening
ECO:0000114
expression library screen evidence
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.
ECO:MCC
TAIR:TED
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.
eco
IEP: differential hybridization
ECO:0000116
Differential hybridization identifies differentially expressed cloned genes. Two different mRNA-derived probes are used to demonstrate RNA expression under a specific condition.
differential hybridization evidence
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.
PMID:14668817
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'.
eco
IEP: subtractive hybridization
ECO:0000118
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.
subtractive hybridization evidence
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'.
PMID:11298187
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.
eco
IMP: analysis of overexpression/ectopic expression phenotype
ECO:0000120
over expression analysis evidence
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.
PMID:22419077
A type of protein assay evidence where sub-cellular localization of a protein within a cell is determined.
eco
ECO:0000122
protein localization evidence
A type of protein assay evidence where sub-cellular localization of a protein within a cell is determined.
GO:0008104
url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019937
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.
eco
ECO:0000124
fusion protein localization evidence
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.
MI:0240
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
eco
IDA: localization of GFP/YFP fusion protein
ECO:0000126
green fluorescent protein fusion protein localization evidence
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.
PMID:9759496
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
eco
IDA: localization of GFP/YFP fusion protein
ECO:0000128
yellow 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.
MI:0368
url:http://www.jbc.org/content/276/31/29188.long
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
GUS staining evidence
eco
IDA: localization of GUS fusion protein
ECO:0000130
beta-glucuronidase 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.
ECO:RCT
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
eco
ECO:0000132
beta-galactosidase 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.
PMID:23681629
A type of direct assay evidence resulting from the activity assessment of transport proteins.
eco
IDA: transport assay
ECO:0000134
transport assay evidence
A type of direct assay evidence resulting from the activity assessment of transport proteins.
PMID:18401524
A type of affinity evidence resulting from the binding of a molecule to a nucleic acid.
eco
ECO:0000136
nucleic acid binding evidence
A type of affinity evidence resulting from the binding of a molecule to a nucleic acid.
GO:0003676
A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer.
eco
IDA: ribohomopolymer binding assay
ECO:0000138
ribohomopolymer binding assay evidence
A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer.
PMC:102612
A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
TLC evidence
eco
IDA: thin layer chromatography
ECO:0000140
thin layer chromatography evidence
A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
ECO:MCC
A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site.
eco
ECO:0000142
protein:ion binding evidence
A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site.
PMID:2377604
A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
eco
IDA: Southwestern analysis
ECO:0000144
Southwestern blot evidence
A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
ECO:RCT
TAIR:TED
A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
eco
IDA: Northwestern analysis
ECO:0000146
Northwestern blot evidence
A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
ECO:RCT
TAIR:TED
eco
ECO:0000148
in vitro binding evidence
true
A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis.
eco
IDA: in vitro reconstitution assay with recombinant protein
ECO:0000150
in vitro transcription reconstitution assay evidence
A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis.
PMID:9237163
A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system.
eco
IDA: in vitro reconstitution assay with recombinant protein
ECO:0000152
in vitro recombinant protein 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.
PMID:9237165
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.
eco
IDA: protein expression in heterologous system
ECO:0000154
heterologous protein expression 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.
ECO:KAV
A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture.
eco
ECO:0000156
protein separation evidence
A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture.
ERO:0000526
eco
IDA: protein separation and direct sequencing
ECO:0000158
protein separation followed by direct sequencing evidence
eco
IDA: protein separation and fragment identification
ECO:0000160
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.
eco
IDA: uptake assay in heterologous system
ECO:0000162
The transporter is a recombinant protein.
heterologous system uptake 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.
ECO:RCT
doi:10.1146/annurev.pp.46.060195.002223
A type of direct assay evidence where electrical properties of cells or tissues are studied.
eco
ECO:0000164
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.
electrophysiology assay evidence
A type of direct assay evidence where electrical properties of cells or tissues are studied.
ECO:KAV
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.
eco
IDA: two-electrode voltage clamp technique
ECO:0000166
two-electrode voltage clamp recording evidence
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.
ECO:SN
PMID:23529422
A type of direct assay evidence resulting from the detection and quantification of transcribed RNA.
eco
ECO:0000168
transcription assay evidence
A type of direct assay evidence resulting from the detection and quantification of transcribed RNA.
MeSH:D014158
url:https://bmcmolbiol.biomedcentral.com/articles/10.1186/1471-2199-15-7
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.
eco
IDA: transcriptional activation assay
ECO:0000170
transcriptional activation assay
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.
url:http://smcg.ccg.unam.mx/enp-unam/05-TranscripYRegulacion/transcription.pdf
A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed.
eco
IMP: analysis of biochemical trait
ECO:0000172
For example, the accumulation of a biosynthetic intermediate.
biochemical trait analysis evidence
A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed.
ECO:RCT
A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined.
eco
IMP: analysis of physiological response
ECO:0000174
Examples include: abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions.
mutant physiological response evidence
A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined.
ECO:RCT
A type of mutant phenotype evidence in which traits arising from a mutation are visually examined.
eco
IMP: analysis of visible trait
ECO:0000176
mutant visible phenotype evidence
A type of mutant phenotype evidence in which traits arising from a mutation are visually examined.
ECO:RCT
A type of evidence in which the location of the gene within the genome provides insight into its function, or provides evolutionary insight.
eco
ECO:0000177
This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis.
genomic context evidence
A type of evidence in which the location of the gene within the genome provides insight into its function, or provides evolutionary insight.
PMID:21609955
A type of direct assay evidence resulting from a sample of microorganisms or living tissue grown in a medium.
eco
ECO:0000178
in vivo assay evidence
A type of direct assay evidence resulting from a sample of microorganisms or living tissue grown in a medium.
ECO:RCT
url:https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=46352
A type of experimental evidence arising from the investigation of an animal model system.
eco
ECO:0000179
animal model system study evidence
A type of experimental evidence arising from the investigation of an animal model system.
ECO:MCC
A type of experimental evidence arising from a controlled investigation that uses human subjects.
eco
ECO:0000180
clinical study evidence
A type of experimental evidence arising from a controlled investigation that uses human subjects.
ECO:MCC
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.
ECO:0005013
eco
ECO:0000181
in vitro assay evidence
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.
ECO:RCT
url:https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=45733
eco
ECO:0000182
Use ECO:0001563 (cell growth assay evidence) in place of this term.
in vitro culture assay evidence
true
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.
in vitro assay
eco
ECO:0000183
cell-free assay evidence
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.
PMID:18453125
A type of specific protein inhibition evidence where the protein under study is an enzyme.
eco
ECO:0000184
enzyme inhibition evidence
A type of specific protein inhibition evidence where the protein under study is an enzyme.
ECO:MCC
A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment
mchibucos
2010-03-18T12:21:31Z
ECO:00000057
eco
ECO:0000200
Such alignments may be pairwise alignments or multiple alignments.
sequence alignment evidence
A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment
url:http://www.geneontology.org/GO.evidence.shtml
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.
mchibucos
2010-03-18T12:30:06Z
ECO:00000060
eco
ortholog evidence
ECO:0000201
Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor.
sequence orthology evidence
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.
url:http://www.geneontology.org/GO.evidence.shtml
A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model.
mchibucos
2010-03-18T12:32:30Z
ECO:00000063
eco
ECO:0000202
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.
match to sequence model evidence
A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model.
ECO:MCC
url:http://www.geneontology.org/GO.evidence.shtml
An assertion method that does not involve human review.
mchibucos
2010-03-18T12:36:04Z
ECO:00000067
eco
ECO:0000203
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.
automatic assertion
An assertion method that does not involve human review.
ECO:MCC
An evidence type that is based on an assertion by the author of a paper, which is read by a curator.
mchibucos
2010-06-21T11:17:21Z
eco
ECO:0000204
author statement
An evidence type that is based on an assertion by the author of a paper, which is read by a curator.
ECO:MCC
A type of inferential evidence that is based on a conclusion drawn by a curator.
mchibucos
2010-08-18T05:55:12Z
eco
ECO:0000205
curator inference
A type of inferential evidence that is based on a conclusion drawn by a curator.
ECO:MCC
A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST).
mchibucos
2010-08-06T04:48:24Z
eco
ECO:0000206
BLAST evidence
A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST).
ECO:MCC
A type of BLAST evidence in which nucleotide sequences are aligned.
mchibucos
2010-08-06T04:49:58Z
eco
ECO:0000207
nucleotide BLAST evidence
A type of BLAST evidence in which nucleotide sequences are aligned.
ECO:MCC
A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned.
mchibucos
2010-08-06T04:50:45Z
eco
ECO:0000208
protein BLAST evidence
A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned.
ECO:MCC
A type of BLAST evidence that is used in an automatic assertion.
mchibucos
2010-08-06T04:55:21Z
eco
ECO:0000209
BLAST evidence used in automatic assertion
true
true
A type of BLAST evidence that is used in an automatic assertion.
ECO:MCC
A type of nucleotide BLAST evidence that is used in an automatic assertion.
mchibucos
2010-08-06T05:09:51Z
eco
ECO:0000210
nucleotide BLAST evidence used in automatic assertion
true
true
A type of nucleotide BLAST evidence that is used in an automatic assertion.
ECO:RCT
A type of protein BLAST evidence that is used in an automatic assertion.
mchibucos
2010-08-06T05:11:04Z
eco
ECO:0000211
protein BLAST evidence used in automatic assertion
true
true
A type of protein BLAST evidence that is used in an automatic assertion.
ECO:RCT
A type of evidence that arises out of the integration of more than one line of evidence.
mchibucos
2010-08-06T05:24:57Z
ECO:0000036
ECO:0000043
eco
inferred from in-silico analysis
ECO:0000212
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.
combinatorial evidence
A type of evidence that arises out of the integration of more than one line of evidence.
ECO:MCC
A type of combinatorial analysis that is used in an automatic assertion.
mchibucos
2010-08-06T05:28:33Z
eco
inferred from in-silico analysis
ECO:0000213
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.
combinatorial evidence used in automatic assertion
true
true
A type of combinatorial analysis that is used in an automatic assertion.
ECO:MCC
A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
mchibucos
2010-10-05T11:16:50Z
eco
ECO:0000214
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 whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
ECO:MCC
A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
mchibucos
2010-10-05T03:41:34Z
eco
ECO:0000215
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 long phylogenetic tree branch lengths following a duplication event.
ECO:MCC
A type of phylogenetic evidence characterized by the absence of key sequence residues.
mchibucos
2010-10-05T03:43:17Z
eco
ECO:0000216
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 type of phylogenetic evidence characterized by the absence of key sequence residues.
ECO:MCC
A means by which a statement is made about an entity.
mchibucos
2010-11-12T04:17:37Z
eco
ECO:0000217
assertion method
A means by which a statement is made about an entity.
ECO:MCC
An assertion method that involves human review.
mchibucos
2010-11-12T04:20:02Z
eco
ECO:0000218
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.
manual assertion
An assertion method that involves human review.
ECO:MCC
A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides.
mchibucos
2010-11-15T12:22:40Z
eco
DNA sequencing
ECO:0000219
nucleotide sequencing assay evidence
A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides.
ECO:MCC
DNA sequencing
OBI:0000626
A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
mchibucos
2010-11-15T01:44:45Z
eco
ECO:0000220
sequencing assay evidence
A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
ECO:MCC
OBI:0600047
A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique.
mchibucos
2010-11-15T02:19:34Z
eco
next generation sequencing evidence
ECO:0000221
Typically thousands to millions of reads are produced in parallel.
high throughput nucleotide sequencing assay evidence
A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique.
ECO:MCC
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.
mchibucos
2010-11-15T02:38:03Z
eco
Solexa sequencing result
ECO:0000222
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.
Illumina sequencing 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.
OBI:0000724
PMID:26000844
Solexa sequencing result
OBI:0000724
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.
mchibucos
2010-11-15T03:50:14Z
pyrosequencing
eco
ECO:0000223
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.
454 pyrosequencing evidence
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.
EFO:0005016
pyrosequencing
OBI:0000730
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.
mchibucos
2010-11-15T04:17:41Z
eco
ECO:0000224
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.
SOLiD sequencing evidence
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.
OBI:0000706
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.
mchibucos
2010-11-15T04:46:31Z
Sanger sequencing
dye terminator sequencing
eco
ECO:0000225
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.
chain termination sequencing evidence
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.
OBI:0000695
A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
mchibucos
2010-11-16T01:29:08Z
MI:0402
ChIP evidence
eco
ECO:0000226
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).
chromatin immunoprecipitation evidence
A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
ECO:MCC
MI:0402
chromatin immunoprecipitation assay
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.
CollecTF
mchibucos
2010-11-16T05:02:00Z
ChIP-PCR evidence
eco
ECO:0000227
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 that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection.
ECO:MCC
ECO:SW
PMID:18388953
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.
mchibucos
2010-11-16T05:26:47Z
ChIP-qPCR evidence
eco
ECO:0000228
chromatin immunoprecipitation-qPCR 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.
url:https://www.diagenode.com/applications/chip-qpcr
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.
CollecTF
mchibucos
2010-11-16T05:30:41Z
ChIP-SEQ evidence
ChIP-seq evidence
eco
ECO:0000229
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 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.
ECO:MCC
ECO:SW
OBI:0000716
PMID:22955991
ChIP-SEQ evidence
OBI:0000716
ChIP-seq evidence
PMID:22955991
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.
CollecTF
mchibucos
2010-11-16T05:43:55Z
MI:0225
ChIP-chip evidence
ChIP-on-chip evidence
eco
ECO:0000230
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 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.
ECO:MCC
ECO:SW
PMID:18388953
PMID:19381927
MI:0225
chromatin immunoprecipitation array
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.
CollecTF
mchibucos
2010-11-16T05:57:20Z
Q-PCR evidence
quantitative PCR evidence
real-time PCR evidence
real-time polymerase chain reaction evidence
eco
qRT-PCR evidence
ECO:0000231
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 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.
ECO:MCC
ECO:SW
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.
mchibucos
2010-11-17T12:27:14Z
3C
chromosome conformation capture
eco
ECO:0000232
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 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.
ECO:MCC
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.
mchibucos
2010-11-17T12:46:15Z
3C
eco
ECO:0000233
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 performing a type of polymerase chain reaction (PCR) in the final product quantitation step.
ECO:MCC
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.
mchibucos
2010-11-19T01:20:28Z
4C
chromosome conformation capture on chip
circularized 3C
eco
ECO:0000234
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 inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray.
ECO:MCC
A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
mchibucos
2010-11-19T01:22:20Z
5C
carbon-copy 3C
eco
ECO:0000235
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-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
ECO:MCC
A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
mchibucos
2010-11-19T03:00:47Z
3C
3C-PCR
eco
ECO:0000236
chromosome conformation capture-PCR evidence
A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
ECO:MCC
A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step.
mchibucos
2010-11-19T03:06:47Z
3C-qPCR
3C-quantitative PCR
3C-real-time PCR
eco
ECO:0000237
chromosome conformation capture-qPCR evidence
A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step.
ECO:MCC
A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation.
mchibucos
2010-11-19T04:24:03Z
eco
ECO:0000238
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.
Hi-C evidence
A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation.
ECO:MCC
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.
mchibucos
2010-11-30T03:22:25Z
3C sequencing
3C-seq
4C sequencing
4C-seq
circularized 3C sequencing
circularized 3C-seq
eco
ECO:0000239
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 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.
ECO:MCC
A type of experimental phenotypic evidence in which the phenotype of an organism is observed after the disruption of a structural feature.
mchibucos
2010-12-06T12:24:16Z
eco
ECO:0000240
anatomical perturbation evidence
A type of experimental phenotypic evidence in which the phenotype of an organism is observed after the disruption of a structural feature.
ECO:MCC
A type of experimental phenotypic evidence in which the phenotype of an organism is observed after modification of the extra-organismal context.
mchibucos
2010-12-06T12:33:58Z
eco
mechanical constraint evidence
ECO:0000241
Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth.
environmental perturbation evidence
A type of experimental phenotypic evidence in which the phenotype of an organism is observed after modification of the extra-organismal context.
ECO:MCC
A type of anatomical perturbation that is based on disruption of tissue.
mchibucos
2010-12-06T12:33:58Z
ablated tissue evidence
eco
ECO:0000242
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.
tissue ablation evidence
A type of anatomical perturbation that is based on disruption of tissue.
ECO:MCC
A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure.
mchibucos
2010-12-06T12:33:58Z
eco
ECO:0000243
tissue grafting evidence
A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure.
ECO:MCC
A type of combinatorial analysis that is used in a manual assertion.
mchibucos
2010-12-09T02:02:12Z
eco
inferred from in-silico analysis
ECO:0000244
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.
combinatorial evidence used in manual assertion
true
true
A type of combinatorial analysis that is used in a manual assertion.
ECO:MCC
A type of computational combinatorial analysis that is used in a manual assertion.
mchibucos
2010-12-09T02:37:54Z
GOECO:RCA
RCA
inferred from reviewed computational analysis
eco
ECO:0000245
computational combinatorial evidence used in manual assertion
http://geneontology.org/page/rca-inferred-reviewed-computational-analysis
true
true
A type of computational combinatorial analysis that is used in a manual assertion.
ECO:MCC
GOECO:RCA
inferred from reviewed computational analysis
RCA
GOECO:RCA
inferred from reviewed computational analysis
GOECO:RCA
A type of computational combinatorial analysis that is used in an automatic assertion.
mchibucos
2010-12-09T02:37:54Z
eco
ECO:0000246
computational combinatorial evidence used in automatic assertion
true
true
A type of computational combinatorial analysis that is used in an automatic assertion.
ECO:MCC
A type of sequence alignment evidence that is used in a manual assertion.
mchibucos
2010-12-09T05:12:27Z
GOECO:ISA
ISA
inferred from sequence alignment
eco
ECO:0000247
sequence alignment evidence used in manual assertion
http://geneontology.org/page/isa-inferred-sequence-alignment
true
true
A type of sequence alignment evidence that is used in a manual assertion.
ECO:RCT
GOECO:ISA
inferred from sequence alignment
ISA
GOECO:ISA
inferred from sequence alignment
GOECO:ISA
A type of sequence alignment evidence that is used in an automatic assertion.
mchibucos
2010-12-09T05:12:27Z
eco
ECO:0000248
sequence alignment evidence used in automatic assertion
true
true
A type of sequence alignment evidence that is used in an automatic assertion.
ECO:RCT
A type of sequence similarity evidence that is used in an automatic assertion.
mchibucos
2010-12-09T05:22:30Z
eco
ECO:0000249
sequence similarity evidence used in automatic assertion
true
true
A type of sequence similarity evidence that is used in an automatic assertion.
ECO:RCT
A type of sequence similarity evidence that is used in a manual assertion.
mchibucos
2010-12-09T05:22:30Z
GOECO:ISS
ISS
inferred from sequence or structural similarity
eco
ECO:0000250
sequence similarity evidence used in manual assertion
http://geneontology.org/page/iss-inferred-sequence-or-structural-similarity
true
true
A type of sequence similarity evidence that is used in a manual assertion.
ECO:MCC
GOECO:ISS
inferred from sequence or structural similarity
ISS
GOECO:ISS
inferred from sequence or structural similarity
GOECO:ISS
A type of similarity evidence that is used in an automatic assertion.
mchibucos
2010-12-09T05:28:12Z
IS
eco
inferred from similarity
ECO:0000251
similarity evidence used in automatic assertion
true
true
A type of similarity evidence that is used in an automatic assertion.
ECO:RCT
A type of similarity evidence that is used in a manual assertion.
mchibucos
2010-12-09T05:28:12Z
IS
eco
inferred from similarity
ECO:0000252
similarity evidence used in manual assertion
true
true
A type of similarity evidence that is used in a manual assertion.
ECO:RCT
A type of genetic similarity evidence that is used in a manual assertion.
mchibucos
2010-12-10T01:42:44Z
IGTS
eco
inferred from genetic similarity
ECO:0000253
genetic similarity evidence used in manual assertion
true
true
A type of genetic similarity evidence that is used in a manual assertion.
ECO:RCT
A type of genetic similarity evidence that is used in an automatic assertion.
mchibucos
2010-12-10T01:42:44Z
IGTS
eco
inferred from genetic similarity
ECO:0000254
genetic similarity evidence used in automatic assertion
true
true
A type of genetic similarity evidence that is used in an automatic assertion.
ECO:RCT
A type of match to sequence model evidence that is used in a manual assertion.
mchibucos
2010-12-10T02:26:35Z
GOECO:ISM
GO_REF:0000011
ISM
inferred from sequence model
eco
ECO:0000255
match to sequence model evidence used in manual assertion
http://geneontology.org/page/ism-inferred-sequence-model
true
true
A type of match to sequence model evidence that is used in a manual assertion.
ECO:RCT
GOECO:ISM
inferred from sequence model
GO_REF:0000011
Hidden Markov Models (TIGR)
ISM
GOECO:ISM
inferred from sequence model
GOECO:ISM
A type of match to sequence model evidence that is used in an automatic assertion.
mchibucos
2010-12-10T02:26:35Z
GO_REF:0000002
GO_REF:0000107
eco
ECO:0000256
match to sequence model evidence used in automatic assertion
true
true
A type of match to sequence model evidence that is used in an automatic assertion.
ECO:RCT
GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms.
GO_REF:0000107
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.
mchibucos
2010-12-10T02:44:34Z
eco
ISS: recognized domains
ECO:0000257
motif similarity evidence used in manual assertion
true
true
A type of motif similarity evidence that is used in a manual assertion.
ECO:RCT
A type of motif similarity evidence that is used in an automatic assertion.
mchibucos
2010-12-10T02:44:34Z
eco
ISS: recognized domains
ECO:0000258
motif similarity evidence used in automatic assertion
true
true
A type of motif similarity evidence that is used in an automatic assertion.
ECO:RCT
A type of match to InterPro member signature evidence that is used in an automatic assertion.
mchibucos
2010-12-10T02:54:51Z
eco
ECO:0000259
match to InterPro member signature evidence used in automatic assertion
true
true
A type of match to InterPro member signature evidence that is used in an automatic assertion.
ECO:RCT
A type of match to InterPro member signature evidence that is used in a manual assertion.
mchibucos
2010-12-10T02:54:51Z
eco
ECO:0000260
match to InterPro member signature evidence used in manual assertion
true
true
A type of match to InterPro member signature evidence that is used in a manual assertion.
ECO:RCT
A type of targeting sequence prediction that is used in an automatic assertion.
mchibucos
2010-12-10T03:02:49Z
eco
ISS: targeting sequence prediction
ECO:0000261
targeting sequence prediction evidence used in automatic assertion
true
true
A type of targeting sequence prediction that is used in an automatic assertion.
ECO:RCT
A type of targeting sequence prediction that is used in a manual assertion.
mchibucos
2010-12-10T03:02:49Z
eco
ISS: targeting sequence prediction
ECO:0000262
targeting sequence prediction evidence used in manual assertion
true
true
A type of targeting sequence prediction that is used in a manual assertion.
ECO:RCT
A type of transmembrane domain prediction that is used in an automatic assertion.
mchibucos
2010-12-10T03:28:35Z
eco
ISS: transmembrane domain prediction
ECO:0000263
transmembrane domain prediction evidence used in automatic assertion
true
true
A type of transmembrane domain prediction that is used in an automatic assertion.
ECO:RCT
A type of transmembrane domain prediction that is used in a manual assertion.
mchibucos
2010-12-10T03:28:35Z
eco
ISS: transmembrane domain prediction
ECO:0000264
transmembrane domain prediction evidence used in manual assertion
true
true
A type of transmembrane domain prediction that is used in a manual assertion.
ECO:RCT
A type of sequence orthology evidence that is used in an automatic assertion.
mchibucos
2010-12-10T03:39:41Z
GO_REF:0000019
GO_REF:0000020
GO_REF:0000035
GO_REF:0000049
eco
Ortholog evidence
ortholog evidence
ECO:0000265
sequence orthology evidence used in automatic assertion
true
true
A type of sequence orthology evidence that is used in an automatic assertion.
ECO:RCT
GO_REF:0000019
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
GO_REF:0000020
Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins.
GO_REF:0000035
Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara
GO_REF:0000049
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.
mchibucos
2010-12-10T03:39:41Z
GOECO:ISO
ISO
inferred from sequence orthology
eco
Ortholog evidence
ortholog evidence
ECO:0000266
sequence orthology evidence used in manual assertion
http://geneontology.org/page/iso-inferred-sequence-orthology
true
true
A type of sequence orthology evidence that is used in a manual assertion.
ECO:MCC
GOECO:ISO
inferred from sequence orthology
ISO
GOECO:ISO
inferred from sequence orthology
GOECO:ISO
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.
CollecTF
mchibucos
2010-12-14T01:57:13Z
MI:0411
ELISA evidence
enzyme-linked immunosorbent assay
eco
ECO:0000267
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 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.
ECO:MCC
ECO:SW
PMID:23949770
MI:0411
enzyme linked immunosorbent assay
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.
mchibucos
2010-12-14T02:07:08Z
FCM
eco
ECO:0000268
flow cytometry 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.
ECO:MCC
A type of experimental evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:36:49Z
GOECO:EXP
EXP
inferred from experiment
eco
ECO:0000269
experimental evidence used in manual assertion
http://geneontology.org/page/exp-inferred-experiment
true
true
A type of experimental evidence that is used in a manual assertion.
ECO:MCC
GOECO:EXP
inferred from experiment
EXP
GOECO:EXP
inferred from experiment
GOECO:EXP
A type of expression pattern evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:46:39Z
GOECO:IEP
IEP
inferred from expression pattern
eco
ECO:0000270
expression evidence used in manual assertion
http://geneontology.org/page/iep-inferred-expression-pattern
true
true
A type of expression pattern evidence that is used in a manual assertion.
ECO:MCC
GOECO:IEP
inferred from expression pattern
IEP
GOECO:IEP
inferred from expression pattern
GOECO:IEP
mchibucos
2010-12-20T05:51:58Z
eco
ECO:0000271
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
true
A type of Affymetrix GeneChip evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:53:36Z
Affymetrix array experiment evidence
eco
ECO:0000272
Affymetrix GeneChip evidence used in manual assertion
true
true
A type of Affymetrix GeneChip evidence that is used in a manual assertion.
ECO:MCC
A type of cDNA to DNA expression microarray evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:55:49Z
ECO:0001178
ECO:0005525
eco
DNA microarray|RNA microarray
ECO:0000273
cDNA to DNA expression microarray evidence used in manual assertion
true
true
A type of cDNA to DNA expression microarray evidence that is used in a manual assertion.
ECO:MCC
A type of differential methylation hybridization evidence that is used in a manual assertion.
mchibucos
2010-12-20T05:58:44Z
CpG island microarray evidence
CpG island microarray evidence used in manual assertion
eco
ECO:0000274
differential methylation hybridization evidence used in manual assertion
true
true
A type of differential methylation hybridization evidence that is used in a manual assertion.
ECO:RCT
A type of expression microarray evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:01:26Z
eco
differential gene expression evidence from microarray experiment
ECO:0000275
expression microarray evidence used in manual assertion
true
true
A type of expression microarray evidence that is used in a manual assertion.
ECO:MCC
A type of cRNA to DNA expression microarray evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:03:28Z
genomic microarray evidence
genomic microarray evidence used in manual assertion
eco
ECO:0000276
cRNA to DNA expression microarray evidence used in manual assertion
true
true
A type of cRNA to DNA expression microarray evidence that is used in a manual assertion.
ECO:RCT
A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
mchibucos
2010-12-20T06:05:20Z
eco
ECO:0000277
Nimblegen array evidence used in manual assertion
true
true
A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
ECO:MCC
A type of array-based sequence capture evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:09:45Z
DNA microarray
oligonucleotide microarray evidence
oligonucleotide microarray evidence used in manual assertion
eco
SNP array evidence
single nucleotide polymorphism array evidence
ECO:0000278
array-based sequence capture evidence used in manual assertion
true
true
A type of array-based sequence capture evidence that is used in a manual assertion.
ECO:MCC
A type of Western blot assay that is used in a manual assertion.
mchibucos
2010-12-20T06:20:01Z
eco
IEP: protein levels (e.g. Western blots)
Western blot expression analysis
protein immunoblot
ECO:0000279
western blot evidence used in manual assertion
true
true
A type of Western blot assay that is used in a manual assertion.
ECO:MCC
A type of protein expression level analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:21:54Z
eco
ECO:0000280
protein expression level evidence used in manual assertion
true
true
A type of protein expression level analysis that is used in a manual assertion.
ECO:MCC
A type of expression library screen evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:24:05Z
eco
IEP: expression library screening
ECO:0000281
expression library screen evidence used in manual assertion
true
true
A type of expression library screen evidence that is used in a manual assertion.
ECO:MCC
A type of heterologous protein expression analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:27:04Z
eco
IDA: protein expression in heterologous system
ECO:0000282
heterologous protein expression evidence used in manual assertion
true
true
A type of heterologous protein expression analysis that is used in a manual assertion.
ECO:MCC
A type of protein expression spatial pattern analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:31:44Z
eco
ECO:0000283
spatial pattern of protein expression evidence used in manual assertion
true
true
A type of protein expression spatial pattern analysis that is used in a manual assertion.
ECO:MCC
A type of protein expression analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:33:46Z
eco
ECO:0000284
protein expression evidence used in manual assertion
true
true
true
A type of protein expression analysis that is used in a manual assertion.
ECO:MCC
A type of DNA to cDNA expression microarray evidence that is used in a manual assertion.
mchibucos
2010-12-20T06:41:33Z
REM evidence
RNA expression microarray evidence
microarray RNA expression level evidence
eco
IEP: transcript levels (e.g. microarray data)
ECO:0000285
DNA to cDNA expression microarray evidence used in manual assertion
true
true
A type of DNA to cDNA expression microarray evidence that is used in a manual assertion.
ECO:MCC
A type of differential hybridization experiment that is used in a manual assertion.
mchibucos
2010-12-20T06:55:14Z
eco
IEP: differential hybridization
ECO:0000287
differential hybridization evidence used in manual assertion
true
true
A type of differential hybridization experiment that is used in a manual assertion.
ECO:MCC
A type of RNA protection assay that is used in a manual assertion.
mchibucos
2010-12-20T06:57:33Z
ribonuclease protection assay
eco
IEP: RNA protection assay|RPA
RNAse protection assay
ECO:0000288
RNA protection assay evidence used in manual assertion
true
true
A type of RNA protection assay that is used in a manual assertion.
ECO:MCC
A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
mchibucos
2010-12-20T06:59:18Z
eco
ECO:0000289
spatial pattern of transcript expression evidence used in manual assertion
true
true
A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
ECO:MCC
A type of subtractive hybridization experiment that is used in a manual assertion.
mchibucos
2010-12-20T07:00:48Z
eco
IEP: subtractive hybridization
ECO:0000290
subtractive hybridization evidence used in manual assertion
true
true
A type of subtractive hybridization experiment that is used in a manual assertion.
ECO:MCC
A type of transcript expression evidence that is used in a manual assertion.
mchibucos
2010-12-20T07:02:08Z
ECO:0000286
transcript expression level evidence
eco
ECO:0000291
transcript expression evidence used in manual assertion
true
true
A type of transcript expression evidence that is used in a manual assertion.
ECO:MCC
A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
mchibucos
2011-01-10T03:36:25Z
anti-sense
eco
ECO:0000292
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.
morpholino experiment evidence
A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
ECO:MCC
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.
mchibucos
2011-01-10T04:23:50Z
MI:0657
SELEX evidence
in vitro selection evidence
eco
in vitro evolution evidence
ECO:0000293
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
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.
ECO:MCC
url:http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment
MI:0657
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).
mchibucos
2011-01-10T06:16:20Z
B1H evidence
eco
ECO:0000294
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.
bacterial one-hybrid evidence
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).
ECO:MCC
A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
mchibucos
2011-01-11T12:54:50Z
ECO:0000357
WTSS
whole transcriptome shotgun sequencing
differential gene expression evidence from RNA-seq experiment
eco
RNA sequencing
ECO:0000295
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.
RNA-seq evidence
A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
ECO:MCC
whole transcriptome shotgun sequencing
PMID:18611170
A type of transcriptional activation assay evidence that is based on transcriptional activation of a green fluorescent protein (GFP) reporter gene.
mchibucos
2011-01-11T02:31:19Z
localization of GFP transcript
eco
ECO:0000296
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 green fluorescent protein (GFP) reporter gene.
ECO:MCC
ECO:RCT
A type of transcriptional activation assay evidence that is based on transcriptional activation of a LacZ reporter gene.
mchibucos
2011-01-11T02:53:19Z
eco
ECO:0000297
This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of LacZ protein".
LacZ transcript localization evidence
A type of transcriptional activation assay evidence that is based on transcriptional activation of a LacZ reporter gene.
ECO:MCC
A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
mchibucos
2011-01-11T03:28:49Z
eco
ECO:0000298
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.
cleavage arrested development evidence
A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
ECO:MCC
A type of cleavage arrested development that arises after treatment with cytochalasin.
mchibucos
2011-01-11T03:30:29Z
eco
ECO:0000299
Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments.
cytochalasin experiment evidence
A type of cleavage arrested development that arises after treatment with cytochalasin.
ECO:MCC
A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
mchibucos
2011-01-11T03:48:50Z
GFP immunolocalization evidence
eco
ECO:0000300
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 data that was generated using green fluorescent protein (GFP) as a marker.
ECO:MCC
A type of immunolocalization evidence that was generated using LacZ protein as a marker.
mchibucos
2011-01-11T04:06:40Z
LacZ protein immunolocalization evidence
eco
ECO:0000301
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 immunolocalization evidence that was generated using LacZ protein as a marker.
ECO:MCC
A type of author statement that is used in a manual assertion.
mchibucos
2011-01-20T02:26:47Z
eco
ECO:0000302
author statement used in manual assertion
true
true
A type of author statement that is used in a manual assertion.
ECO:MCC
A type of non-traceable author statement that is used in a manual assertion.
mchibucos
2011-01-20T02:29:50Z
GOECO:NAS
NAS
non-traceable author statement
eco
ECO:0000303
non-traceable author statement used in manual assertion
http://geneontology.org/page/nas-non-traceable-author-statement
true
true
A type of non-traceable author statement that is used in a manual assertion.
ECO:MCC
GOECO:NAS
non-traceable author statement
NAS
GOECO:NAS
non-traceable author statement
GOECO:NAS
A type of traceable author statement that is used in a manual assertion.
mchibucos
2011-01-20T02:31:03Z
GOECO:TAS
TAS
traceable author statement
eco
ECO:0000304
traceable author statement used in manual assertion
http://geneontology.org/page/tas-traceable-author-statement
true
true
A type of traceable author statement that is used in a manual assertion.
ECO:MCC
GOECO:TAS
traceable author statement
TAS
GOECO:TAS
traceable author statement
GOECO:TAS
A type of curator inference that is used in a manual assertion.
mchibucos
2011-01-20T02:33:32Z
GOECO:IC
IC
inferred by curator
eco
ECO:0000305
curator inference used in manual assertion
http://geneontology.org/page/ic-inferred-curator
true
true
A type of curator inference that is used in a manual assertion.
ECO:MCC
GOECO:IC
inferred by curator
IC
GOECO:IC
inferred by curator
GOECO:IC
A type of inference from background scientific knowledge that is used in a manual assertion.
mchibucos
2011-01-20T02:35:11Z
eco
ECO:0000306
inference from background scientific knowledge used in manual assertion
true
true
A type of inference from background scientific knowledge that is used in a manual assertion.
ECO:MCC
A type of no biological data found that is used in a manual assertion.
mchibucos
2011-01-20T02:43:18Z
GOECO:ND
ND
no biological data available
eco
ECO:0000307
no biological data found used in manual assertion
http://geneontology.org/page/nd-no-biological-data-available
true
true
A type of no biological data found that is used in a manual assertion.
ECO:MCC
GOECO:ND
no biological data available
ND
GOECO:ND
no biological data available
GOECO:ND
A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
mchibucos
2011-02-04T05:41:26Z
eco
ECO:0000308
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.
biological aspect of ancestor evidence
A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
ECO:MCC
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.
mchibucos
2011-02-17T01:33:09Z
CAGE
eco
ECO:0000309
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 a cap-trapper system.
ECO:MCC
CAGE
PMID:16489339
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.
mchibucos
2011-02-17T01:33:34Z
eco
nanoCAGE
ECO:0000310
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 transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching.
ECO:MCC
nanoCAGE
PMID:20543846
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.
mchibucos
2011-03-02T05:24:13Z
eco
ECO:0000311
imported information
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.
ECO:MCC
A type of imported information that is used in a manual assertion.
mchibucos
2011-03-02T05:29:44Z
eco
ECO:0000312
imported information used in manual assertion
true
true
A type of imported information that is used in a manual assertion.
ECO:MCC
A type of imported information that is used in an automatic assertion.
mchibucos
2011-03-02T05:33:43Z
eco
ECO:0000313
imported information used in automatic assertion
true
true
A type of imported information that is used in an automatic assertion.
ECO:MCC
A type of direct assay evidence that is used in a manual assertion.
mchibucos
2011-10-28T04:59:31Z
GOECO:IDA
inferred from direct assay
eco
IDA
ECO:0000314
direct assay evidence used in manual assertion
http://geneontology.org/page/ida-inferred-direct-assay
true
true
A type of direct assay evidence that is used in a manual assertion.
ECO:MCC
GOECO:IDA
inferred from direct assay
inferred from direct assay
GOECO:IDA
IDA
GOECO:IDA
A type of mutant phenotype evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:12:49Z
GOECO:IMP
eco
IMP
inferred from mutant phenotype
ECO:0000315
mutant phenotype evidence used in manual assertion
http://geneontology.org/page/imp-inferred-mutant-phenotype
true
true
A type of mutant phenotype evidence that is used in a manual assertion.
ECO:MCC
GOECO:IMP
inferred from mutant phenotype
IMP
GOECO:IMP
inferred from mutant phenotype
GOECO:IMP
A type of genetic interaction experiment evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:14:42Z
GOECO:IGI
IGI
inferred from genetic interaction
eco
ECO:0000316
genetic interaction evidence used in manual assertion
http://geneontology.org/page/igi-inferred-genetic-interaction
true
true
A type of genetic interaction experiment evidence that is used in a manual assertion.
ECO:MCC
GOECO:IGI
inferred from genetic interaction
IGI
GOECO:IGI
inferred from genetic interaction
GOECO:IGI
A type of genomic context evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:22:53Z
GOECO:IGC
IGC
inferred from genomic context
eco
ECO:0000317
genomic context evidence used in manual assertion
http://geneontology.org/page/igc-inferred-genomic-context
IGC
GOECO:IGC
inferred from genomic context
GOECO:IGC
true
true
A type of genomic context evidence that is used in a manual assertion.
ECO:MCC
GOECO:IGC
inferred from genomic context
A type of biological aspect of ancestor evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:23:51Z
GOECO:IBA
IBA
inferred from biological aspect of ancestor
eco
ECO:0000318
biological aspect of ancestor evidence used in manual assertion
http://geneontology.org/page/iba-inferred-biological-aspect-ancestor
true
true
A type of biological aspect of ancestor evidence that is used in a manual assertion.
ECO:MCC
GOECO:IBA
inferred from biological aspect of ancestor
IBA
GOECO:IBA
inferred from biological aspect of ancestor
GOECO:IBA
A type of biological aspect of descendant evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:25:09Z
GOECO:IBD
IBD
inferred from biological aspect of descendant
eco
ECO:0000319
biological aspect of descendant evidence used in manual assertion
http://geneontology.org/page/ibd-inferred-biological-aspect-descendent
true
true
A type of biological aspect of descendant evidence that is used in a manual assertion.
ECO:MCC
GOECO:IBD
inferred from biological aspect of descendant
IBD
GOECO:IBD
inferred from biological aspect of descendant
GOECO:IBD
A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:25:48Z
GOECO:IKR
GOECO:IMR
IKR
IMR
inferred from key residues
inferred from missing residues
eco
ECO:0000320
phylogenetic determination of loss of key residues evidence used in manual assertion
http://geneontology.org/page/ikr-inferred-key-residues
true
true
A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
ECO:MCC
GOECO:IKR
inferred from key residues
GOECO:IMR
inferred from missing residues
IKR
GOECO:IKR
IMR
GOECO:IKR
inferred from key residues
GOECO:IKR
inferred from missing residues
GOECO:IKR
A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
mchibucos
2011-10-28T05:26:42Z
GOECO:IRD
IRD
inferred from rapid divergence
eco
ECO:0000321
rapid divergence from ancestral sequence evidence used in manual assertion
http://geneontology.org/page/ird-inferred-rapid-divergence
true
true
A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
ECO:MCC
GOECO:IRD
inferred from rapid divergence
IRD
GOECO:IRD
inferred from rapid divergence
GOECO:IRD
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.
mchibucos
2011-12-13T12:04:48Z
GO_REF:0000037
GO_REF:0000039
GO_REF:0000041
eco
ECO:0000322
imported manually asserted information used in automatic 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.
ECO:MCC
GO_REF:0000037
Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.
GO_REF:0000039
Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.
GO_REF:0000041
IEA (UniProt UniPathway)
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.
mchibucos
2011-12-13T02:06:25Z
GO_REF:0000038
GO_REF:0000040
eco
ECO:0000323
imported automatically asserted information used in automatic assertion
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.
ECO:MCC
GO_REF:0000038
Gene Ontology annotation based on automatic assignment of UniProtKB keywords in UniProtKB/TrEMBL entries.
GO_REF:0000040
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.
mchibucos
2012-02-23T12:01:43Z
ECO:0001122
ECO:0005024
ECO:MCC
radiologic test evidence
eco
ECO:0000324
imaging assay evidence
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.
mchibucos
2012-05-16T11:46:27Z
chromatographic evidence
eco
ECO:0000325
chromatography evidence
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.
ECO:MCC
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.
mchibucos
2012-06-08T11:03:59Z
eco
ECO:0000326
transcript splice pattern evidence
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.
ECO:MCC
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
mchibucos
2012-06-08T11:11:24Z
eco
ECO:0000327
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 whole transcript, rather than its constituent features.
ECO:MCC
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.
mchibucos
2012-06-08T11:21:57Z
eco
ECO:0000328
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.
coding sequence 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.
ECO:MCC
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.
mchibucos
2012-06-08T11:40:03Z
eco
ECO:0000329
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 used in manual assertion
true
true
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.
ECO:MCC
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.
mchibucos
2012-06-08T11:43:47Z
eco
ECO:0000330
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.
coding sequence splice pattern evidence used in manual assertion
true
true
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.
ECO:MCC
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.
mchibucos
2012-06-08T11:48:09Z
eco
ECO:0000331
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.
coding sequence splice pattern evidence used in automatic assertion
true
true
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.
ECO:MCC
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.
mchibucos
2012-06-08T11:49:17Z
eco
ECO:0000332
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 used in automatic assertion
true
true
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.
ECO:MCC
A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
mchibucos
2012-07-31T02:56:43Z
SDS-PAGE evidence
eco
ECO:0000333
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 gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
ECO:MCC
PubMed:4861258
url:http://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html
url:http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Protein/protein18.html
A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined.
mchibucos
2012-07-31T03:19:32Z
eco
ECO:0000334
An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system.
particle size and count assay 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.
ECO:MCC
A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
mchibucos
2012-07-31T03:52:46Z
eco
ECO:0000335
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.
substance quantification evidence
A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
ECO:MCC
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.
mchibucos
2012-08-24T12:03:58Z
fitness profiling
eco
ECO:0000336
competitive growth assay evidence
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.
GOC:MAH
PMID:14718172
PMID:20537132
fitness profiling
GOC:MAH
PMID:20537132
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.
mchibucos
2012-08-24T12:11:51Z
ECO:0005026
eco
ECO:0000337
Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch.
gel electrophoresis evidence
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.
ECO:MCC
wikipedia:Gel_electrophoresis
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.
mchibucos
2012-08-24T12:34:01Z
PFGE
eco
ECO:0000338
pulsed-field gel electrophoresis evidence
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.
PMID:6373014
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.
mchibucos
2012-08-24T12:42:37Z
2-D agarose gel electrophoresis
eco
ECO:0000339
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 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.
PMID:16118435
PMID:8594382
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.
mchibucos
2012-08-24T01:27:58Z
minichromosome maintenance assay evidence
eco
ECO:0000340
Loss per generation is determined by comparing colony numbers on selective and non-selective media.
plasmid maintenance assay 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.
ECO:MCC
PMID:6323245
minichromosome maintenance assay evidence
PMID:6323245
A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
mchibucos
2012-08-24T01:48:24Z
eco
ECO:0000341
specific protein inhibition by antibody evidence
A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
ECO:MCC
A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
mchibucos
2013-04-03T04:22:05Z
eco
ECO:0000342
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 RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
ECO:MCC
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.
mchibucos
2013-04-03T04:41:48Z
eco
ECO:0000343
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 from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
ECO:MCC
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.
mchibucos
2013-04-03T04:50:46Z
eco
ECO:0000344
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
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.
ECO:MCC
mchibucos
2013-04-03T05:10:34Z
eco
ECO:0000345
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.
mchibucos
2013-04-04T04:37:35Z
eco
ECO:0000346
Support of intron position by RNA-seq alignment evidence used in manual assertion
true
true
A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
ECO:MCC
A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
mchibucos
2013-04-04T04:38:45Z
eco
ECO:0000347
Support of intron position by RNA-seq alignment evidence used in automatic assertion
true
true
A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
ECO:MCC
A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
mchibucos
2013-04-04T04:40:19Z
eco
ECO:0000348
Full support of intron position by RNA-seq alignment evidence used in automatic assertion
true
true
A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
ECO:MCC
A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
mchibucos
2013-04-04T04:41:34Z
eco
ECO:0000349
Full support of intron position by RNA-seq alignment evidence used in manual assertion
true
true
A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
ECO:MCC
A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
mchibucos
2013-04-04T04:42:53Z
eco
ECO:0000350
Partial support of intron position by RNA-seq alignment evidence used in automatic assertion
true
true
A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
ECO:MCC
A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
mchibucos
2013-04-04T04:43:56Z
eco
ECO:0000351
Partial support of intron position by RNA-seq alignment evidence used in manual assertion
true
true
A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
ECO:MCC
A type of evidence that is used in an manual assertion.
mchibucos
eco
ECO:0000352
evidence used in manual assertion
true
true
A type of evidence that is used in an manual assertion.
ECO:MCC
A type of physical interaction evidence that is used in a manual assertion.
mchibucos
2013-10-31T21:01:27Z
GOECO:IPI
IPI
inferred from physical interaction
eco
ECO:0000353
physical interaction evidence used in manual assertion
http://geneontology.org/page/ipi-inferred-physical-interaction
true
true
A type of physical interaction evidence that is used in a manual assertion.
ECO:MCC
GOECO:IPI
inferred from physical interaction
IPI
GOECO:IPI
inferred from physical interaction
GOECO:IPI
A type of gene neighbors evidence that is used in a manual assertion.
mchibucos
2013-11-19T13:37:24Z
inferred from genome cluster
GO_REF:0000025
eco
ICL
ECO:0000354
gene neighbors evidence used in manual assertion
true
true
A type of gene neighbors evidence that is used in a manual assertion.
ECO:MCC
GO_REF:0000025
operon structure as IGC evidence
A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
mchibucos
2014-04-22T17:02:31Z
eco
ECO:0000355
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.
phylogenetic distribution evidence
A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
ECO:MCC
PMID:21238344
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.
mchibucos
2014-09-26T16:25:47Z
eco
ECO:0000358
differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact)
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.
PMID:19725948
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.
mchibucos
2014-09-26T16:26:48Z
eco
ECO:0000359
differential geneset expression evidence from RNA-seq 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.
PMC:2881125
mchibucos
2014-09-26T16:39:11Z
eco
ECO:0000360
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.
mchibucos
2015-07-14T11:19:37Z
eco
ECO:0000361
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.
inferential evidence
A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
ECO:MCC
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.
mchibucos
2015-07-14T11:24:27Z
eco
ECO:0000362
evidence based on computational logical inference
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.
ECO:MCC
GOC:MC
A type of evidence based on computational logical inference that is used in automatic assertion.
mchibucos
2015-07-14T11:35:08Z
GO_REF:0000108
eco
ECO:0000363
evidence based on computational logical inference used in automatic assertion
true
true
A type of evidence based on computational logical inference that is used in automatic assertion.
ECO:MCC
GO_REF:0000108
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.
mchibucos
2015-07-14T11:44:19Z
eco
ECO:0000364
evidence based on logical inference from manual annotation used in automatic assertion
A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
ECO:MCC
A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
mchibucos
2015-07-14T11:45:25Z
eco
ECO:0000366
evidence based on logical inference from automatic 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.
ECO:MCC
A type of evidence that is used in an automatic assertion.
cjm
GOECO:IEA
GO_REF:0000003
GO_REF:0000004
GO_REF:0000023
IEA
inferred from electronic annotation
eco
ECO:0000501
evidence used in automatic assertion
http://geneontology.org/page/automatically-assigned-evidence-codes
true
true
A type of evidence that is used in an automatic assertion.
ECO:cjm
GOECO:IEA
inferred from electronic annotation
GO_REF:0000003
Gene Ontology annotation based on Enzyme Commission mapping.
GO_REF:0000004
Gene Ontology annotation based on Swiss-Prot keyword mapping.
GO_REF:0000023
Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.
IEA
GOECO:IEA
inferred from electronic annotation
GOECO:IEA
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001001
3D cell culture evidence
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.
PMID:21042962
url:http://volttecnologia.com.br/wp-content/uploads/2016/03/Drug-discovery.pdf
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001002
[3H]arachidonic acid release assay evidence
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.
ISBN:0323152295
PMID:20693009
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001003
[3H]-thymidine incorporation 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.
OBI:0000669
url:http://www.scientistsolutions.com/forum/cell-culture-and-tissue-culture-proliferationapoptosis/3h-thymidine-incorporation-assay-rat-1a
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).
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001004
51Cr release 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).
PMC:3929704
url:http://www4.mpbio.com/ecom/docs/proddata.nsf/5f64ffd4f38c2fda8525645d00769d68/53d2a75653615bab852568cb00572ff3?OpenDocument
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
7-AAD staining evidence
7-amino-actinomycin D staining evidence
eco
ECO:0001005
7-aminoactinomycin staining evidence
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.
ECO:RCT
A type of cell-based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001006
adhesion assay evidence
A type of cell-based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells.
PMID:15576904
PMID:21909903
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
Adoptive immunotherapy
passive immunization
eco
ECO:0001007
adoptive cell transfer evidence
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.
ECO:SN
url:http://jco.ascopubs.org/content/23/10/2346.full.pdf+html
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001008
alamarBlue assay evidence
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.
PMC:3478843
url:https://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/cell-profilteration-assay-protocols/cell-viability-with-alamarblue.html
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
Allotransplantation
allografting
tissue grafting
eco
ECO:0001009
allograft transplantation experiment evidence
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.
ECO:SN
url:http://www.nature.com/subjects/allograft
url:http://www.organdonor.gov/about/terms_and_topics/
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001010
anion-exchange chromatography 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.
ECO:SN
PMID:20978968
url:http://www.bio-rad.com/en-us/applications-technologies/anion-exchange-chromatography
url:http://www.uta.edu/faculty/sawasthi/Enzymology-4351-5324/Class%20Syllabus%20Enzymology/Ion%20Exchange%20Chromatography-1.pdf
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001011
annexin-V staining evidence
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.
PMC:3169266
A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001012
behavioral assay evidence
A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning.
PMID:24462904
A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001013
blocking monoclonal antibody evidence
A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies.
PMID:11292349
url:http://www.sciencedirect.com/science/article/pii/S0140673600034966
A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001014
blocking peptide evidence
A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets.
ECO:RCT
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001015
blocking polyclonal antibody evidence
A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001016
blood test evidence
A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
ECO:SN
url:https://www.nhlbi.nih.gov/health/health-topics/topics/bdt
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001017
Boyden chamber assay evidence
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.
PMID:13872176
PMID:15576901
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
ECO:0005010
cell proliferation marker detection assay evidence
5-bromo-2'-deoxyuridine incorporation assay evidence
BUdR incorporation assay evidence
BrdU incorporation assay evidence
BrdUrd incorporation assay evidence
eco
ECO:0001018
bromodeoxyuridine incorporation assay evidence
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.
PMID:23690005
A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001019
caspase 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.
PMID:18314058
PMID:25086023
A type of cell-based assay evidence resulting from the quantification of a sample of cells.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001020
cell counting evidence
A type of cell-based assay evidence resulting from the quantification of a sample of cells.
ECO:RCT
A type of cell-based assay evidence resulting from the quantification of cell permeability.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001021
cell permeability assay evidence
A type of cell-based assay evidence resulting from the quantification of cell permeability.
PMID:16962665
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
CFDA-SE staining evidence
CFSE-staining evidence
eco
ECO:0001022
carboxyfluorescein diacetate succinimidyl ester staining evidence
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.
PMC:3185625
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
CLIA evidence
eco
ECO:0001023
chemiluminescence-linked immunoassay 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.
PMID:659901
A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001024
chimeric protein evidence
A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product.
PMID:22588898
PMID:25832756
A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001025
co-electrophoresis evidence
A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions.
PMID:7668395
A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001026
co-localization evidence
A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location.
PMC:3074624
A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001027
colony counting evidence
A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish.
PMID:16558698
PMID:23457446
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001028
co-sedimentation assay evidence
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.
MI:0027
A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001029
comet assay evidence
A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration.
OBI:0302736
PMID:10737956
A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001030
conditional knockout evidence
A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal.
PMC:3572410
A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001031
conditional knockin evidence
A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation.
PMID:16832820
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001032
constitutively active mutant evidence
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.
PMID:12217490
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
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001033
cross-linking evidence
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
PMID:15530987
PMID:19241040
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001034
crystallography evidence
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.
MI:0114
A type of histochemistry evidence resulting from localizing chemical components of cells and organelles on histological sections.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001035
cytochemistry evidence
A type of histochemistry evidence resulting from localizing chemical components of cells and organelles on histological sections.
PMID:11597006
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001036
cytochrome C release assay evidence
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.
PMID:10914021
PMID:12815469
A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
DAPI staining evidence
diaminophenylindole staining
eco
ECO:0001037
4',6-diamidino-2-phenylindole staining evidence
A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence.
PMID:8580206
url:https://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/protocols/dapi-imaging-protocol.html
A type of experimental phenotypic evidence resulting from a mutation in which there is a removal of one or more contiguous nucleotides.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
ECO:0005510
eco
ECO:0001038
deletion mutation evidence
A type of experimental phenotypic evidence resulting from a mutation in which there is a removal of one or more contiguous nucleotides.
SO:0000159
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001039
DNA laddering assay evidence
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.
PMC:4401164
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.
CollecTF
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
RNA dot blot
ECO:0001040
RNA dot blot assay evidence
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.
ECO:SW
PMID:21424648
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001042
dominant-negative mutant evidence
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.
PMC:2217636
PMID:8018332
A type of Edman degradation evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:59:00Z
eco
ECO:0001043
Edman degradation evidence used in manual assertion
true
true
A type of Edman degradation evidence that is used in a manual assertion.
ECO:MCC
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001044
Edman degradation evidence
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.
OBI:0000705
doi:10.3891/acta.chem.scand.04-0283
A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001045
eTag assay evidence
A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters.
PMID:15137949
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001046
filter binding assay evidence
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.
PMID:23028069
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001047
fluorescence in situ hybridization evidence
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.
PMC:346675
PMID:6812046
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
FRET
eco
ECO:0001048
fluorescence resonance energy transfer 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.
PMID:11516318
PMID:15696158
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001049
gel-filtration 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.
CHMO:0001011
doi:10.1038/nmeth0506-410
A type of histology evidence resulting from the identification of chemical components in cells and tissues.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001050
histochemistry evidence
A type of histology evidence resulting from the identification of chemical components in cells and tissues.
MMO:0000497
A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001051
histology evidence
A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues.
OBI:0600020
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.
mchibucos
2014-03-16T11:30:54Z
HPLC evidence
eco
ECO:0001052
high-performance liquid chromatography evidence
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.
PMID:16376355
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001053
immunocytochemistry 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.
MI:1200
OBI:0001986
A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001054
immunodepletion evidence
A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample.
BAO:0002505
A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001055
immunohistochemistry evidence
A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections.
OBI:0001986
A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001056
induced mutation evidence
A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation.
OBI:0001154
A type of acetylation assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001057
in vitro acetylation assay evidence
A type of acetylation assay evidence used in an in vitro experiment.
ECO:SN
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
A type of cleavage assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001058
in vitro cleavage assay evidence
A type of cleavage assay evidence used in an in vitro experiment.
PMID:21121091
A type of deubiquitination assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001059
in vitro deubiquitination assay evidence
A type of deubiquitination assay evidence used in an in vitro experiment.
ECO:SN
PMID:19692941
SIB:PG
A type of deacetylation assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001060
in vitro deacetylation assay evidence
A type of deacetylation assay evidence used in an in vitro experiment.
ECO:SN
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
A type of defarnesylation assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001061
in vitro defarnesylation assay evidence
A type of defarnesylation assay evidence used in an in vitro experiment.
ECO:SN
PMID:16126733
SIB:PG
A type of demethylation assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001062
in vitro demethylation assay evidence
A type of demethylation assay evidence used in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Demethylation
A type of desumoylation assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001063
in vitro desumoylation assay evidence
A type of desumoylation assay evidence used in an in vitro experiment.
ECO:SN
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
A type of farnesylation assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001064
in vitro farnesylation assay evidence
A type of farnesylation assay evidence used in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Farnesyltransferase
A type of methylation assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001065
in vitro methylation assay evidence
A type of methylation assay evidence used in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Methylation
A type of palmitoylation assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001066
in vitro palmitoylation assay evidence
A type of palmitoylation assay evidence used in an in vitro experiment.
ECO:SN
PMID:17077383
SIB:PG
A type of phosphatase assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001067
in vitro phosphatase assay evidence
A type of phosphatase assay evidence used in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Phosphatase
A type of protein kinase assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001068
in vitro protein kinase assay evidence
A type of protein kinase assay evidence used in an in vitro experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Protein_kinase
url:http://en.wikipedia.org/wiki/Protein_phosphorylation
A type of polyADP-ribosylation assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001069
in vitro polyADP-ribosylation assay evidence
A type of polyADP-ribosylation assay evidence used in an in vitro experiment.
ECO:SN
PMID:21870253
SIB:PG
A type of sumoylation assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001070
in vitro sumoylation assay evidence
A type of sumoylation assay evidence used in an in vitro experiment.
ECO:SN
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
A type of transcription assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001071
in vitro transcription assay evidence
A type of transcription assay evidence used in an in vitro experiment.
ECO:SN
ECO:SW
PMID:21125481
SIB:PG
A type of translation assay evidence used in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001072
in vitro translation assay evidence
A type of translation assay evidence used in an in vitro experiment.
ECO:SN
PMID:18230759
SIB:PG
A type of ubiquitination assay evidenceused in an in vitro experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001073
in vitro ubiquitination assay evidence
A type of ubiquitination assay evidenceused in an in vitro experiment.
ECO:SN
PMID:19692941
SIB:PG
A type of acetylation assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001074
in vivo acetylation assay evidence
A type of acetylation assay evidence used in an in vivo experiment.
ECO:SN
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
A type of cleavage assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001075
in vivo cleavage assay evidence
A type of cleavage assay evidence used in an in vivo experiment.
ECO:SN
PMID:22154596
A type of deacetylation assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001076
in vivo deacetylation assay evidence
A type of deacetylation assay evidence used in an in vivo experiment.
ECO:SN
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
A type of defarnesylation assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001077
in vivo defarnesylation assay evidence
A type of defarnesylation assay evidence used in an in vivo experiment.
ECO:SN
PMID:15556768
PMID:16507103
SIB:PG
A type of demethylation assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001078
in vivo demethylation assay evidence
A type of demethylation assay evidence used in an in vivo experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Demethylation
A type of deubiquitination assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001079
in vivo deubiquitination assay evidence
A type of deubiquitination assay evidence used in an in vivo experiment.
ECO:SN
PMID:19692941
SIB:PG
A type of desumoylation assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001080
in vivo desumoylation assay evidence
A type of desumoylation assay evidence used in an in vivo experiment.
ECO:SN
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
A type of farnesylation assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001081
in vivo farnesylation assay evidence
A type of farnesylation assay evidence used in an in vivo experiment.
ECO:SN
PMID:9030603
SIB:PG
A type of methylation assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001082
in vivo methylation assay evidence
A type of methylation assay evidence used in an in vivo experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Methylation
A type of palmitoylation assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001083
in vivo palmitoylation assay evidence
A type of palmitoylation assay evidence used in an in vivo experiment.
ECO:SN
PMID:10329400
SIB:PG
A type of phosphatase assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001084
in vivo phosphatase assay evidence
A type of phosphatase assay evidence used in an in vivo experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Phosphatase
A type of protein kinase assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001085
in vivo protein kinase assay evidence
A type of protein kinase assay evidence used in an in vivo experiment.
ECO:SN
SIB:PG
url:http://en.wikipedia.org/wiki/Protein_kinase
url:http://en.wikipedia.org/wiki/Protein_phosphorylation
A type of sumoylation assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001086
in vivo sumoylation assay evidence
A type of sumoylation assay evidence used in an in vivo experiment.
ECO:SN
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
A type of transcription assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001087
in vivo transcription assay evidence
A type of transcription assay evidence used in an in vivo experiment.
ECO:SN
PMID:12181418
SIB:PG
A type of translation assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001088
in vivo translation assay evidence
A type of translation assay evidence used in an in vivo experiment.
ECO:SN
PMID:24901308
SIB:PG
A type of ubiquitination assay evidence used in an in vivo experiment.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001089
in vivo ubiquitination assay evidence
A type of ubiquitination assay evidence used in an in vivo experiment.
ECO:SN
PMID:19692941
SIB:PG
A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001090
knockin evidence
A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence.
PMID:18077807
PMID:21800101
A type of genetic transformation evidence resulting from the removal of a particular gene (or genes), disrupting the function and allowing for functional analysis.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001091
knockout evidence
A type of genetic transformation evidence resulting from the removal of a particular gene (or genes), disrupting the function and allowing for functional analysis.
PMC:2782548
A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001092
lipid binding assay evidence
A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid.
PMID:22848065
PMID:23681540
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
LUMIER assay
eco
ECO:0001093
luminescence-based mammalian interactome mapping assay evidence
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.
MI:0729
PMID:15761153
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001094
macroscopy 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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001095
mammalian 2-hybrid 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.
ECO:RCT
PMID:9043710
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001096
mass spectrometry evidence
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.
OBI:0000470
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001097
medical imaging evidence
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.
url:http://www.fda.gov/Radiation-EmittingProducts/RadiationEmittingProductsandProcedures/MedicalImaging/ucm2005914.htm
A type of direct assay evidence where a microscope was used to view a sample.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001098
microscopy evidence
A type of direct assay evidence where a microscope was used to view a sample.
ECO:MCC
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
ECO:0001135
wound healing assay evidence
eco
ECO:0001099
motility wound healing assay evidence
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium
eco
ECO:0001100
MTS assay evidence
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.
NBK:144065
PMID:1867954
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
eco
ECO:0001101
MTT assay evidence
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.
NBK:144065
PMID:6606682
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).
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001102
multiplex bead-based immunoassay evidence
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).
PMC:1534009
A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001103
natural variation mutant evidence
A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits.
ECO:RCT
A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001104
nuclear fragmentation evidence
A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death.
PMID:16738861
A type of structure determination evidence resulting from the use of an MRI to provide chemical information about tissue metabolites.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
NMR spectroscopy
eco
ECO:0001105
nuclear magnetic resonance spectroscopy evidence
A type of structure determination evidence resulting from the use of an MRI to provide chemical information about tissue metabolites.
PMID:16428685
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001106
nuclease protection assay 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.
PMID:17486122
PMID:18428580
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001107
nucleotide analog incorporation assay evidence
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.
PMC:3149870
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001108
phage display 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.
MI:0084
PMID:11680867
A type of protein assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001109
phosphoamino acid analysis evidence
A type of protein assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis.
PMID:11680867
PMID:18429115
SIB:PG
mchibucos
2014-03-16T11:30:54Z
phosphopeptide affinity enrichment evidence
eco
ECO:0001110
peptide affinity enrichment evidence
A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001111
physical examination evidence
A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample.
ECO:RCT
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
phosphopeptide array evidence
eco
ECO:0001112
peptide array evidence
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.
PMID:21243154
A type of experimental phenotypic evidence resulting from the change in a single nucleotide.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001113
point mutation evidence
A type of experimental phenotypic evidence resulting from the change in a single nucleotide.
SO:1000008
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001114
propidium iodide staining evidence
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.
PMID:17406435
A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001115
fluorescence evidence
A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore.
url:http://www.nature.com/subjects/biological-fluorescence
A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001116
protein dot blot assay evidence
A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged.
doi:10.1007/978-94-009-0951-9_24
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001117
protein microarray evidence
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.
PMC:1828913
A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001118
protein sequencing assay evidence
A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein.
ERO:0001287
A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001119
quantitative mass spectrometry evidence
A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes.
PMID:22665296
A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
radioassay
radioisotopic assay
eco
ECO:0001120
radioisotope assay evidence
A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant.
ISBN:978-3-642-50036-7
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001121
radioimmunoassay evidence
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.
MeSH:D011863
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001123
resonant mirror biosensor evidence
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.
PMID:19151938
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001124
restriction fragment detection evidence
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.
doi:10.1007/978-94-009-0951-9_24
url:http://www.ncbi.nlm.nih.gov/probe/docs/techrflp/
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001126
spectrophotometry evidence
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.
MMO:0000173
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
SPR evidence
eco
ECO:0001127
Plasmons are generated by an incident light beam.
surface plasmon resonance evidence
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.
ECO:SW
PMID:11578932
PMID:19151937
PMID:8574707
SPR evidence
PMID:11578932
A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001128
syngeneic transplantation experiment evidence
A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin.
PMID:18469352
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
Tumor necrosis factor - alpha converting enzyme activity assay
eco
ECO:0001129
TACE activity assay 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.
PMC:1808921
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001130
tissue microarray evidence
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.
PMID:11770905
A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001131
transgenic organism evidence
A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification.
OBI:1000048
A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001132
tryptic phosphopeptide mapping assay evidence
A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate.
PMID:18429120
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
TUNEL assay evidence
TdT-mediated dUTP-biotin nick end labeling assay
terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence
eco
ECO:0001133
terminal deoxynucleotidyl transferase dUTP nick end labeling 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.
PMID:22566045
A type of direct assay evidence resulting from the analysis of a urine sample.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
eco
ECO:0001134
urine test evidence
A type of direct assay evidence resulting from the analysis of a urine sample.
ECO:RCT
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
ECO:0005009
metabolic cell proliferation assay evidence
eco
ECO:0001136
WST-1 assay evidence
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.
PMID:18417231
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.
SIB:PG
mchibucos
2014-03-16T11:30:54Z
Xenograft transplantation
Xenografting
Xenotransplantation
tissue grafting
eco
ECO:0001137
xenotransplantation experiment 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.
ECO:SN
url:http://ilarjournal.oxfordjournals.org/content/37/1/16.full.pdf+html
url:http://www.fda.gov/BiologicsBloodVaccines/Xenotransplantation/
A type of 3D cell culture evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:18:35Z
eco
ECO:0001138
3D cell culture evidence used in manual assertion
true
true
A type of 3D cell culture evidence that is used in a manual assertion.
ECO:MCC
A type of 51Cr release assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:20:55Z
eco
ECO:0001139
51Cr release assay evidence used in manual assertion
true
true
A type of 51Cr release assay evidence that is used in a manual assertion.
ECO:MCC
A type of 7-aminoactinomycin staining evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:22:01Z
7-AAD staining evidence
7-amino-actinomycin D staining evidence
eco
ECO:0001140
7-aminoactinomycin staining evidence used in manual assertion
true
true
A type of 7-aminoactinomycin staining evidence that is used in a manual assertion.
ECO:MCC
A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:31:52Z
eco
ECO:0001141
[3H]-thymidine incorporation assay evidence used in manual assertion
true
true
A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion.
ECO:MCC
A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:32:44Z
eco
ECO:0001142
[3H]arachidonic acid release assay evidence used in manual assertion
true
true
A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion.
ECO:MCC
A type of adhesion assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:33:38Z
eco
ECO:0001143
adhesion assay evidence used in manual assertion
true
true
A type of adhesion assay evidence that is used in a manual assertion.
ECO:MCC
A type of adoptive cell transfer evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:36:19Z
Adoptive immunotherapy
passive immunization
eco
ECO:0001144
adoptive cell transfer evidence used in manual assertion
true
true
A type of adoptive cell transfer evidence that is used in a manual assertion.
ECO:MCC
A type of alamarBlue assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:37:21Z
eco
ECO:0001145
alamarBlue assay evidence used in manual assertion
true
true
A type of alamarBlue assay evidence that is used in a manual assertion.
ECO:MCC
A type of allograft transplantation experiment evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:38:22Z
Allotransplantation
allografting
eco
tissue grafting
ECO:0001146
allograft transplantation experiment evidence used in manual assertion
true
true
A type of allograft transplantation experiment evidence that is used in a manual assertion.
ECO:MCC
A type of anion-exchange chromatography evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:44:30Z
eco
ECO:0001147
anion-exchange chromatography evidence used in manual assertion
true
true
A type of anion-exchange chromatography evidence that is used in a manual assertion.
ECO:MCC
A type of annexin-V staining evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:52:01Z
eco
ECO:0001148
annexin-V staining evidence used in manual assertion
true
true
A type of annexin-V staining evidence that is used in a manual assertion.
ECO:MCC
A type of behavioral assay evidence used that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:53:38Z
eco
ECO:0001149
behavioral assay evidence used in manual assertion
true
true
A type of behavioral assay evidence used that is used in a manual assertion.
ECO:MCC
A type of blocking monoclonal antibody evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:54:44Z
eco
ECO:0001150
blocking monoclonal antibody evidence used in manual assertion
true
true
A type of blocking monoclonal antibody evidence that is used in a manual assertion.
ECO:MCC
A type of blocking peptide evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T15:55:33Z
eco
ECO:0001151
blocking peptide evidence used in manual assertion
true
true
A type of blocking peptide evidence that is used in a manual assertion.
ECO:MCC
A type of blocking polyclonal antibody evidence tthat is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:01:39Z
eco
ECO:0001152
blocking polyclonal antibody evidence used in manual assertion
true
true
A type of blocking polyclonal antibody evidence tthat is used in a manual assertion.
ECO:MCC
A type of blood test evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:02:47Z
eco
ECO:0001153
blood test evidence used in manual assertion
true
true
A type of blood test evidence that is used in a manual assertion.
ECO:MCC
A type of Boyden chamber assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:03:53Z
eco
ECO:0001154
Boyden chamber assay evidence used in manual assertion
true
true
A type of Boyden chamber assay evidence that is used in a manual assertion.
ECO:MCC
A type of bromodeoxyuridine incorporation assay evidence used in manual assertion.
SIB:PG
mchibucos
2014-03-17T16:04:49Z
5-bromo-2'-deoxyuridine incorporation assay evidence
BUdR incorporation assay evidence
BrdU incorporation assay evidence
BrdUrd incorporation assay evidence
eco
ECO:0001155
bromodeoxyuridine incorporation assay evidence used in manual assertion
true
true
A type of bromodeoxyuridine incorporation assay evidence used in manual assertion.
ECO:MCC
A type of caspase assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:06:06Z
eco
ECO:0001156
caspase assay evidence used in manual assertion
true
true
A type of caspase assay evidence that is used in a manual assertion.
ECO:MCC
A type of cell counting evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:07:13Z
eco
ECO:0001157
cell counting evidence used in manual assertion
true
true
A type of cell counting evidence that is used in a manual assertion.
ECO:MCC
A type of cell permeability assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:07:58Z
eco
ECO:0001158
cell permeability assay evidence used in manual assertion
true
true
A type of cell permeability assay evidence that is used in a manual assertion.
ECO:MCC
A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:08:54Z
CFDA-SE staining evidence
CFSE-staining evidence
eco
ECO:0001159
carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion
true
true
A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion.
ECO:MCC
A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:09:55Z
CLIA evidence
eco
ECO:0001160
chemiluminescence-linked immunoassay evidence used in manual assertion
true
true
A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion.
ECO:MCC
A type of chimeric protein evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:10:40Z
eco
ECO:0001161
chimeric protein evidence used in manual assertion
true
true
A type of chimeric protein evidence that is used in a manual assertion.
ECO:MCC
A type of co-electrophoresis evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:11:22Z
eco
ECO:0001162
co-electrophoresis evidence used in manual assertion
true
true
A type of co-electrophoresis evidence that is used in a manual assertion.
ECO:MCC
A type of co-localization evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:12:04Z
eco
ECO:0001163
co-localization evidence used in manual assertion
true
true
A type of co-localization evidence that is used in a manual assertion.
ECO:MCC
A type of co-sedimentation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:12:55Z
eco
ECO:0001164
co-sedimentation assay evidence used in manual assertion
true
true
A type of co-sedimentation assay evidence that is used in a manual assertion.
ECO:MCC
A type of colony counting evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:14:57Z
eco
ECO:0001165
colony counting evidence used in manual assertion
true
true
A type of colony counting evidence that is used in a manual assertion.
ECO:MCC
A type of comet assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:16:01Z
eco
ECO:0001166
comet assay evidence used in manual assertion
true
true
A type of comet assay evidence that is used in a manual assertion.
ECO:MCC
A type of conditional knockin evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:17:22Z
eco
ECO:0001167
conditional knockin evidence used in manual assertion
true
true
A type of conditional knockin evidence that is used in a manual assertion.
ECO:MCC
A type of conditional knockout evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:17:58Z
eco
ECO:0001168
conditional knockout evidence used in manual assertion
true
true
A type of conditional knockout evidence that is used in a manual assertion.
ECO:MCC
A type of constitutively active mutant evidence that is used a in manual assertion.
SIB:PG
mchibucos
2014-03-17T16:20:23Z
eco
ECO:0001169
constitutively active mutant evidence used in manual assertion
true
true
A type of constitutively active mutant evidence that is used a in manual assertion.
ECO:MCC
A type of cross-linking evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:21:29Z
eco
ECO:0001170
cross-linking evidence used in manual assertion
true
true
A type of cross-linking evidence that is used in a manual assertion.
ECO:MCC
A type of crystallography evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:22:20Z
eco
ECO:0001171
crystallography evidence used in manual assertion
true
true
A type of crystallography evidence that is used in a manual assertion.
ECO:MCC
A type of cytochemistry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:23:10Z
eco
ECO:0001172
cytochemistry evidence used in manual assertion
true
true
A type of cytochemistry evidence that is used in a manual assertion.
ECO:MCC
A type of cytochrome C release assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:23:53Z
eco
ECO:0001173
cytochrome C release assay evidence used in manual assertion
true
true
A type of cytochrome C release assay evidence that is used in a manual assertion.
ECO:MCC
A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:25:03Z
DAPI staining evidence
eco
ECO:0001174
4',6-diamidino-2-phenylindole staining evidence used in manual assertion
true
true
A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion.
ECO:MCC
A type of deletion evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:25:54Z
eco
ECO:0001175
deletion mutation evidence used in manual assertion
true
true
A type of deletion evidence that is used in a manual assertion.
ECO:MCC
A type of DNA laddering assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:26:46Z
eco
ECO:0001176
DNA laddering assay evidence used in manual assertion
true
true
A type of DNA laddering assay evidence that is used in a manual assertion.
ECO:MCC
A type of RNA dot blot assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:45:52Z
RNA dot blot evidence
eco
ECO:0001177
RNA dot blot assay evidence used in manual assertion
true
true
A type of RNA dot blot assay evidence that is used in a manual assertion.
ECO:MCC
A type of dominant-negative mutant evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:47:44Z
eco
ECO:0001179
dominant-negative mutant evidence used in manual assertion
true
true
A type of dominant-negative mutant evidence that is used in a manual assertion.
ECO:MCC
A type of eTag assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T16:59:39Z
eco
ECO:0001180
eTag assay evidence used in manual assertion
true
true
A type of eTag assay evidence that is used in a manual assertion.
ECO:MCC
A type of filter binding assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:03:28Z
eco
ECO:0001181
filter binding assay evidence used in manual assertion
true
true
A type of filter binding assay evidence that is used in a manual assertion.
ECO:MCC
A type of fluorescence in situ hybridization evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:04:20Z
eco
ECO:0001182
fluorescence in situ hybridization evidence used in manual assertion
true
true
A type of fluorescence in situ hybridization evidence that is used in a manual assertion.
ECO:MCC
A type of fluorescence resonance energy transfer evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:05:22Z
FRET evidence
eco
ECO:0001183
fluorescence resonance energy transfer evidence used in manual assertion
true
true
A type of fluorescence resonance energy transfer evidence that is used in a manual assertion.
ECO:MCC
A type of gel-filtration evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:06:14Z
eco
ECO:0001184
gel-filtration evidence used in manual assertion
true
true
A type of gel-filtration evidence that is used in a manual assertion.
ECO:MCC
A type of histochemistry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:07:19Z
eco
ECO:0001185
histochemistry evidence used in manual assertion
true
true
A type of histochemistry evidence that is used in a manual assertion.
ECO:MCC
A type of immunocytochemistry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:12:39Z
eco
ECO:0001186
immunocytochemistry evidence used in manual assertion
true
true
A type of immunocytochemistry evidence that is used in a manual assertion.
ECO:MCC
A type of histology evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:09:50Z
eco
ECO:0001187
histology evidence used in manual assertion
true
true
A type of histology evidence that is used in a manual assertion.
ECO:MCC
A type of immunodepletion evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:16:19Z
eco
ECO:0001188
immunodepletion evidence used in manual assertion
true
true
A type of immunodepletion evidence that is used in a manual assertion.
ECO:MCC
A type of immunohistochemistry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:17:22Z
eco
ECO:0001189
immunohistochemistry evidence used in manual assertion
true
true
A type of immunohistochemistry evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro acetylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:19:24Z
eco
ECO:0001190
in vitro acetylation assay evidence used in manual assertion
true
true
A type of in vitro acetylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro cleavage assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:21:22Z
eco
ECO:0001191
in vitro cleavage assay evidence used in manual assertion
true
true
A type of in vitro cleavage assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro deacetylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:23:42Z
eco
ECO:0001192
in vitro deacetylation assay evidence used in manual assertion
true
true
A type of in vitro deacetylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro defarnesylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:25:45Z
eco
ECO:0001193
in vitro defarnesylation assay evidence used in manual assertion
true
true
A type of in vitro defarnesylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro demethylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:27:00Z
eco
ECO:0001194
in vitro demethylation assay evidence used in manual assertion
true
true
A type of in vitro demethylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro desumoylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:29:01Z
eco
ECO:0001195
in vitro desumoylation assay evidence used in manual assertion
true
true
A type of in vitro desumoylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro deubiquitination assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:29:48Z
eco
ECO:0001196
in vitro deubiquitination assay evidence used in manual assertion
true
true
A type of in vitro deubiquitination assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro farnesylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:30:50Z
eco
ECO:0001197
in vitro farnesylation assay evidence used in manual assertion
true
true
A type of in vitro farnesylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro methylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:31:54Z
eco
ECO:0001198
in vitro methylation assay evidence used in manual assertion
true
true
A type of in vitro methylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro palmitoylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:32:57Z
eco
ECO:0001199
in vitro palmitoylation assay evidence used in manual assertion
true
true
A type of in vitro palmitoylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro phosphatase assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:34:16Z
eco
ECO:0001200
in vitro phosphatase assay evidence used in manual assertion
true
true
A type of in vitro phosphatase assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:34:57Z
eco
ECO:0001201
in vitro polyADP-ribosylation assay evidence used in manual assertion
true
true
A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro protein kinase assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:39:57Z
eco
ECO:0001202
in vitro protein kinase assay evidence used in manual assertion
true
true
A type of in vitro protein kinase assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro sumoylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:41:25Z
eco
ECO:0001203
in vitro sumoylation assay evidence used in manual assertion
true
true
A type of in vitro sumoylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro transcription assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:44:40Z
eco
ECO:0001204
in vitro transcription assay evidence used in manual assertion
true
true
A type of in vitro transcription assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro translation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:46:30Z
eco
ECO:0001205
in vitro translation assay evidence used in manual assertion
true
true
A type of in vitro translation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vitro ubiquitination assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:47:18Z
eco
ECO:0001206
in vitro ubiquitination assay evidence used in manual assertion
true
true
A type of in vitro ubiquitination assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo acetylation assay evidence that is used in manual assertion.
SIB:PG
mchibucos
2014-03-17T17:48:56Z
eco
ECO:0001207
in vivo acetylation assay evidence used in manual assertion
true
true
A type of in vivo acetylation assay evidence that is used in manual assertion.
ECO:MCC
A type of in vivo cleavage assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:49:43Z
eco
ECO:0001208
in vivo cleavage assay evidence used in manual assertion
true
true
A type of in vivo cleavage assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo deacetylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:50:47Z
eco
ECO:0001209
in vivo deacetylation assay evidence used in manual assertion
true
true
A type of in vivo deacetylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo defarnesylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:52:41Z
eco
ECO:0001210
in vivo defarnesylation assay evidence used in manual assertion
true
true
A type of in vivo defarnesylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo demethylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:53:40Z
eco
ECO:0001211
in vivo demethylation assay evidence used in manual assertion
true
true
A type of in vivo demethylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo desumoylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:54:36Z
eco
ECO:0001212
in vivo desumoylation assay evidence used in manual assertion
true
true
A type of in vivo desumoylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo deubiquitination assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:56:28Z
eco
ECO:0001213
in vivo deubiquitination assay evidence used in manual assertion
true
true
A type of in vivo deubiquitination assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo farnesylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T17:57:18Z
eco
ECO:0001214
in vivo farnesylation assay evidence used in manual assertion
true
true
A type of in vivo farnesylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo methylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:03:16Z
eco
ECO:0001215
in vivo methylation assay evidence used in manual assertion
true
true
A type of in vivo methylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo palmitoylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:04:07Z
eco
ECO:0001216
in vivo palmitoylation assay evidence used in manual assertion
true
true
A type of in vivo palmitoylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo phosphatase assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:06:08Z
eco
ECO:0001217
in vivo phosphatase assay evidence used in manual assertion
true
true
A type of in vivo phosphatase assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo protein kinase assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:07:58Z
eco
ECO:0001218
in vivo protein kinase assay evidence used in manual assertion
true
true
A type of in vivo protein kinase assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo sumoylation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:09:49Z
eco
ECO:0001219
in vivo sumoylation assay evidence used in manual assertion
true
true
A type of in vivo sumoylation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo transcription assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:11:20Z
eco
ECO:0001220
in vivo transcription assay evidence used in manual assertion
true
true
A type of in vivo transcription assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo translation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:42:50Z
eco
ECO:0001221
in vivo translation assay evidence used in manual assertion
true
true
A type of in vivo translation assay evidence that is used in a manual assertion.
ECO:MCC
A type of in vivo ubiquitination assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:44:11Z
eco
ECO:0001222
in vivo ubiquitination assay evidence used in manual assertion
true
true
A type of in vivo ubiquitination assay evidence that is used in a manual assertion.
ECO:MCC
A type of induced mutation evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:45:56Z
eco
ECO:0001223
induced mutation evidence used in manual assertion
true
true
A type of induced mutation evidence that is used in a manual assertion.
ECO:MCC
A type of knockin evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:49:35Z
eco
ECO:0001224
knockin evidence used in manual assertion
true
true
A type of knockin evidence that is used in a manual assertion.
ECO:MCC
A type of knockout evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:51:31Z
eco
ECO:0001225
knockout evidence used in manual assertion
true
true
A type of knockout evidence that is used in a manual assertion.
ECO:MCC
A type of lipid binding assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:52:19Z
eco
ECO:0001226
lipid binding assay evidence used in manual assertion
true
true
A type of lipid binding assay evidence that is used in a manual assertion.
ECO:MCC
A type of LUMIER assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:55:16Z
LUMIER assay evidence
eco
ECO:0001227
luminescence-based mammalian interactome mapping assay evidence used in manual assertion
true
true
A type of LUMIER assay evidence that is used in a manual assertion.
ECO:MCC
A type of macroscopy evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:56:21Z
eco
ECO:0001228
macroscopy evidence used in manual assertion
true
true
A type of macroscopy evidence that is used in a manual assertion.
ECO:MCC
A type of mammalian 2-hybrid assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:57:25Z
eco
ECO:0001229
mammalian 2-hybrid assay evidence used in manual assertion
true
true
A type of mammalian 2-hybrid assay evidence that is used in a manual assertion.
ECO:MCC
A type of mass spectrometry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T18:59:50Z
eco
ECO:0001230
mass spectrometry evidence used in manual assertion
true
true
A type of mass spectrometry evidence that is used in a manual assertion.
ECO:MCC
A type of medical imaging evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:04:43Z
eco
ECO:0001231
medical imaging evidence used in manual assertion
true
true
A type of medical imaging evidence that is used in a manual assertion.
ECO:MCC
A type of microscopy evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:05:37Z
eco
ECO:0001232
microscopy evidence used in manual assertion
true
true
A type of microscopy evidence that is used in a manual assertion.
ECO:MCC
A type of motility wound healing assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:08:13Z
ECO:0001262
wound healing assay evidence used in manual assertion
eco
ECO:0001233
motility wound healing assay evidence used in manual assertion
true
true
A type of motility wound healing assay evidence that is used in a manual assertion.
ECO:MCC
A type of MTS assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:08:51Z
eco
3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium
ECO:0001234
MTS assay evidence used in manual assertion
true
true
A type of MTS assay evidence that is used in a manual assertion.
ECO:MCC
A type of MTT assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:13:17Z
eco
3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
ECO:0001235
MTT assay evidence used in manual assertion
true
true
A type of MTT assay evidence that is used in a manual assertion.
ECO:MCC
A type of multiplex bead-based immunoassay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:14:03Z
eco
ECO:0001236
multiplex bead-based immunoassay evidence used in manual assertion
true
true
A type of multiplex bead-based immunoassay evidence that is used in a manual assertion.
ECO:MCC
A type of natural variation mutant evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:15:48Z
eco
ECO:0001237
natural variation mutant evidence used in manual assertion
true
true
A type of natural variation mutant evidence that is used in a manual assertion.
ECO:MCC
A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:18:50Z
NMR spectroscopy evidence
eco
ECO:0001238
nuclear magnetic resonance spectroscopy evidence used in manual assertion
true
true
A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion.
ECO:MCC
A type of nuclear fragmentation evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:19:55Z
eco
ECO:0001239
nuclear fragmentation evidence used in manual assertion
true
true
A type of nuclear fragmentation evidence that is used in a manual assertion.
ECO:MCC
A type of nuclease protection assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:23:41Z
eco
ECO:0001240
nuclease protection assay evidence used in manual assertion
true
true
A type of nuclease protection assay evidence that is used in a manual assertion.
ECO:MCC
A type of nucleotide analog incorporation assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:25:17Z
eco
ECO:0001241
nucleotide analog incorporation assay evidence used in manual assertion
true
true
A type of nucleotide analog incorporation assay evidence that is used in a manual assertion.
ECO:MCC
A type of phage display evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:27:17Z
eco
ECO:0001242
phage display evidence used in manual assertion
true
true
A type of phage display evidence that is used in a manual assertion.
ECO:MCC
A type of phosphoamino acid analysis evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:28:59Z
eco
ECO:0001243
phosphoamino acid analysis evidence used in manual assertion
true
true
A type of phosphoamino acid analysis evidence that is used in a manual assertion.
ECO:MCC
A type of peptide affinity enrichment evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T19:30:13Z
eco
phosphopeptide affinity enrichment evidence
ECO:0001244
peptide affinity enrichment evidence used in manual assertion
true
true
A type of peptide affinity enrichment evidence that is used in a manual assertion.
ECO:MCC
A type of peptide array evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:16:45Z
eco
phosphopeptide array evidence
ECO:0001245
peptide array evidence used in manual assertion
true
true
A type of peptide array evidence that is used in a manual assertion.
ECO:MCC
A type of physical examination evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:17:27Z
eco
ECO:0001246
physical examination evidence used in manual assertion
true
true
A type of physical examination evidence that is used in a manual assertion.
ECO:MCC
A type of point mutation evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:18:10Z
eco
ECO:0001247
point mutation evidence used in manual assertion
true
true
A type of point mutation evidence that is used in a manual assertion.
ECO:MCC
A type of propidium iodide staining evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:18:58Z
eco
ECO:0001248
propidium iodide staining evidence used in manual assertion
true
true
A type of propidium iodide staining evidence that is used in a manual assertion.
ECO:MCC
A type of protein detection by fluorescence evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:19:35Z
eco
ECO:0001249
fluorescence evidence used in manual assertion
true
true
A type of protein detection by fluorescence evidence that is used in a manual assertion.
ECO:MCC
A type of protein dot blot assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:20:30Z
eco
ECO:0001250
protein dot blot assay evidence used in manual assertion
true
true
A type of protein dot blot assay evidence that is used in a manual assertion.
ECO:MCC
A type of protein microarray evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:21:11Z
eco
ECO:0001251
protein microarray evidence used in manual assertion
true
true
A type of protein microarray evidence that is used in a manual assertion.
ECO:MCC
A type of protein sequencing assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:22:08Z
eco
ECO:0001252
protein sequencing assay evidence used in manual assertion
true
true
A type of protein sequencing assay evidence that is used in a manual assertion.
ECO:MCC
A type of quantitative mass spectrometry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:23:15Z
eco
ECO:0001253
quantitative mass spectrometry evidence used in manual assertion
true
true
A type of quantitative mass spectrometry evidence that is used in a manual assertion.
ECO:MCC
A type of radioisotope assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:27:05Z
radioassay evidence
radioisotopic assay evidence
eco
ECO:0001254
radioisotope assay evidence used in manual assertion
true
true
A type of radioisotope assay evidence that is used in a manual assertion.
ECO:MCC
A type of radioimmunoassay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:28:04Z
eco
ECO:0001255
radioimmunoassay evidence used in manual assertion
true
true
A type of radioimmunoassay evidence that is used in a manual assertion.
ECO:MCC
A type of imaging assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:00Z
eco
radiologic test evidence
ECO:0001256
imaging assay evidence used in manual assertion
true
true
A type of imaging assay evidence that is used in a manual assertion.
ECO:MCC
A type of restriction fragment detection evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:05Z
eco
ECO:0001257
restriction fragment detection evidence used in manual assertion
true
true
A type of restriction fragment detection evidence that is used in a manual assertion.
ECO:MCC
A type of spectrophotometry evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:09Z
eco
ECO:0001258
spectrophotometry evidence used in manual assertion
true
true
A type of spectrophotometry evidence that is used in a manual assertion.
ECO:MCC
A type of syngeneic transplantation experiment evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:13Z
eco
ECO:0001259
syngeneic transplantation experiment evidence used in manual assertion
true
true
A type of syngeneic transplantation experiment evidence that is used in a manual assertion.
ECO:MCC
A type of xenotransplantation experiment evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:18Z
xenograft transplantation evidence
xenografting evidence
xenotransplantation evidence
eco
tissue grafting
ECO:0001260
xenotransplantation experiment evidence used in manual assertion
true
true
A type of xenotransplantation experiment evidence that is used in a manual assertion.
ECO:MCC
A type of WST-1 assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:22Z
metabolic cell proliferation assay evidence
eco
ECO:0001261
WST-1 assay evidence used in manual assertion
true
true
A type of WST-1 assay evidence that is used in a manual assertion.
ECO:MCC
A type of urine test evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:30Z
eco
ECO:0001263
urine test evidence used in manual assertion
true
true
A type of urine test evidence that is used in a manual assertion.
ECO:MCC
A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:34Z
TUNEL assay evidence
TdT-mediated dUTP-biotin nick end labeling assay evidence
terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence
eco
ECO:0001264
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion
true
true
A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence assay evidence that is used in a manual assertion.
ECO:MCC
A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:38Z
eco
ECO:0001265
tryptic phosphopeptide mapping assay evidence used in manual assertion
true
true
A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion.
ECO:MCC
A type of transgenic organism evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:41Z
eco
ECO:0001266
transgenic organism evidence used in manual assertion
true
true
A type of transgenic organism evidence that is used in a manual assertion.
ECO:MCC
A type of tissue microarray evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:45Z
eco
ECO:0001267
tissue microarray evidence used in manual assertion
true
true
A type of tissue microarray evidence that is used in a manual assertion.
ECO:MCC
A type of TACE activity assay evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:49Z
Tumor necrosis factor - alpha converting enzyme activity assay evidence
eco
ECO:0001268
TACE activity assay evidence used in manual assertion
true
true
A type of TACE activity assay evidence that is used in a manual assertion.
ECO:MCC
A type of surface plasmon resonance evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:54Z
SPR evidence
eco
ECO:0001269
surface plasmon resonance evidence used in manual assertion
true
true
A type of surface plasmon resonance evidence that is used in a manual assertion.
ECO:MCC
A type of restriction landmark genome scanning evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:29:58Z
RLGS evidence
restriction landmark genome scanning evidence
eco
ECO:0001270
restriction landmark genomic scanning evidence used in manual assertion
true
true
A type of restriction landmark genome scanning evidence that is used in a manual assertion.
ECO:MCC
A type of resonant mirror biosensor evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T20:30:02Z
eco
ECO:0001271
resonant mirror biosensor evidence used in manual assertion
true
true
A type of resonant mirror biosensor evidence that is used in a manual assertion.
ECO:MCC
A type of high-performance liquid chromatography evidence that is used in a manual assertion.
mchibucos
2014-03-16T20:49:54Z
HPLC evidence
eco
ECO:0001272
high-performance liquid chromatography evidence used in manual assertion
true
true
A type of high-performance liquid chromatography evidence that is used in a manual assertion.
ECO:MCC
A type of ectopic expression evidence that is used in a manual assertion.
SIB:PG
mchibucos
2014-03-17T22:34:56Z
eco
IMP: analysis of overexpression/ectopic expression phenotype
ECO:0001273
ectopic expression evidence used in manual assertion
true
true
A type of ectopic expression evidence that is used in a manual assertion.
ECO:MCC
A type of direct assay evidence where acetylated residues are detected in a protein.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001546
acetylation assay evidence
A type of direct assay evidence where acetylated residues are detected in a protein.
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
A type of direct assay evidence where the cleavage of a protein into protein fragments by a protease is detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001547
cleavage assay evidence
A type of direct assay evidence where the cleavage of a protein into protein fragments by a protease is detected.
PMID:21121091
PMID:22154596
A type of direct assay evidence where the removal of acetyl groups are detected in a protein.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001548
deacetylation assay evidence
A type of direct assay evidence where the removal of acetyl groups are detected in a protein.
SIB:PG
url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml
A type of direct assay evidence where the removal of farnesyl groups from a protein is detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001549
defarnesylation assay evidence
A type of direct assay evidence where the removal of farnesyl groups from a protein is detected.
PMID:15556768
PMID:16126733
PMID:16507103
SIB:PG
A type of direct assay evidence where the removal of methyl groups from a substrate (RNA/DNA or protein) is detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001550
demethylation assay evidence
A type of direct assay evidence where the removal of methyl groups from a substrate (RNA/DNA or protein) is detected.
SIB:PG
url:http://en.wikipedia.org/wiki/Demethylation
A type of direct assay evidence where the removal of sumo groups from a protein is detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001551
desumoylation assay evidence
A type of direct assay evidence where the removal of sumo groups from a protein is detected.
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
A type of direct assay evidence where the removal of ubiquitin groups from a protein is detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001552
deubiquitination assay evidence
A type of direct assay evidence where the removal of ubiquitin groups from a protein is detected.
PMID:19692941
SIB:PG
A type of direct assay evidence where farnesylated residues in proteins are detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001553
farnesylation assay evidence
A type of direct assay evidence where farnesylated residues in proteins are detected.
PMID:9030603
SIB:PG
url:http://en.wikipedia.org/wiki/Farnesyltransferase
A type of direct assay evidence where methylated residues of a substarte (RNA/DNA or protein) are detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001554
methylation assay evidence
A type of direct assay evidence where methylated residues of a substarte (RNA/DNA or protein) are detected.
SIB:PG
url:http://en.wikipedia.org/wiki/Methylation
A type of direct assay evidence where palmitoylated residues in a protein are detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001555
palmitoylation assay evidence
A type of direct assay evidence where palmitoylated residues in a protein are detected.
PMID:10329400
PMID:17077383
SIB:PG
A type of direct assay evidence where the removal of phosphatase groups from a protein is detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001556
phosphatase assay evidence
A type of direct assay evidence where the removal of phosphatase groups from a protein is detected.
SIB:PG
url:http://en.wikipedia.org/wiki/Phosphatase
A type of direct assay evidence where ADP-ribosylated residues in proteins are detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001557
polyADP-ribosylation assay evidence
A type of direct assay evidence where ADP-ribosylated residues in proteins are detected.
PMID:21870253
PMID:2820766
SIB:PG
A type of direct assay evidence where phosphorylated residues in proteins are detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001558
protein kinase assay evidence
A type of direct assay evidence where phosphorylated residues in proteins are detected.
SIB:PG
url:http://en.wikipedia.org/wiki/Protein_kinase
url:http://en.wikipedia.org/wiki/Protein_phosphorylation
A type of direct assay evidence where sumoylated residues on a protein are detected.
ECO_AssayCleanup
jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001559
sumoylation assay evidence
A type of direct assay evidence where sumoylated residues on a protein are detected.
SIB:PG
url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/
A type of direct assay evidence where de novo protein synthesis is detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001561
translation assay evidence
A type of direct assay evidence where de novo protein synthesis is detected.
PMID:18230759
PMID:24901308
SIB:PG
A type of direct assay evidence where ubiquitinated residues on a protein are detected.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001562
ubiquitination assay evidence
A type of direct assay evidence where ubiquitinated residues on a protein are detected.
PMID:19692941
SIB:PG
A type of direct assay evidence where biological cell development, i.e. an increase in cell mass and size are measured.
ECO_AssayCleanup
mchibucos / jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001563
cell growth assay evidence
A type of direct assay evidence where biological cell development, i.e. an increase in cell mass and size are measured.
GO:0016049
PMID:11057898
A type of direct assay evidence resulting from the study of cells.
jbmunro
2017-11-30T14:00:00Z
eco
ECO:0001565
cell-based assay evidence
A type of protein-binding evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
swolfish
2015-06-05T14:36:00Z
PBM evidence
eco
ECO:0001601
protein-binding microarray evidence
A type of protein-binding evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
PMID:22146299
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.
swolfish
2015-06-08T11:51:37Z
eco
vital staining evidence
ECO:0001603
cell staining evidence
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.
GOC:MAH
vital staining evidence
GOC:MAH
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.
CollecTF
swolfish
2015-10-29T15:53:45Z
eco
SEAP reporter assay
Secreted Embryonic Alkaline Phosphatase reporter assay
ECO:0001801
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 selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing.
ECO:SW
PMID:11823238
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.
CollecTF
swolfish
2015-10-29T15:57:10Z
beta-gal reporter gene assay
beta-galactosidase assay evidence
eco
lacZ reporter gene assay
ECO:0001802
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 lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium.
ECO:SW
PMID:20439410
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.
CollecTF
swolfish
2015-10-29T16:06:42Z
CAT reporter gene assay
eco
ECO:0001803
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 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.
ECO:SW
PMID:1630936
CAT reporter gene assay
PMID:1630936
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.
CollecTF
swolfish
2015-10-29T16:11:02Z
GUS reporter gene assay
eco
ECO:0001804
beta-glucuronidase 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.
ECO:SW
A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence.
CollecTF
swolfish
2015-10-29T16:15:39Z
eco
ECO:0001805
luciferase 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.
ECO:SW
PMID:17623934
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.
CollecTF
swolfish
2015-10-29T16:37:36Z
ChIP-exo
eco
ECO:0001806
chromatin immunoprecipitation- exonuclease evidence
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.
ECO:SW
PMID:25249628
ChIP-exo
PMID:25249628
A type of electrophoretic mobility shift that is used in a manual assertion.
swolfish
2015-11-03T12:13:17Z
EMSA evidence
IDA: electrophoretic mobility shift assay
eco
gel retardation assay
ECO:0001807
electrophoretic mobility shift assay evidence used in manual assertion
true
true
A type of electrophoretic mobility shift that is used in a manual assertion.
ECO:SW
A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion.
swolfish
2015-11-03T12:22:46Z
RT-PCR evidence
qRT-PCR evidence
eco
ECO:0001808
reverse transcription polymerase chain reaction evidence used in manual assertion
true
true
A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion.
ECO:SW
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.
CollecTF
swolfish
2015-11-03T13:48:49Z
eco
DNA affinity purification
ECO:0001809
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.
DNA affinity chromatography evidence
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.
ECO:SW
PMID:11694305
PMID:11725488
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.
CollecTF
swolfish
2015-11-03T13:55:15Z
eco
DNase protection
ECO:0001810
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.
DNAse footprinting evidence
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.
ECO:SW
PMID:212715
PMID:22194258
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.
CollecTF
swolfish
2015-11-03T14:01:36Z
FA
eco
FP
Fluorescence polarization
ECO:0001811
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.
fluorescence anisotropy evidence
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.
ECO:SW
PMID:20232898
FP
PMCID:3277431
PMID:20232898
Fluorescence polarization
PMCID:3277431
PMID:20232898
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.
CollecTF
swolfish
2015-11-03T14:05:37Z
genomic SELEX
eco
ECO:0001812
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 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.
ECO:SW
PMID:20541015
PMID:21720957
genomic SELEX
PMID:20541015
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.
CollecTF
swolfish
2015-11-03T14:11:06Z
HSQC
eco
ECO:0001813
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 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.
ECO:SW
PMID:19856946
HSQC
PMID:19856946
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.
CollecTF
swolfish
2015-11-03T14:24:04Z
eco
MPE Fe(II) footprinting
MPE-EDTA Fe(II) footprinting
Methidiumpropyl-EDTA Fe(II) footprinting
ECO:0001814
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting 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.
ECO:SW
PMID:6225070
MPE Fe(II) footprinting
PMID:6225070
MPE-EDTA Fe(II) footprinting
PMID:6225070
Methidiumpropyl-EDTA Fe(II) footprinting
PMID:6225070
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.
CollecTF
swolfish
2015-11-04T08:37:51Z
1,10-Phenanthroline-copper footprinting
eco
OP-Cu Complex
ECO:0001815
copper-phenanthroline 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.
ECO:SW
PMID:11691942
1,10-Phenanthroline-copper footprinting
PMID:1384472
OP-Cu Complex
PMID:1384472
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.
CollecTF
swolfish
2015-11-04T08:58:42Z
GFP reporter gene assay
eco
GFP promoter fusion
green fluorescent protein promoter fusion
ECO:0001816
green fluorescent protein reporter gene assay 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.
ECO:SW
PMID:11989662
GFP reporter gene assay
PMID:11989662
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.
CollecTF
swolfish
2015-11-04T09:05:56Z
GST pull-down assay
eco
ECO:0001817
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 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.
ECO:SW
PMID:26096507
GST pull-down assay
PMID:26096507
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.
CollecTF
swolfish
2015-11-04T09:20:26Z
eco
ECO:0001818
hydroxyl-radical footprinting 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.
ECO:SW
PMID:18546600
PMID:19378159
PMID:3090544
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.
CollecTF
swolfish
2015-11-04T09:33:18Z
eco
ECO:0001819
The most commonly used radiolabel is 32P.
primer extension assay evidence
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.
ECO:SW
PMID:23378648
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.
CollecTF
swolfish
2015-11-04T09:48:38Z
RACE PCR
eco
ECO:0001820
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
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.
ECO:SW
PMID:17498297
RACE PCR
PMI:17498297
CollecTF
swolfish
2015-11-04T10:15:57Z
eco
ECO:0001821
Use ECO:0000295 (RNA-seq evidence) in place of this term.
RNA sequencing assay evidence
true
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.
CollecTF
swolfish
2015-11-04T10:48:59Z
eco
ECO:0001822
survival rate analysis evidence
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.
ECO:SW
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.
CollecTF
swolfish
2015-11-04T10:56:22Z
eco
ECO:0001823
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.
x-ray crystallography evidence
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.
ECO:SW
PMID:23135450
PMID:24648090
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.
CollecTF
swolfish
2015-11-05T15:56:13Z
DamID
eco
ECO:0001824
The methylation tag is detected with methylation-sensitive restriction enzymes, DpnI and DpnII.
DNA adenine methyltransferase identification evidence
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.
ECO:SW
PMID:16938559
PMID:17545983
PMID:19588092
DamID
PMID:19588092
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.
CollecTF
swolfish
2015-11-05T16:06:20Z
ITC
eco
ECO:0001825
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 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.
ECO:SW
PMID:10527727
ITC
PMID:10527727
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.
CollecTF
swolfish
2015-11-05T16:13:36Z
eco
UV footprinting
ultraviolet footprinting
ECO:0001826
ultraviolet light footprinting 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.
ECO:SW
PMID:2842760
PMID:7602584
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.
CollecTF
swolfish
2015-11-05T16:16:27Z
eco
methylation interference footprinting
ECO:0001827
premethylation interference footprinting evidence
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.
ECO:SW
PMID:1583685
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.
swolfish
2015-11-10T14:40:16Z
eco
ECO:0001828
visual sequence inspection 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.
ECO:SW
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.
CollecTF
swolfish
2015-11-10T14:55:36Z
FURTA
eco
Fluorescence polarization
ECO:0001829
ferric uptake regulator titration assay evidence
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.
ECO:SW
PMID:10713425
PMID:7642488
PMID:8107138
FURTA
PMID:10713425
Fluorescence polarization
PMID:15689115
A type of cell-based assay evidence resulting from analyzing the ability of cells to survive or live successfully.
snadendla
2015-02-13T12:08:01Z
eco
ECO:0005004
cell viability assay evidence
A type of cell-based assay evidence resulting from analyzing the ability of cells to survive or live successfully.
NBK:144065
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.
snadendla
2015-02-11T16:27:13Z
eco
ECO:0005007
cell proliferation assay evidence
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.
ECO:RCT
GO:0008283
PMID:11057898
A type of cell proliferation assay evidence resulting from the measure of DNA synthesis in the presece of a label.
snadendla
2015-02-11T16:30:10Z
eco
ECO:0005008
DNA synthesis cell proliferation assay evidence
A type of cell proliferation assay evidence resulting from the measure of DNA synthesis in the presece of a label.
PMC:3908118
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.
snadendla
2015-02-11T16:47:30Z
eco
ECO:0005011
ATP bioluminescence 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.
PMID:15344559
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.
snadendla
2015-02-12T11:39:35Z
eco
ECO:0005012
cytotoxicity assay evidence
snadendla
2015-02-12T13:26:55Z
eco
ECO:0005014
Use children of ECO:0001565 (cell-based assay evidence) in place of this term.
in vitro cell based assay evidence
true
A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image.
snadendla
2015-02-19T11:48:57Z
eco
ECO:0005019
staining evidence
A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image.
ECO:RCT
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.
snadendla
2015-02-19T13:10:20Z
eco
ECO:0005021
chemotaxis assay evidence
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.
PMC:3667641
A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA.
snadendla
2015-03-16T15:33:50Z
eco
ECO:0005027
genetic transformation evidence
A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA.
ECO:RCT
A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures.
snadendla
2015-03-20T12:16:17Z
eco
ECO:0005031
structure determination evidence
A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures.
ECO:RCT
A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image.
snadendla
2015-03-20T12:21:48Z
eco
ECO:0005033
electron microscopy evidence
A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image.
ECO:RCT
A type of cell-based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis.
snadendla
2015-04-07T21:58:24Z
eco
ECO:0005034
apoptotic assay evidence
A type of cell-based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis.
ECO:RCT
A type of polyADP-ribosylation assay evidence used in an in vivo experiment.
snadendla
2015-06-15T15:35:05Z
eco
ECO:0005500
in vivo polyADP-ribosylation assay evidence
A type of polyADP-ribosylation assay evidence used in an in vivo experiment.
ECO:SN
PMID:2820766
SIB:PG
A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion.
snadendla
2015-06-15T15:37:23Z
eco
ECO:0005501
in vivo polyADP-ribosylation assay evidence used in manual assertion
true
true
A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion.
ECO:SN
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.
snadendla
2015-06-26T11:46:15Z
eco
ECO:0005502
ex vivo assay evidence
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.
ECO:SN
PMID:16305312
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf
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.
CollecTF
snadendla
2015-10-01T16:23:20Z
2D PAGE
2D-PAGE
eco
ECO:0005503
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 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.
ECO:SW
url:http://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html
A type of experimental evidence resulting from the use of a spectrometer.
snadendla
2015-08-14T15:48:08Z
eco
ECO:0005504
spectrometry evidence
A type of experimental evidence resulting from the use of a spectrometer.
ECO:RCT
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.
CollecTF
snadendla
2015-10-09T13:51:52Z
eco
ECO:0005505
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 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.
ECO:SW
PMID:17337630
A type of point mutation evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another.
snadendla
2015-09-18T16:52:34Z
eco
ECO:0005506
missense mutation 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.
SO:0001583
A type of point mutation evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon.
snadendla
2015-09-18T16:55:32Z
eco
ECO:0005507
nonsense mutation evidence
A type of point mutation evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon.
url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations
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.
snadendla
2015-09-18T17:01:12Z
eco
ECO:0005508
silent mutation evidence
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.
url:http://www.sciencemag.org/news/2006/12/sound-silent-mutation
A type of experimental phenotypic evidence resulting from a mutation in which there is an insertion of an additional nucleotide, or nucleotides.
snadendla
2015-09-18T17:02:03Z
eco
ECO:0005509
insertion mutation evidence
A type of experimental phenotypic evidence resulting from a mutation in which there is an insertion of an additional nucleotide, or nucleotides.
GO:0070705
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.
snadendla
2015-09-18T17:03:25Z
eco
ECO:0005511
duplication mutation evidence
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.
SO:1000035
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.
snadendla
2015-09-18T17:05:49Z
eco
ECO:0005512
frameshift mutation evidence
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.
url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations
A type of experimental phenotypic evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated.
snadendla
2015-09-18T17:06:34Z
eco
ECO:0005513
repeat expansion mutation evidence
A type of experimental phenotypic evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated.
PMID:9397685
url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations
A type of experimental phenotypic evidence resulting from a mutation in which there is a change in nucleotides at a splice site
snadendla
2015-09-18T17:07:29Z
eco
ECO:0005514
splice site mutation evidence
A type of experimental phenotypic evidence resulting from a mutation in which there is a change in nucleotides at a splice site
ECO:RCT
A type of experimental phenotypic evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome
snadendla
2015-09-18T17:08:01Z
eco
ECO:0005515
translocation mutation evidence
A type of experimental phenotypic evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome
ECO:RCT
A type of experimental evidence resulting from the detection and analysis of molecular markers.
snadendla
2015-09-24T15:54:21Z
eco
ECO:0005516
molecule detection assay evidence
A type of experimental evidence resulting from the detection and analysis of molecular markers.
ECO:RCT
A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins.
snadendla
2015-09-25T14:27:40Z
eco
ECO:0005517
protein detection assay evidence
A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins.
ECO:RCT
A type of molecule detection assay evidence resulting from the detection of specific RNAs.
snadendla
2015-09-25T14:43:53Z
eco
ECO:0005518
RNA detection assay evidence
A type of molecule detection assay evidence resulting from the detection of specific RNAs.
ECO:RCT
A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA.
snadendla
2015-09-25T19:33:25Z
eco
ECO:0005519
DNA detection assay evidence
A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA.
ECO:RCT
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.
CollecTF
snadendla
2015-09-28T16:01:01Z
IRIS
SRIB
Spectral Reflectance Imaging Biosensor
eco
ECO:0005520
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 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.
ECO:SW
PMID:21587155
PMID:24271115
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.
CollecTF
snadendla
2015-09-28T17:16:56Z
eco
ECO:0005521
S1 nuclease protection assay 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.
ECO:SW
PMID:21390683
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.
snadendla
2015-09-30T10:03:03Z
eco
ECO:0005522
DNA dot blot assay evidence
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.
PMID:18265189
A type of DNA dot blot assay evidence that is used in a manual assertion.
snadendla
2015-09-30T10:04:00Z
eco
ECO:0005523
DNA dot blot assay evidence used in manual assertion
true
true
A type of DNA dot blot assay evidence that is used in a manual assertion.
ECO:SN
ECO:SW
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.
CollecTF
snadendla
2015-09-30T10:51:56Z
MALDI-TOF Mass Spectrometry
MALDI-TOF-MS
eco
ECO:0005526
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 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.
ECO:SW
PMID:21964792
PMID:25354905
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion.
snadendla
2015-09-30T10:58:51Z
MALDI-TOF mass spectrometry evidence
MALDI-TOF-MS evidence
eco
ECO:0005527
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
true
true
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion.
ECO:SN
ECO:SW
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.
CollecTF
snadendla
2015-09-30T11:34:41Z
site directed mutagenesis
eco
ECO:0005528
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.
site-directed mutagenesis evidence
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.
ECO:SW
PMID:21204030
PMID:24011050
PMID:3541892
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.
CollecTF
snadendla
2015-09-30T11:55:03Z
eco
ECO:0005529
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.
random mutagenesis evidence
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.
ECO:SW
PMID:15153637
PMID:18265275
A type of random mutagenesis evidence that is used in a manual assertion.
snadendla
2015-09-30T11:57:00Z
eco
ECO:0005530
random mutagenesis evidence used in manual assertion
true
true
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.
CollecTF
snadendla
2015-09-30T15:04:45Z
eco
ECO:0005531
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.
motif discovery evidence
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.
ECO:SW
PMID:10812473
PMID:16845028
PMID:8211139
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.
PMID:19892760
PMID:23032607
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.
CollecTF
snadendla
2015-10-09T14:12:54Z
eco
ECO:0005532
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.
consensus search evidence
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.
ECO:SW
PMID:15130839
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'.
CollecTF
snadendla
2015-09-30T16:23:02Z
eco
ECO:0005533
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).
phylogenetic footprinting evidence
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'.
ECO:SW
PMID:16477324
PMID:3199442
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.
CollecTF
snadendla
2015-10-09T14:30:38Z
eco
ECO:0005534
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 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.
ECO:SW
PMID:10854408
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.
CollecTF
snadendla
2015-10-01T11:58:36Z
eco
ECO:0005535
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 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.
ECO:SW
PMID:17117497
PMID:2014171
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.
CollecTF
snadendla
2015-10-09T15:04:35Z
PSSM motif search
PSSM
eco
ECO:0005536
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 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.
ECO:SW
PMID:10812473
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.
CollecTF
snadendla
2015-10-28T15:31:28Z
eco
ECO:0005537
xylE reporter gene assay 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.
ECO:SW
PMID:2592344
snadendla
2015-11-17T15:15:50Z
eco
ECO:0005538
computationally derived logical inference
true
snadendla
2015-11-17T15:17:47Z
eco
ECO:0005539
computationally derived logical inference used in automatic assertion
true
snadendla
2015-11-17T15:24:42Z
eco
ECO:0005540
computationally derived logical inference from automatic assertion used in automatic assertion
true
snadendla
2015-11-17T15:32:03Z
eco
ECO:0005541
computationally derived logical inference from manual assertion used in automatic assertion
true
A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion.
snadendla
2015-12-16T15:32:41Z
eco
ECO:0005542
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
true
true
A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion.
ECO:SN
PMID:19450514
A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion.
snadendla
2015-12-16T15:45:01Z
eco
ECO:0005543
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
true
true
A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion.
ECO:SN
PMID:22232657
A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion.
snadendla
2015-12-18T16:20:49Z
eco
ECO:0005544
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
true
A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion.
ECO:SN
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.
snadendla
2015-12-16T15:57:37Z
eco
ECO:0005545
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
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.
ECO:SN
PMID:15660128
A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion.
snadendla
2015-12-16T16:05:15Z
eco
ECO:0005546
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 paralogy evidence used in manual assertion
true
A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion.
ECO:SN
PMID:15660128
A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion.
snadendla
2015-12-16T16:07:42Z
eco
ECO:0005547
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
true
true
A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion.
ECO:SN
PMID:17876790
A type of biological system reconstruction based solely on background scientific knowledge of that biological system.
snadendla
2015-12-18T15:32:15Z
eco
ECO:0005548
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 based solely on background scientific knowledge of that biological system.
ECO:SN
PMID:17876790
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.
snadendla
2015-12-18T15:49:46Z
eco
ECO:0005549
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 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.
ECO:SN
PMID:15660128
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.
snadendla
2015-12-18T16:24:08Z
eco
ECO:0005550
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 paralogy 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.
ECO:SN
PMID:15660128
A type of biological system reconstruction evidence that uses experimental evidence as support.
snadendla
2015-12-18T16:34:13Z
eco
ECO:0005551
biological system reconstruction evidence by experimental evidence
A type of biological system reconstruction evidence that uses experimental evidence as support.
ECO:SN
PMID:19450514
PMID:22232657
A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment.
snadendla
2015-12-18T16:35:13Z
eco
ECO:0005552
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
A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment.
ECO:SN
PMID:22232657
A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species.
snadendla
2015-12-18T16:36:44Z
eco
ECO:0005553
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
A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species.
ECO:SN
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).
snadendla
2016-02-08T14:30:46Z
eco
ECO:0005554
pairwise sequence alignment evidence
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).
ECO:SN
url:http://www.ebi.ac.uk/Tools/psa/
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.
CollecTF
snadendla
2016-02-08T14:31:24Z
eco
ECO:0005555
multiple sequence alignment evidence
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.
ECO:SN
url:http://www.ebi.ac.uk/Tools/msa/
A type of multiple sequence alignment evidence that is used in a manual assertion.
snadendla
2016-02-08T14:59:18Z
eco
ECO:0005556
multiple sequence alignment evidence used in manual assertion
true
true
A type of multiple sequence alignment evidence that is used in a manual assertion.
ECO:SN
A type of multiple sequence alignment evidence that is used in an automatic assertion.
snadendla
2016-02-08T15:00:50Z
eco
ECO:0005557
multiple sequence alignment evidence used in automatic assertion
true
true
A type of multiple sequence alignment evidence that is used in an automatic assertion.
ECO:SN
A type of motif discovery evidence that is used in a manual assertion.
snadendla
2016-02-08T15:07:47Z
eco
ECO:0005558
motif discovery evidence used in manual assertion
true
true
A type of motif discovery evidence that is used in a manual assertion.
ECO:SN
A type of motif discovery evidence that is used in an automatic assertion.
snadendla
2016-02-08T15:08:19Z
eco
ECO:0005559
motif discovery evidence used in automatic assertion
true
true
A type of motif discovery evidence that is used in an automatic assertion.
ECO:SN
A type of pairwise sequence alignment evidence that is used in a manual assertion.
snadendla
2016-02-08T15:17:05Z
eco
ECO:0005560
pairwise sequence alignment evidence used in manual assertion
true
true
A type of pairwise sequence alignment evidence that is used in a manual assertion.
ECO:SN
A type of pairwise sequence alignment evidence that is used in an automatic evidence.
snadendla
2016-02-08T15:17:52Z
eco
ECO:0005561
pairwise sequence alignment evidence used in automatic assertion
true
true
A type of pairwise sequence alignment evidence that is used in an automatic evidence.
ECO:SN
A type of protein kinase assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated kinase substrate.
snadendla
2016-02-09T12:05:29Z
eco
ECO:0005562
in-gel protein kinase assay evidence
A type of protein kinase assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated kinase substrate.
PMID:12372853
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.
snadendla
2016-02-09T12:40:03Z
eco
ECO:0005563
macroscopic current trace evidence
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.
ECO:SN
PMID:17938230
url:http://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch03.pdf
A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane.
snadendla
2016-02-09T12:43:07Z
eco
ECO:0005564
current density evidence
A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane.
ECO:SN
url:http://circres.ahajournals.org/content/102/11/1298.full
url:http://www.bem.fi/book/04/04.htm
snadendla
2016-02-09T12:45:42Z
eco
ECO:0005565
single channel conductance evidence
true
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.
snadendla
2016-02-09T12:46:54Z
eco
ECO:0005566
sustained current evidence
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.
ECO:SN
url:http://www.nature.com/ncomms/journal/v3/n2/full/ncomms1717.html
snadendla
2016-02-09T12:48:17Z
eco
ECO:0005567
steady state activation curve evidence
true
snadendla
2016-02-09T12:50:45Z
eco
ECO:0005568
steady state inactivation curve evidence
true
snadendla
2016-02-09T12:57:16Z
eco
ECO:0005569
window current trace evidence
true
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.
snadendla
2016-02-09T12:58:18Z
eco
ECO:0005570
use dependence of inactivation 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.
ECO:SN
url:http://circres.ahajournals.org/content/89/8/700.full
A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell.
snadendla
2016-02-12T13:58:32Z
birnlex:2278
current clamp voltage recording evidence
eco
ECO:0005571
current clamp recording evidence
A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell.
ECO:SN
url:http://www.nature.com/nprot/journal/v4/n8/full/nprot.2009.91.html
birnlex:2278
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.
snadendla
2016-02-12T14:06:40Z
birnlex:2281
eco
ECO:0005572
whole-cell voltage clamp recording evidence
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.
ECO:SN
url:http://circres.ahajournals.org/content/72/1/91.full.pdf
birnlex:2281
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.
snadendla
2016-02-12T14:07:39Z
birnlex:2283
cell-attached patch-clamp recording evidence
eco
ECO:0005573
cell-attached single-channel recording evidence
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.
ECO:SN
url:http://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch04.pdf
birnlex:2283
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.
snadendla
2016-02-12T14:16:53Z
birnlex:2286
cell-detached inside-out patch-clamp recording evidence
eco
ECO:0005574
cell-detached inside-out single-channel recording evidence
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.
ECO:SN
url:http://www.acnp.org/g4/GN401000005/CH005.html
birnlex:2286
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.
snadendla
2016-02-12T14:17:46Z
birnlex:2287
eco
ECO:0005575
reconstituted bilayer single-channel patch recording evidence
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.
ECO:SN
url:http://nanion.de/images/stories/papers/Bilayers_lab-on-a-chip08.pdf
birnlex:2287
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.
snadendla
2016-02-12T14:18:36Z
birnlex:2279
voltage clamp current recording evidence
eco
ECO:0005576
voltage clamp recording evidence
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.
ECO:SN
url:http://neurobio.drexelmed.edu/GaoWeb/Resources/Recording%20_Techniques.pdf
url:http://www.acnp.org/g4/GN401000005/CH005.html
birnlex:2279
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.
snadendla
2016-02-12T14:19:21Z
birnlex:2293
eco
ECO:0005577
electroencephalography recording evidence
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.
ECO:SN
url:http://www.jove.com/science-education/5420/electro-encephalography-eeg
birnlex:2293
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.
snadendla
2016-02-12T15:20:47Z
eco
ECO:0005578
super-resolution microscopy evidence
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.
ECO:SN
url:http://journal.frontiersin.org/article/10.3389/fncel.2015.00007/full
A type of immunogold labelling evidence that is used in a manual assertion.
snadendla
2016-02-12T15:38:03Z
IDA: immunogold labelling
eco
ECO:0005579
immunogold labelling evidence used in manual assertion
true
true
A type of immunogold labelling evidence that is used in a manual assertion.
ECO:SN
A type of flow cytometry evidence that is used in a manual assertion.
snadendla
2016-02-12T16:04:23Z
FCM
eco
ECO:0005580
flow cytometry evidence used in manual assertion
true
true
A type of flow cytometry evidence that is used in a manual assertion.
ECO:SN
A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion.
snadendla
2016-02-12T16:23:38Z
ELISA evidence|enzyme-linked immunosorbent assay evidence
eco
ECO:0005581
enzyme-linked immunoabsorbent assay evidence used in manual assertion
true
true
A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion.
ECO:SN
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).
snadendla
2016-03-02T10:47:25Z
cell-detached outside-out patch-clamp evidence
eco
ECO:0005582
cell-detached outside-out single-channel recording evidence
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).
ECO:SN
url:http://www.nature.com/nprot/journal/v2/n11/full/nprot.2007.403.html
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.
snadendla
2016-03-02T11:29:32Z
eco
ECO:0005583
cut-open oocyte voltage clamp 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.
ECO:SN
PMID:9711615
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).
snadendla
2016-03-02T11:33:48Z
eco
ECO:0005584
macropatch 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).
ECO:SN
url:http://jxb.oxfordjournals.org/content/50/Special_Issue/1037.full.pdf
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.
snadendla
2016-03-02T12:33:07Z
eco
ECO:0005585
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 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.
ECO:SN
PMID:20805795
A type of high throughput mass spectrometry evidence that is used in a manual assertion.
snadendla
2016-03-02T12:50:02Z
eco
ECO:0005586
high throughput mass spectrometry evidence used in manual assertion
true
A type of high throughput mass spectrometry evidence that is used in a manual assertion.
ECO:SN
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.
snadendla
2016-03-17T12:29:45Z
eco
ECO:0005587
confocal microscopy evidence
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.
ECO:SN
url:http://www.physics.emory.edu/faculty/weeks//lab/papers/ebbe05.pdf
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.
snadendla
2016-03-17T12:30:27Z
eco
ECO:0005588
wide-field microscopy evidence
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.
ECO:SN
url:http://jcb.rupress.org/content/172/1/9.full
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048960/
url:http://zeiss-campus.magnet.fsu.edu/articles/livecellimaging/techniques.html
A type confocal microscopy evidence that is used in a manual assertion.
snadendla
2016-03-17T12:32:24Z
eco
ECO:0005589
confocal microscopy evidence used in manual assertion
true
true
A type confocal microscopy evidence that is used in a manual assertion.
ECO:SN
A type of wide-field microscopy evidence that is used in a manual assertion.
snadendla
2016-03-17T12:34:42Z
eco
ECO:0005590
wide-field microscopy evidence used in manual assertion
true
true
A type of wide-field microscopy evidence that is used in a manual assertion.
ECO:SN
A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles.
snadendla
2016-03-17T15:43:00Z
eco
ECO:0005591
immunogold labelling electron microscopy assay evidence
A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles.
ECO:SN
PMID:4110101
A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion.
snadendla
2016-03-17T16:39:37Z
eco
ECO:0005592
immunogold labelling electron microscopy assay evidence used in manual assertion
true
true
true
A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion.
ECO:SN
A type of direct assay evidence that involves the use of antibodies to detect biomolecules.
snadendla
2016-03-17T17:07:33Z
eco
ECO:0005593
immunodetection assay evidence
A type of direct assay evidence that involves the use of antibodies to detect biomolecules.
ECO:SN
A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody.
snadendla
2016-03-17T17:11:34Z
eco
ECO:0005594
immunoperoxidase immunolocalization evidence
A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody.
ECO:SN
A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion.
snadendla
2016-03-17T17:14:05Z
eco
ECO:0005595
immunoperoxidase immunolocalization evidence used in manual assertion
true
true
A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion.
ECO:SN
A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody.
snadendla
2016-03-17T17:16:38Z
Immunoperoxidase labelling electron microscopy
eco
ECO:0005596
immunoperoxidase immunolocalization electron microscopy evidence
A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody.
ECO:SN
A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion.
snadendla
2016-03-17T17:23:56Z
immunoperoxidase labelling electron microscopy evidence
eco
ECO:0005597
immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion
true
true
true
A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion.
ECO:SN
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.
snadendla
2016-03-18T11:53:56Z
eco
ECO:0005598
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 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.
ECO:SN
url:http://www.bristol.ac.uk/synaptic/research/techniques/widefield.html
A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
snadendla
2016-03-18T11:55:40Z
wide-field epifluorescence microscopy
eco
ECO:0005599
immunofluorescence wide-field microscopy evidence
A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
ECO:SN
url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057135
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.
snadendla
2016-03-18T12:48:42Z
eco
ECO:0005600
This allows visualization of sub cellular distribution of biomolecules of interest.
immunofluorescence confocal 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.
ECO:SN
url:http://www.physics.emory.edu/faculty/weeks/confocal/
url:https://www.hycultbiotech.com/media/wysiwyg/protocol_Immunofluorescence.pdf
A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion.
snadendla
2016-03-18T12:52:04Z
eco
ECO:0005601
immunofluorescence confocal microscopy evidence used in manual assertion
true
true
true
A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion.
ECO:SN
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.
snadendla
2016-03-18T13:02:29Z
eco
ECO:0005602
protein expression level evidence based on western blot
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.
ECO:SN
A type of mass spectrometry evidence where one or more protein analyses are performed.
snadendla
2016-03-18T13:11:37Z
eco
ECO:0005603
protein mass spectrometry evidence
A type of mass spectrometry evidence where one or more protein analyses are performed.
ECO:SN
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.
snadendla
2016-03-29T15:40:54Z
eco
ECO:0005604
cross-streak test evidence
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.
ECO:SN
url:www.jstor.org/stable/3792785
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.
snadendla
2016-03-29T16:02:22Z
eco
ECO:0005605
disk diffusion test evidence
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.
ECO:SN
url:http://www.cdc.gov/nczved/resources/cholera/ch9.pdf
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.
snadendla
2016-03-29T16:59:17Z
eco
ECO:0005606
cell transfection experiment evidence
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.
ECO:SN
url:http://ch.promega.com/resources/product-guides-and-selectors/protocols-and-applications-guide/transfection/
url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911531/
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.
snadendla
2016-03-31T15:51:10Z
eco
ECO:0005607
tethered cell assay evidence
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.
ECO:SN
PMID:1103143
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.
snadendla
2016-03-31T16:42:35Z
Temporal assay
eco
ECO:0005608
tumble frequency assay evidence
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.
ECO:SN
PMID:4576832
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.
snadendla
2016-03-31T16:45:29Z
eco
ECO:0005609
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.
capillary assay evidence
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.
ECO:SN
PMID:4632978
A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion.
snadendla
2016-03-31T17:00:03Z
eco
ECO:0005610
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 used in manual assertion
true
true
A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion.
ECO:SN
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.
snadendla
2016-04-12T16:55:16Z
IED
inferred from experimental data
eco
ECO:0005611
inference from experimental data evidence
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.
ECO:SN
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.
snadendla
2016-04-12T17:09:43Z
IPM
inferred from phenotype manipulation
eco
ECO:0005612
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 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.
ECO:SN
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.
snadendla
2016-04-12T17:24:00Z
IAGP
inferred by association of genotype from phenotype
eco
ECO:0005613
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 natural variation mutant evidence used in manual assertion where alleles are directly linked to phenotype and Mendelian diseases as a result of various experiments.
ECO:SN
A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion.
snadendla
2016-05-06T11:03:08Z
2D-PAGE evidence
eco
ECO:0005614
two-dimensional polyacrylamide gel electrophoresis evidence used in manual assertion
true
true
A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion.
ECO:SN
A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-06T11:05:59Z
eco
SEAP reporter assay
secreted embryonic alkaline phosphatase reporter assay
ECO:0005615
alkaline phosphatase reporter gene assay evidence used in manual assertion
true
true
A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-06T11:08:57Z
beta-gal reporter gene assay evidence
eco
lacZ reporter gene assay
ECO:0005616
beta-galactosidase reporter gene assay evidence used in manual assertion
true
true
A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-06T11:11:07Z
CAT reporter gene assay evidence
eco
ECO:0005617
chloramphenicol acetyltransferase reporter gene assay evidence used in manual assertion
true
true
A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion.
snadendla
2016-05-06T11:17:04Z
ChIP-chip evidence
ChIP-on-chip evidence
eco
ECO:0005618
chromatin immunoprecipitation-chip evidence used in automatic assertion
true
true
A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion.
ECO:SN
A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion.
snadendla
2016-05-06T11:22:25Z
ChIP-exo evidence
eco
ECO:0005619
chromatin immunoprecipitation- exonuclease evidence used in automatic assertion
true
true
A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion.
ECO:SN
A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion.
snadendla
2016-05-06T11:25:01Z
ChIP-PCR evidence
eco
ECO:0005620
chromatin immunoprecipitation-PCR evidence used in manual assertion
true
true
A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion.
ECO:SN
A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion.
snadendla
2016-05-06T11:29:13Z
ChIP-SEQ evidence
ChIP-seq evidence
eco
ECO:0005621
chromatin immunoprecipitation-seq evidence used in automatic assertion
true
true
A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion.
ECO:SN
A type of comparative genomics motif search evidence that is used in a manual assertion.
snadendla
2016-05-06T14:49:36Z
eco
ECO:0005622
comparative genomics motif search evidence used in manual assertion
true
true
A type of comparative genomics motif search evidence that is used in a manual assertion.
ECO:SN
A type of comparative genomics motif search evidence that is used in an automatic assertion.
snadendla
2016-05-06T14:52:21Z
eco
ECO:0005623
comparative genomics motif search evidence used in automatic assertion
true
true
A type of comparative genomics motif search evidence that is used in an automatic assertion.
ECO:SN
A type of consensus search evidence that is used in a manual assertion.
snadendla
2016-05-06T14:54:53Z
eco
ECO:0005624
consensus search evidence used in manual assertion
true
true
A type of consensus search evidence that is used in a manual assertion.
ECO:SN
A type of consensus search evidence that is used in an automatic assertion.
snadendla
2016-05-06T14:58:22Z
eco
ECO:0005625
consensus search evidence used in automatic assertion
true
true
A type of consensus search evidence that is used in an automatic assertion.
ECO:SN
A type of copper-phenanthroline footprinting evidence that is used in a manual assertion.
snadendla
2016-05-06T15:01:25Z
1,10-phenanthroline-copper footprinting evidence
eco
OP-Cu Complex
ECO:0005626
copper-phenanthroline footprinting evidence used in manual assertion
true
true
A type of copper-phenanthroline footprinting evidence that is used in a manual assertion.
ECO:SN
A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion.
snadendla
2016-05-06T15:05:14Z
DamID evidence
eco
ECO:0005627
DNA adenine methyltransferase identification evidence used in manual assertion
true
true
A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion.
ECO:SN
A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion.
snadendla
2016-05-06T15:06:46Z
DamID evidence
eco
ECO:0005628
DNA adenine methyltransferase identification evidence used in automatic assertion
true
true
A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion.
ECO:SN
A type of DNA affinity chromatography evidence that is used in a manual assertion.
snadendla
2016-05-06T15:08:40Z
DNA affinity purification evidence
eco
ECO:0005629
DNA affinity chromatography evidence used in manual assertion
true
true
A type of DNA affinity chromatography evidence that is used in a manual assertion.
ECO:SN
A type of cDNA to DNA expression microarray evidence that is used in an automatic assertion.
snadendla
2016-05-06T15:31:51Z
DNA microarray evidence
RNA microarray evidence
eco
ECO:0005630
cDNA to DNA expression microarray evidence used in automatic assertion
true
true
A type of cDNA to DNA expression microarray evidence that is used in an automatic assertion.
ECO:SN
A type of DNAse footprinting evidence that is used in a manual assertion.
snadendla
2016-05-06T15:35:41Z
DNase protection evidence
eco
ECO:0005631
DNAse footprinting evidence used in manual assertion
true
true
A type of DNAse footprinting evidence that is used in a manual assertion.
ECO:SN
A type of fluorescence anisotropy evidence that is used in a manual assertion.
snadendla
2016-05-06T15:45:40Z
FA evidence
eco
FP
fluorescence polarization
ECO:0005632
fluorescence anisotropy evidence used in manual assertion
true
true
A type of fluorescence anisotropy evidence that is used in a manual assertion.
ECO:SN
A type of ferric uptake regulator titration assay evidence that is used in a manual assertion.
snadendla
2016-05-06T15:49:18Z
FURTA evidence
eco
ECO:0005633
ferric uptake regulator titration assay evidence used in manual assertion
true
true
A type of ferric uptake regulator titration assay evidence that is used in a manual assertion.
ECO:SN
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion.
snadendla
2016-05-06T16:41:30Z
genomic SELEX evidence
eco
ECO:0005634
genomic systematic evolution of ligands by exponential amplification evidence used in manual assertion
true
true
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion.
ECO:SN
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion.
snadendla
2016-05-06T16:43:03Z
genomic SELEX evidence
eco
ECO:0005635
genomic systematic evolution of ligands by exponential amplification evidence used in automatic assertion
true
true
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion.
ECO:SN
A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-06T16:46:32Z
GFP reporter gene assay evidence
eco
GFP promoter fusion
green fluorescent protein promoter fusion
ECO:0005636
green fluorescent protein reporter gene assay evidence used in manual assertion
true
true
A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion.
snadendla
2016-05-06T16:48:29Z
GFP reporter gene assay evidence
eco
GFP promoter fusion
green fluorescent protein promoter fusion
ECO:0005637
green fluorescent protein reporter gene assay evidence used in automatic assertion
true
true
A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion.
ECO:SN
A type of cell growth regulation assay evidence that is used in a manual assertion.
snadendla
2016-05-06T16:52:15Z
eco
growth curve analysis
ECO:0005638
cell growth regulation assay evidence used in manual assertion
true
true
A type of cell growth regulation assay evidence that is used in a manual assertion.
ECO:SN
A type of cell growth regulation assay evidence that is used in an automatic assertion.
snadendla
2016-05-06T16:53:28Z
eco
growth curve analysis
ECO:0005639
cell growth regulation assay evidence used in automatic assertion
true
true
A type of cell growth regulation assay evidence that is used in an automatic assertion.
ECO:SN
A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion.
snadendla
2016-05-06T16:56:39Z
GST pull-down assay evidence
eco
ECO:0005640
glutathione S-transferase pull-down assay evidence used in manual assertion
true
true
A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion.
ECO:SN
A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-06T16:58:29Z
GUS reporter gene assay evidence
eco
ECO:0005641
beta-glucuronidase reporter gene assay evidence used in manual assertion
true
true
A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion.
snadendla
2016-05-06T23:10:13Z
HSQC evidence
eco
ECO:0005642
heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
true
true
A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion.
ECO:SN
A type of hydroxyl-radical footprinting evidence that is used in a manual assertion.
snadendla
2016-05-06T23:14:48Z
eco
ECO:0005643
hydroxyl-radical footprinting evidence used in manual assertion
true
true
A type of hydroxyl-radical footprinting evidence that is used in a manual assertion.
ECO:SN
A type of immunoprecipitation evidence that is used in a manual assertion.
snadendla
2016-05-06T23:20:49Z
IDA: immunoprecipitation
eco
ECO:0005644
immunoprecipitation evidence used in manual assertion
true
true
A type of immunoprecipitation evidence that is used in a manual assertion.
ECO:SN
A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion.
snadendla
2016-05-06T23:27:58Z
IRIS evidence
SRIB evidence
spectral reflectance imaging biosensor evidence
eco
ECO:0005645
interferometric reflectance imaging sensor evidence used in manual assertion
true
true
A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion.
ECO:SN
A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion.
snadendla
2016-05-06T23:29:23Z
IRIS evidence
SRIB evidence
spectral reflectance imaging biosensor evidence
eco
ECO:0005646
interferometric reflectance imaging sensor evidence used in automatic assertion
true
true
A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion.
ECO:SN
A type of isothermal titration calorimetry evidence that is used in a manual assertion.
snadendla
2016-05-06T23:36:26Z
ITC evidence
eco
ECO:0005647
isothermal titration calorimetry evidence used in manual assertion
true
true
A type of isothermal titration calorimetry evidence that is used in a manual assertion.
ECO:SN
A type of luciferase reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-06T23:44:52Z
eco
ECO:0005648
luciferase reporter gene assay evidence used in manual assertion
true
true
A type of luciferase reporter gene assay evidence that is used in a manual assertion.
ECO:SN
A type of machine learning prediction of motif instance evidence that is used in a manual assertion.
snadendla
2016-05-06T23:51:30Z
eco
ECO:0005649
machine learning prediction of motif instance evidence used in manual assertion
true
true
A type of machine learning prediction of motif instance evidence that is used in a manual assertion.
ECO:SN
A type of machine learning prediction of motif instance evidence that is used in an automatic assertion.
snadendla
2016-05-06T23:54:00Z
eco
ECO:0005650
machine learning prediction of motif instance evidence used in automatic assertion
true
true
A type of machine learning prediction of motif instance evidence that is used in an automatic assertion.
ECO:SN
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion.
snadendla
2016-05-06T23:57:30Z
MALDI-TOF mass spectrometry evidence
MALDI-TOF-MS evidence
eco
ECO:0005651
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in automatic assertion
true
true
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion.
ECO:SN
A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion.
snadendla
2016-05-09T14:42:28Z
MPE-EDTA Fe(II) footprinting evidence
Methidiumpropyl-EDTA Fe(II) footprinting evidence
eco
MPE Fe(II) footprinting
ECO:0005652
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in manual assertion
true
true
A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion.
ECO:SN
A type of northern assay evidence that is used in a manual assertion.
snadendla
2016-05-09T14:48:03Z
RNA blot evidence
northern assay evidence
eco
IEP: transcript levels (e.g. Northerns)
ECO:0005653
northern assay evidence used in manual assertion
true
true
A type of northern assay evidence that is used in a manual assertion.
ECO:SN
A type of phylogenetic footprinting evidence that is used in a manual assertion.
snadendla
2016-05-09T14:50:52Z
eco
ECO:0005654
phylogenetic footprinting evidence used in manual assertion
true
true
A type of phylogenetic footprinting evidence that is used in a manual assertion.
ECO:SN
A type of phylogenetic footprinting evidence that is used in an automatic assertion.
snadendla
2016-05-09T14:51:55Z
eco
ECO:0005655
phylogenetic footprinting evidence used in automatic assertion
true
true
A type of phylogenetic footprinting evidence that is used in an automatic assertion.
ECO:SN
A type of premethylation interference footprinting evidence that is used in a manual assertion.
snadendla
2016-05-09T14:55:25Z
eco
methylation interference footprinting
ECO:0005656
premethylation interference footprinting evidence used in manual assertion
true
true
A type of premethylation interference footprinting evidence that is used in a manual assertion.
ECO:SN
A type of primer extension assay evidence that is used in a manual assertion.
snadendla
2016-05-09T14:58:38Z
eco
ECO:0005657
primer extension assay evidence used in manual assertion
true
true
A type of primer extension assay evidence that is used in a manual assertion.
ECO:SN
A type of position-specific scoring matrix motif search evidence that is used in a manual assertion.
snadendla
2016-05-09T15:01:31Z
PSSM motif search evidence
eco
ECO:0005658
position-specific scoring matrix motif search evidence used in manual assertion
true
true
A type of position-specific scoring matrix motif search evidence that is used in a manual assertion.
ECO:SN
A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion.
snadendla
2016-05-09T15:02:31Z
PSSM motif search evidence
eco
ECO:0005659
position-specific scoring matrix motif search evidence used in automatic assertion
true
true
A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion.
ECO:SN
A type of quantitative polymerase chain reaction evidence that is used in a manual assertion.
snadendla
2016-05-09T15:09:01Z
Q-PCR evidence
quantitative PCR evidence
real-time PCR evidence
real-time polymerase chain reaction evidence
eco
ECO:0005660
quantitative polymerase chain reaction evidence used in manual assertion
true
true
A type of quantitative polymerase chain reaction evidence that is used in a manual assertion.
ECO:SN
A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion.
snadendla
2016-05-09T15:19:20Z
RACE PCR evidence
eco
ECO:0005661
rapid amplification of cDNA ends polymerase chain reaction evidence used in manual assertion
true
true
A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion.
ECO:SN
A type of regular expression motif search evidence that is used in a manual assertion.
snadendla
2016-05-09T16:13:55Z
eco
ECO:0005662
regular expression motif search evidence used in manual assertion
true
true
A type of regular expression motif search evidence that is used in a manual assertion.
ECO:SN
A type of regular expression motif search evidence that is used in an automatic assertion.
snadendla
2016-05-09T16:15:03Z
eco
ECO:0005663
regular expression motif search evidence used in automatic assertion
true
true
A type of regular expression motif search evidence that is used in an automatic assertion.
ECO:SN
snadendla
2016-05-09T16:18:35Z
eco
ECO:0005664
Use ECO:0006068 (RNA-seq evidence used in manual assertion) in place of this term.
RNA sequencing assay evidence used in manual assertion
true
snadendla
2016-05-09T16:19:38Z
eco
ECO:0005665
Use ECO:0006069 (RNA-seq evidence used in automatic assertion) in place of this term.
RNA sequencing assay evidence used in automatic assertion
true
A type of S1 nuclease protection assay evidence that is used in a manual assertion.
snadendla
2016-05-09T16:22:58Z
eco
ECO:0005666
S1 nuclease protection assay evidence used in manual assertion
true
true
A type of S1 nuclease protection assay evidence that is used in a manual assertion.
ECO:SN
A type of site-directed mutagenesis evidence that is used in a manual assertion.
snadendla
2016-05-09T16:29:13Z
site directed mutagenesis evidence
eco
ECO:0005667
site-directed mutagenesis evidence used in manual assertion
true
true
A type of site-directed mutagenesis evidence that is used in a manual assertion.
ECO:SN
A type of survival rate analysis evidence that is used in a manual assertion.
snadendla
2016-05-09T16:31:08Z
eco
ECO:0005668
survival rate analysis evidence used in manual assertion
true
true
A type of survival rate analysis evidence that is used in a manual assertion.
ECO:SN
A type of ultraviolet light footprinting evidence that is used in a manual assertion.
snadendla
2016-05-09T16:33:44Z
eco
UV footprinting
ECO:0005669
ultraviolet light footprinting evidence used in manual assertion
true
true
A type of ultraviolet light footprinting evidence that is used in a manual assertion.
ECO:SN
A type of x-ray crystallography evidence that is used in a manual assertion.
snadendla
2016-05-10T11:53:00Z
eco
ECO:0005670
x-ray crystallography evidence used in manual assertion
true
true
A type of x-ray crystallography evidence that is used in a manual assertion.
ECO:SN
A type of x-ray crystallography evidence that is used in an automatic assertion.
snadendla
2016-05-10T11:54:03Z
eco
ECO:0005671
x-ray crystallography evidence used in automatic assertion
true
true
A type of x-ray crystallography evidence that is used in an automatic assertion.
ECO:SN
A type of xylE reporter gene assay evidence that is used in a manual assertion.
snadendla
2016-05-10T11:57:15Z
eco
ECO:0005672
xylE reporter gene assay evidence used in manual assertion
true
true
A type of xylE reporter gene assay evidence that is used in a manual assertion.
ECO:SN
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.
CollecTF
snadendla
2016-05-10T12:57:41Z
eco
ECO:0005673
ad-hoc qualitative phenotype observation evidence
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.
ECO:SN
PMID:15150239
A type of ad-hoc qualitative phenotype observation that is used in a manual assertion.
snadendla
2016-05-10T14:28:47Z
eco
ECO:0005674
ad-hoc qualitative phenotype observation evidence used in manual assertion
true
true
A type of ad-hoc qualitative phenotype observation that is used in a manual assertion.
ECO:SN
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.
CollecTF
snadendla
2016-05-10T14:30:50Z
eco
ECO:0005675
ad-hoc quantitative phenotype observation evidence
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.
ECO:SN
PMID:15150239
A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion.
snadendla
2016-05-10T14:34:50Z
eco
ECO:0005676
ad-hoc quantitative phenotype observation evidence used in manual assertion
true
true
A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion.
ECO:SN
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.
critical dilution assay
spot assay
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 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.
http://www.sciencedirect.com/science/article/pii/016770129400068I
A type of enzyme assay evidence that is used in a manual assertion.
IDA: enzyme assays
eco
ECO:0005801
enzyme assay evidence used in manual assertion
true
A type of enzyme assay evidence that is used in a manual assertion.
ECO:SN
A type of cell transfection experiment evidence that is used in a manual assertion.
eco
ECO:0005802
cell transfection experiment evidence used in manual assertion
true
A type of cell transfection experiment evidence that is used in a manual assertion.
ECO:SN
A type of direct assay evidence where the motility of a cell or cells is determined.
eco
ECO:0005803
motility assay evidence
A type of direct assay evidence where the motility of a cell or cells is determined.
ECO:SN
A type of immunofluorescence evidence that is used in a manual assertion.
IDA: immunofluorescence
eco
ECO:0005804
immunofluorescence evidence used in manual assertion
true
A type of immunofluorescence evidence that is used in a manual assertion.
ECO:SN
A type of yeast 2-hybrid evidence that is used in a manual assertion.
IPI: yeast two-hybrid assay
eco
ECO:0005805
yeast 2-hybrid evidence used in manual assertion
true
A type of yeast 2-hybrid evidence that is used in a manual assertion.
ECO:SN
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.
rctauber
2016-06-15T08:42:16Z
eco
ECO:0006001
Cya fusion reporter assay evidence
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.
PMID:10217833
PMID:14702323
A type of Cya fusion reporter assay evidence that is used in a manual assertion.
CollecTF
rctauber
2010-06-15T08:44:10Z
eco
ECO:0006002
Cya fusion reporter assay evidence used in manual assertion
true
A type of Cya fusion reporter assay evidence that is used in a manual assertion.
ECO:RCT
A type of electron microscopy evidence that is used in a manual assertion.
rctauber
2016-10-12T12:32:29Z
eco
ECO:0006003
electron microscopy evidence used in manual assertion
true
A type of electron microscopy evidence that is used in a manual assertion.
ECO:RCT
A type of super-resolution microscopy evidence that is used in a manual assertion.
rctauber
2016-10-12T12:32:29Z
eco
ECO:0006004
super-resolution microscopy evidence used in manual assertion
true
A type of super-resolution microscopy evidence that is used in a manual assertion.
ECO:RCT
A type of fractionation evidence that is used in a manual assertion.
rctauber
2016-10-12T12:32:29Z
eco
ECO:0006005
fractionation evidence used in manual assertion
true
A type of fractionation evidence that is used in a manual assertion.
ECO:RCT
A type of electrophysiology assay evidence that is used in a manual assertion.
rctauber
2016-10-12T12:32:29Z
eco
ECO:0006006
electrophysiology assay evidence used in manual assertion
true
A type of electrophysiology assay evidence that is used in a manual assertion.
ECO:RCT
A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion.
rctauber
2016-10-21T11:55:53Z
ChIP-chip evidence
ChIP-on-chip evidence
eco
ECO:0006007
chromatin immunoprecipitation-chip evidence used in manual assertion
true
A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion.
ECO:RCT
A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion.
rctauber
2016-10-21T11:55:53Z
ChIP-exo
eco
ECO:0006008
chromatin immunoprecipitation- exonuclease evidence used in manual assertion
true
A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion.
ECO:RCT
A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion.
rctauber
2016-10-21T11:55:53Z
ChIP-SEQ evidence
ChIP-seq evidence
eco
ECO:0006009
chromatin immunoprecipitation-seq evidence used in manual assertion
true
A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion.
ECO:RCT
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.
rctauber
2016-10-21T12:28:17Z
ultraviolet light cross-linking RNA binding evidence
eco
ECO:0006010
mRNA interactome capture evidence
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.
PMID:27729395
A type of mRNA interactome capture evidence that is used in a manual assertion.
rctauber
2016-10-21T12:28:17Z
ultraviolet light cross-linking RNA binding evidence
eco
ECO:0006011
mRNA interactome capture evidence used in manual assertion
true
A type of mRNA interactome capture evidence that is used in a manual assertion.
ECO:RCT
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.
rctauber
2016-11-28T11:44:05Z
eco
ECO:0006012
patch-clamp recording evidence
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.
ECO:RCT
A type of patch-clamp recording evidence that is used in a manual assertion.
rctauber
2016-11-28T11:44:05Z
eco
ECO:0006013
patch-clamp recording evidence used in manual assertion
A type of patch-clamp recording evidence that is used in a manual assertion.
ECO:RCT
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.
rctauber
2016-11-28T11:44:05Z
eco
ECO:0006014
whole-cell patch-clamp recording evidence
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.
PMID:27341060
A type of whole-cell patch-clamp recording evidence that is used in a manual assertion.
rctauber
2016-11-28T11:44:05Z
eco
ECO:0006015
whole-cell patch-clamp recording evidence used in manual assertion
A type of whole-cell patch-clamp recording evidence that is used in a manual assertion.
ECO:RCT
A type of traceable author statement that is based on a publication about a clinical study.
rctauber
2016-11-30T09:44:47Z
published clinical study evidence
eco
ECO:0006016
traceable author statement from published clinical study
A type of traceable author statement from published clinical study that is used in a manual assertion.
rctauber
2016-11-30T09:44:47Z
published clinical study evidence
PCS
eco
ECO:0006017
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
http://human-phenotype-ontology.github.io/documentation.html#annot
true
PCS
HPO:PCS
A type of curator inference that is based on the individual clinical experience of a clinician
rctauber
2016-11-30T09:44:47Z
individual clinical experience evidence
eco
ECO:0006018
inference based on individual clinical experience
A type of inference based on individual clinical experience that is used in a manual assertion.
rctauber
2016-11-30T09:44:47Z
individual clinical experience evidence
ICE
eco
ECO:0006019
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
http://human-phenotype-ontology.github.io/documentation.html#annot
true
ICE
HPO:ICE
A type of cell proliferation assay evidence in which biofilm growth is monitored and detected from attachment to development.
rctauber
2016-12-05T09:33:18Z
biofilm assay evidence
eco
ECO:0006020
biofilm formation assay evidence
A type of cell proliferation assay evidence in which biofilm growth is monitored and detected from attachment to development.
PMID:10547784
A type of biofilm formation assay evidence that is used in a manual assertion.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006021
biofilm formation assay evidence used in manual assertion
true
A type of biofilm formation assay evidence that is used in a manual assertion.
ECO:RCT
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.
rctauber
2016-12-05T09:33:18Z
96-well biofilm assay evidence
eco
ECO:0006022
microtiter plate biofilm assay evidence
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.
PMID:10547784
A type of microtiter plate biofilm assay evidence that is used in a manual assertion.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006023
microtiter plate biofilm assay evidence used in manual assertion
true
A type of microtiter plate biofilm assay evidence that is used in a manual assertion.
ECO:RCT
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.
rctauber
2016-12-05T09:33:18Z
ALI biofilm assay evidence
eco
ECO:0006024
Tilting of the plate positions the air-liquid interface on a clear portion to improve visability.
air-liquid interface assay evidence
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.
PMID:18770545
A type of air-liquid interface assay evidence that is used in a manual assertion.
rctauber
2016-12-05T09:33:18Z
ALI biofilm assay evidence
eco
ECO:0006025
air-liquid interface assay evidence used in manual assertion
true
A type of air-liquid interface assay evidence that is used in a manual assertion.
ECO:RCT
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.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006026
The plates commonly contain different carbon sources or antibiotic treatments to observe properties of the cells.
colony biofilm assay evidence
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.
PMID:18770545
A type of colony biofilm assay evidence that is used in a manual assertion.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006027
colony biofilm assay evidence used in manual assertion
true
A type of colony biofilm assay evidence that is used in a manual assertion.
ECO:RCT
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.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006028
Kadouri drip-fed biofilm assay evidence
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.
PMID:18770545
A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion.
rctauber
2016-12-05T09:33:18Z
eco
ECO:0006029
Kadouri drip-fed biofilm assay evidence used in manual assertion
true
A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion.
ECO:RCT
A type of co-immunoprecipitation evidence that is used in a manual assertion.
rctauber
2016-01-13T11:32:26Z
IPI: co-immunoprecipitation
eco
ECO:0006030
co-immunoprecipitation evidence used in manual assertion
true
true
A type of co-immunoprecipitation evidence that is used in a manual assertion.
ECO:RCT
A type of immunolocalization evidence that is used in a manual assertion.
rctauber
2017-01-23T07:54:37Z
IDA: immunolocalization
eco
ECO:0006031
immunolocalization evidence used in manual assertion
true
A type of immunolocalization evidence that is used in a manual assertion.
ECO:RCT
A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators.
rctauber
2017-01-23T11:58:48Z
optogenetic actuator evidence
eco
ECO:0006032
optogenetic evidence
A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators.
GOC:DOS
PMID:17035522
A type of optogenetic evidence that is used in a manual assertion.
rctauber
2017-01-23T11:58:48Z
optogenetic actuator evidence
eco
ECO:0006033
optogenetic evidence used in manual assertion
true
A type of optogenetic evidence that is used in a manual assertion.
ECO:RCT
A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor.
rctauber
2017-01-23T11:58:48Z
eco
ECO:0006034
Examples include sensors for ion concentration and potential difference across a membrane.
fluorescent sensor evidence
A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor.
GOC:DOS
A type of fluorescent sensor evidence that is used in a manual assertion.
rctauber
2017-01-23T11:58:48Z
eco
ECO:0006035
fluorescent sensor evidence used in manual assertion
true
A type of fluorescent sensor evidence that is used in a manual assertion.
ECO:RCT
A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor.
rctauber
2017-01-23T11:58:48Z
optogenetic sensor evidence
eco
ECO:0006036
genetically encoded fluorescent sensor evidence
A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor.
GOC:DOS
A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion.
rctauber
2017-01-23T11:58:48Z
optogenetic sensor evidence
eco
ECO:0006037
genetically encoded fluorescent sensor evidence used in manual assertion
true
A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion.
ECO:RCT
A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors.
rctauber
2017-01-23T11:58:48Z
electrophysiology - optical assay evidence
eco
ECO:0006038
Examples include genetically encoded sensors that detect potential difference across plasma membrane.
genetically encoded fluorescent electrophysiology assay evidence
A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors.
GOC:DOS
A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion.
rctauber
2017-01-23T11:58:48Z
electrophysiology - optical assay evidence
eco
ECO:0006039
genetically encoded fluorescent electrophysiology assay evidence used in manual assertion
true
true
A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion.
ECO:RCT
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.
rctauber
2017-01-23T11:58:48Z
eco
ECO:0006040
Examples include the genetically encoded calcium indicator GCaMP.
genetically encoded fluorescent ion concentration sensor assay evidence
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.
GOC:DOS
A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion.
rctauber
2017-01-23T11:58:48Z
eco
ECO:0006041
genetically encoded fluorescent ion concentration sensor assay evidence used in manual assertion
true
A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion.
ECO:RCT
A type of cell fractionation evidence that is used in a manual assertion.
rctauber
2017-02-21T07:26:28Z
IDA: cell fractionation
eco
ECO:0006042
cell fractionation evidence used in manual assertion
true
A type of cell fractionation evidence that is used in a manual assertion.
ECO:RCT
A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons.
rctauber
2017-02-21T07:26:28Z
eco
ECO:0006043
extracellular recording evidence
A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons.
url:http://www.nature.com/subjects/extracellular-recording
A type of extracellular recording evidence that is used in a manual assertion.
rctauber
2017-02-21T07:26:28Z
eco
ECO:0006044
extracellular recording evidence used in manual assertion
true
A type of extracellular recording evidence that is used in a manual assertion.
ECO:RCT
A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron.
rctauber
2017-02-21T07:26:28Z
eco
ECO:0006045
single-unit extracellular recording evidence
A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron.
doi:10.1385/0-89603-185-3:1
A type of single-unit extracellular recording evidence that is used in a manual assertion.
rctauber
2017-02-21T07:26:28Z
eco
ECO:0006046
single-unit extracellular recording evidence used in manual assertion
true
A type of single-unit extracellular recording evidence that is used in a manual assertion.
ECO:RCT
A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes.
rctauber
2017-02-21T07:26:28Z
local field potential recording evidence
eco
ECO:0006047
field potential recording evidence
A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes.
ECO:RCT
A type of field potential recording evidence that is used in a manual assertion.
rctauber
2017-02-21T07:26:28Z
eco
local field potential recording evidence
ECO:0006048
field potential recording evidence used in manual assertion
true
A type of field potential recording evidence that is used in a manual assertion.
ECO:RCT
A type of genetic transformation evidence that is used in a manual assertion
rctauber
02-21-2017T18:98:58Z
eco
ECO:0006049
genetic transformation evidence used in manual assertion
true
A type of genetic transformation evidence that is used in a manual assertion
ECO:RCT
A type of anti-sense experiment evidence that is used in a manual assertion.
rctauber
02-21-2017T18:98:58Z
IMP: anti-sense experiments
eco
ECO:0006050
anti-sense experiment evidence used in manual assertion
true
A type of anti-sense experiment evidence that is used in a manual assertion.
ECO:RCT
A type of morpholino experiment evidence that is used in a manual assertion.
rctauber
02-21-2017T18:98:58Z
anti-sense evidence
eco
ECO:0006051
morpholino experiment evidence used in manual assertion
true
A type of morpholino experiment evidence that is used in a manual assertion.
ECO:RCT
A type of RNAi evidence that is used in a manual assertion.
rctauber
02-21-2017T18:98:58Z
IMP: RNAi experiment
eco
ECO:0006052
RNAi evidence used in manual assertion
true
A type of RNAi evidence that is used in a manual assertion.
ECO:RCT
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.
dosumis
2017-03-07T08:51:02Z
eco
ECO:0006053
pharmacological assay evidence
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.
GOC:DOS
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.
rctauber
2017-03-07T08:51:02Z
eco
ECO:0006054
pharmacological assay evidence used in manual assertion
true
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.
GOC:DOS
A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
mchibucos
2017-03-28T14:48:39Z
HT evidence
high-throughput evidence
high throughput cell biology evidence
high throughput screening evidence
eco
ECO:0006055
Some relevant articles include: PMID: 23340846, doi:10.1038/nmeth0607-523
high throughput evidence
A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
ECO:MCC
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.
rctauber
2017-03-28T14:48:39Z
HT evidence
high-throughput evidence
GOECO:HTP
HTP
inferred from high throughput experiment
eco
high throughput cell biology evidence
high throughput screening evidence
ECO:0006056
high throughput evidence used in manual assertion
true
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.
ECO:RCT
GOECO:HTP
inferred from high throughput experiment
HTP
GOECO:HTP
inferred from high throughput experiment
GOECO:HTP
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.
rctauber
2017-03-28T14:48:39Z
HT evidence
high-throughput evidence
eco
high throughput cell biology evidence
high throughput screening evidence
ECO:0006057
high throughput evidence used in automatic assertion
true
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.
ECO:RCT
A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
mchibucos
2017-03-28T14:48:39Z
eco
omics experiment
ECO:0006058
HT methodologies may incorporate techniques from optics, chemistry, biology or image analysis (https://en.wikipedia.org/wiki/High_throughput_biology)
high throughput cell biology evidence
A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
ECO:MCC
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.
rctauber
2017-03-28T14:48:39Z
eco
omics experiment
ECO:0006059
high throughput cell biology evidence used in manual assertion
true
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.
ECO:RCT
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.
rctauber
2017-03-28T14:48:39Z
eco
omics experiment
ECO:0006060
high throughput cell biology evidence used in automatic assertion
true
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.
ECO:RCT
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.
rctauber
2017-05-15T08:57:07Z
wide-field epifluorescence microscopy evidence
eco
ECO:0006061
immunofluorescence wide-field microscopy evidence used in manual assertion
true
true
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.
ECO:SN
url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057135
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.
rctauber
2017-05-15T09:01:19Z
eco
ECO:0006062
wide-field fluorescence microscopy evidence used in manual assertion
true
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.
ECO:SN
url:http://www.bristol.ac.uk/synaptic/research/techniques/widefield.html
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.
rctauber
2017-05-15T09:03:49Z
eco
IMP: analysis of overexpression/ectopic expression phenotype
ECO:0006063
over expression analysis evidence used in manual assertion
true
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.
PMID:22419077
A type of cell-free assay evidence that is used in a manual assertion.
rctauber
2017-05-15T09:08:17Z
in vitro assay evidence
eco
ECO:0006064
cell-free assay evidence used in manual assertion
true
A type of cell-free assay evidence that is used in a manual assertion.
PMID:18453125
rctauber
2017-05-15T09:11:13Z
eco
ECO:0006065
Use children of ECO:0001565 (cell-based assay evidence) in place of this term.
in vitro cell based assay evidence used in manual assertion
true
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.
dosumis
rctauber
2017-05-16T10:55:40Z
FRAP evidence
eco
ECO:0006066
FRAP is a fluorescence microscopy-based technique.
fluorescence recovery after photobleaching evidence
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.
PMID:26314367
FRAP is a fluorescence microscopy-based technique.
PMID:26314367
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.
rctauber
2017-05-16T10:55:40Z
FRAP evidence
eco
ECO:0006067
fluorescence recovery after photobleaching evidence used in manual assertion
true
A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
rctauber
2017-06-28T10:37:02Z
WTSS evidence
whole transcriptome shotgun sequencing
eco
RNA sequencing|differential gene expression evidence from RNA-seq experiment
ECO:0006068
RNA-seq evidence used in manual assertion
true
A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
ECO:MCC
A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
rctauber
2017-06-28T10:37:02Z
WTSS evidence
whole transcriptome shotgun sequencing
eco
RNA sequencing|differential gene expression evidence from RNA-seq experiment
ECO:0006069
RNA-seq evidence used in automatic assertion
true
A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
ECO:MCC
A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
dosumis
rctauber
2017-07-05T09:59:10Z
immunolabelling electron microscopy evidence
eco
ECO:0006070
immuno-labelling electron microscopy evidence
A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
PMID:25151300
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.
PMID:25151300
dosumis
rctauber
2017-07-05T09:59:10Z
immunolabelling electron microscopy evidence
eco
ECO:0006071
immuno-labelling electron microscopy evidence used in manual assertion
true
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.
PMID:25151300
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.
dosumis
rctauber
2017-07-05T09:59:10Z
eco
ECO:0006072
immunofluorescence super resolution microscopy evidence
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.
PMID:19245833
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.
dosumis
rctauber
2017-07-05T09:59:10Z
eco
ECO:0006073
immunofluorescence super resolution microscopy evidence used in manual assertion
true
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.
PMID:19245833
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.
rctauber
2017-09-14T09:19:19
IPI: co-purification
eco
ECO:0006074
co-purification evidence used in manual assertion
true
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.
TAIR:TED
A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities.
rctauber
2017-09-14T09:19:20
eco
ligand binding evidence
ECO:0006075
affinity evidence used in manual assertion
true
A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities.
ECO:MCC
A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex.
rctauber
2017-09-14T09:19:21
eco
ECO:0006076
protein binding evidence used in manual assertion
true
true
A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex.
GO:0005515
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.
rctauber
2017-09-14T09:19:22
eco
ECO:0006077
hybrid interaction evidence used in manual assertion
true
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.
ECO:MCC
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.
rctauber
2017-09-14T09:19:23
eco
ECO:0006078
immunological assay evidence used in manual assertion
true
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.
ERO:0001362
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.
rctauber
2017-09-14T09:19:24
IPI: yeast one-hybrid assay
eco
ECO:0006079
yeast one-hybrid evidence used in manual assertion
true
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.
ECO:MCC
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.
rctauber
2017-09-14T09:19:25
IPI: split-ubiquitin assay
eco
ECO:0006080
split-ubiquitin assay evidence used in manual assertion
true
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.
PMID:15064465
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.
rctauber
2017-09-14T09:19:26
IPI: far-Western analysis
eco
ECO:0006081
far-Western blotting evidence used in manual assertion
true
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.
PMID:18079728
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.
rctauber
2017-09-14T09:19:27
IDA: affinity chromatography
eco
ECO:0006082
affinity chromatography evidence used in manual assertion
true
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.
ECO:MCC
A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid.
rctauber
2017-09-14T09:19:28
eco
ECO:0006083
nucleic acid binding evidence used in manual assertion
true
A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid.
GO:0003676
A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer.
rctauber
2017-09-14T09:19:29
IDA: ribohomopolymer binding assay
eco
ECO:0006084
ribohomopolymer binding assay evidence used in manual assertion
true
A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer.
PMC:102612
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.
rctauber
2017-09-14T09:19:30
eco
ECO:0006085
protein:ion binding evidence used in manual assertion
true
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.
PMID:2377604
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.
rctauber
2017-09-14T09:19:31
IDA: Southwestern analysis
eco
ECO:0006086
Southwestern blot evidence used in manual assertion
true
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.
ECO:RCT
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.
rctauber
2017-09-14T09:19:32
IDA: Northwestern analysis
eco
ECO:0006087
Northwestern blot evidence used in manual assertion
true
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.
ECO:RCT
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.
rctauber
2017-09-14T09:19:33
SELEX evidence
in vitro selection evidence
eco
in vitro evolution evidence
ECO:0006088
systematic evolution of ligands by exponential amplification evidence used in manual assertion
true
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.
ECO:MCC
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).
rctauber
2017-09-14T09:19:34
B1H evidence
eco
ECO:0006089
bacterial one-hybrid evidence used in manual assertion
true
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).
ECO:MCC
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.
rctauber
2017-09-14T09:19:35
PBM evidence
eco
ECO:0006090
protein-binding microarray evidence used in manual assertion
true
true
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.
PMID:22146299
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.
rctauber
2017-09-14T09:19:36
IGI: functional complementation
eco
ECO:0006091
functional complementation evidence used in manual assertion
true
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.
PMID:27403640
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.
rctauber
2017-09-14T09:19:37
eco
ECO:0006092
transgenic rescue experiment evidence used in manual assertion
true
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.
url:http://www.nature.com/gt/journal/v11/n15/full/3302282a.html
A type of transient rescue experiment evidence that is used in a manual assertion.
rctauber
2017-09-14T09:19:38
eco
ECO:0006093
transient rescue experiment evidence used in manual assertion
true
A type of transient rescue experiment evidence that is used in a manual assertion.
ECO:RCT
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.
rctauber
2017-09-14T09:19:39
IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)
eco
ECO:0006094
suppressor/enhancer interaction evidence used in manual assertion
true
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.
url:http://www.wormbook.org/chapters/www:geneticsuppression/geneticsuppression.html
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.
rctauber
2017-09-14T09:19:40
IGI: double mutant analysis
eco
ECO:0006095
double mutant phenotype evidence used in manual assertion
true
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.
ECO:RCT
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.
rctauber
2017-09-14T09:19:41
IGI: epistatic interactions
eco
ECO:0006096
epistatic interaction evidence used in manual assertion
true
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.
PMID:18852697
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.
rctauber
2017-09-14T09:19:42
IGI: functional complementation in heterologous system
eco
ECO:0006097
functional complementation in heterologous system evidence used in manual assertion
true
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.
TAIR:TED
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.
pgaudet
rctauber
2017-09-18T07:58:28
Ts mutation evidence
eco
ECO:0006098
temperature-sensitive mutant phenotype evidence
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.
GOC:PG
PMID:19596904
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.
pgaudet
rctauber
2017-09-18T07:58:28
Ts mutation evidence
eco
ECO:0006099
temperature-sensitive mutant phenotype evidence used in manual assertion
true
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.
GOC:PG
PMID:19596904
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.
pgaudet
rctauber
2017-09-18T07:58:28
eco
ECO:0006100
recessive mutant phenotype evidence
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.
GOC:PG
NBK:21578
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.
pgaudet
rctauber
2017-09-18T07:58:28
eco
ECO:0006101
recessive mutant phenotype evidence used in manual assertion
true
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.
GOC:PG
NBK:21578
A type of high throughput evidence derived from high throughput analysis of differences in alleles of a corresponding gene.
GOC
rctauber
2017-10–05T07:39:47Z
eco
ECO:0007000
high throughput mutant phenotype evidence
A type of high throughput evidence derived from high throughput analysis of differences in alleles of a corresponding gene.
GO:IMP
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.
GOC
rctauber
2017-10–05T07:39:47Z
GOECO:HMP
HMP
inferred from high throughput mutant phenotype
eco
ECO:0007001
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
true
true
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.
GO:IMP
GOECO:HMP
inferred from high throughput mutant phenotype
HMP
GOECO:HMP
inferred from high throughput mutant phenotype
GOECO:HMP
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.
GOC
rctauber
2017-10–05T07:39:47Z
eco
ECO:0007002
high throughput genetic interaction evidence
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.
PMID:11822023
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.
GOC
rctauber
2017-10–05T07:39:47Z
GOECO:HGI
HGI
inferred from high throughput genetic interaction
eco
ECO:0007003
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
true
true
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.
PMID:11822023
GOECO:HGI
inferred from high throughput genetic interaction
HGI
GOECO:HGI
inferred from high throughput genetic interaction
GOECO:HGI
A type of high throughput evidence derived from the high throughput direct measurement of some aspect of a biological feature.
GOC
rctauber
2017-10–05T07:39:47Z
eco
ECO:0007004
high throughput direct assay evidence
A type of high throughput evidence derived from the high throughput direct measurement of some aspect of a biological feature.
ECO:MCC
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.
GOC
rctauber
2017-10–05T07:39:47Z
GOECO:HDA
HDA
inferred from high throughput direct assay
eco
ECO:0007005
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
true
true
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.
ECO:MCC
GOECO:HDA
inferred from high throughput direct assay
HDA
GOECO:HDA
inferred from high throughput direct assay
GOECO:HDA
A type of high throughput evidence derived from the high throughput characterization of gene expression.
GOC
rctauber
2017-10–05T07:39:47Z
eco
ECO:0007006
high throughput expression pattern evidence
A type of high throughput evidence derived from the high throughput characterization of gene expression.
GO:IEP
A type of high throughput evidence that is used in a manual assertion derived from the high throughput characterization of gene expression.
GOC
rctauber
2017-10–05T07:39:47Z
GOECO:HEP
HEP
inferred from high throughput expression pattern
eco
ECO:0007007
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
true
true
A type of high throughput evidence that is used in a manual assertion derived from the high throughput characterization of gene expression.
GO:IEP
GOECO:HEP
inferred from high throughput expression pattern
HEP
GOECO:HEP
inferred from high throughput expression pattern
GOECO:HEP
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.
fjungo
rctauber
2017-12-15T10:46:19Z
radioactive ligand binding assay evidence
radiometric ligand-binding assay evidence
competitive binding assay evidence
eco
ECO:0007008
radioligand binding assay evidence
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.
PMID:27471749
A type of radioligand binding assay evidence that is used in a manual assertion.
rctauber
2017-12-15T10:48:44Z
radioactive ligand binding assay evidence
eco
competitive binding assay evidence
ECO:0007009
radioligand binding assay evidence used in manual assertion
true
A type of radioligand binding assay evidence that is used in a manual assertion.
ECO:RCT
A type of inferential evidence resulting from a conclusion drawn by the author of the publication.
rctauber
2018-02-08T09:11:07Z
eco
ECO:0007010
author inference
A type of inferential evidence resulting from a conclusion drawn by the author of the publication.
ECO:RCT
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.
sbello
rctauber
2018-02-15T11:17:11Z
eco
ECO:0007011
combinatorial evidence from author knowledge and experimental evidence
true
true
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.
ECO:RCT
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.
ZFIN
rctauber
2018-02-15T11:17:11Z
eco
ECO:0007012
combinatorial evidence from curator knowledge and experimental evidence
true
true
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.
ECO:RCT
A type of combinatorial evidence from author knowledge and experimental evidence that is used in a manual assertion.
rctauber
2018-02-15T11:22:10Z
eco
ECO:0007013
combinatorial evidence from author knowledge and experimental evidence used in manual assertion
true
true
A type of combinatorial evidence from author knowledge and experimental evidence that is used in a manual assertion.
ECO:RCT
A type of combinatorial evidence from curator knowledge and experimental evidence that is used in a manual assertion.
rctauber
2018-02-15T11:22:10Z
eco
ECO:0007014
combinatorial evidence from curator knowledge and experimental evidence used in manual assertion
true
true
true
A type of combinatorial evidence from curator knowledge and experimental evidence that is used in a manual assertion.
ECO:RCT
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.
SynGO
rctauber
2018-02-28T12:11:00Z
eco
ECO:0007015
voltammetry evidence
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.
ECO:JBM
PMID:28127962
A type of voltammetry evidence that is used in a manual assertion.
rctauber
2018-02-28T12:12:34Z
eco
ECO:0007016
voltammetry evidence used in manual assertion
true
A type of voltammetry evidence that is used in a manual assertion.
ECO:RCT
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.
SynGO
rctauber
2018-03-02T09:01:00Z
eco
ECO:0007017
photoconversion evidence
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.
ECO:RCT
PMID:28574633
A type of photoconversion evidence that is used in a manual assertion.
rctauber
2018-03-02T09:05:04Z
eco
ECO:0007018
photoconversion evidence used in manual assertion
true
A type of photoconversion evidence that is used in a manual assertion.
ECO:RCT
A type of immunological assay evidence that involves observation of visible clumping of antibody and antigen into a complex.
OMP
snadendla
2018-03-14T12:44:11Z
agglutination assay evidence
ECO:0007019
agglutination test evidence
A type of immunological assay evidence that involves observation of visible clumping of antibody and antigen into a complex.
URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC380037/
A type of agglutination test evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
agglutination assay evidence
ECO:0007020
agglutination test evidence used in manual assertion
true
A type of agglutination test evidence that is used in a manual assertion.
ECO:RCT
A type of agglutination test evidence that involves observaiton of visible clumping of antibody and antigen into a complex on a slide.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007021
slide agglutination test evidence
A type of agglutination test evidence that involves observaiton of visible clumping of antibody and antigen into a complex on a slide.
URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC380037/
A type of slide agglutination test evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007022
slide agglutination test evidence used in manual assertion
true
A type of slide agglutination test evidence that is used in a manual assertion.
ECO:RCT
A type of agglutination test evidence that results in detection of nonagglutinating antibodies or complement proteins on red blood cells in vivo.
OMP
snadendla
2018-03-14T12:44:11Z
direct antihuman globulin test (DAT)
ECO:0007023
direct Coombs test evidence
A type of agglutination test evidence that results in detection of nonagglutinating antibodies or complement proteins on red blood cells in vivo.
URL:https://courses.lumenlearning.com/microbiology/chapter/agglutination-assays/
direct Coombs test evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
direct antihuman globulin test (DAT)
ECO:0007024
direct Coombs test evidence used in manual assertion
true
direct Coombs test evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
indirect antiglobulin test (IAT)
ECO:0007025
indirect Coombs test evidence
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.
URL:https://courses.lumenlearning.com/microbiology/chapter/agglutination-assays/
A type of indirect Coombs test evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
indirect antiglobulin test (IAT)
ECO:0007026
indirect Coombs test evidence used in manual assertion
true
A type of indirect Coombs test evidence that is used in a manual assertion.
ECO:RCT
A type of agglutination test evidence where some bacteria and viruses cross-link red blood cells and clump together.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007027
direct hemagglutination assay evidence
A type of agglutination test evidence where some bacteria and viruses cross-link red blood cells and clump together.
URL:https://courses.lumenlearning.com/microbiology/chapter/agglutination-assays/
A type of direct hemagglutination assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007028
direct hemagglutination assay evidence used in manual assertion
true
A type of direct hemagglutination assay evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007029
viral hemagglutination inhibition assay evidence
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.
URL:https://courses.lumenlearning.com/microbiology/chapter/agglutination-assays/
A type of viral hemagglutination inhibition assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007030
viral hemagglutination inhibition assay evidence used in manual assertion
true
A type of viral hemagglutination inhibition assay evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007031
compement fixation assay evidence
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.
URL:http://laboratoryinfo.com/complement-fixation-test/
A type of compement fixation assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007032
compement fixation assay evidence used in manual assertion
true
A type of compement fixation assay evidence that is used in a manual assertion.
ECO:RCT
A type of immunogical assay evidence that results in detection of specific neutralizing antibodies in a sample.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007033
neutralization test assay evidence
A type of immunogical assay evidence that results in detection of specific neutralizing antibodies in a sample.
PMID:24899440
url:http://www.creative-biolabs.com/drug-discovery/therapeutics/neutralization-assay.htm?gclid=Cj0KEQjwqvvLBRDIt-D7q7iqiOcBEiQAxi68ERRz00a0x9sWSKSLDu7d5-kMi4AdiLNdUq1mXzePdywaArli8P8HAQ)
A type of neutralization test assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007034
neutralization test assay evidence used in manual assertion
true
A type of neutralization test assay evidence that is used in a manual assertion.
ECO:RCT
A type of transport assay evidence where the rate of copper transport is estimated.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007035
copper transport assay evidence
A type of transport assay evidence where the rate of copper transport is estimated.
URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689948/
A type of copper transport assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007036
copper transport assay evidence used in manual assertion
true
A type of copper transport assay evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
CTC staining
ECO:0007037
5-cyano-2,3-ditolyl tetrazolium chloride staining evidence
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.
PMID:1622256
A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
CTC staining
ECO:0007038
5-cyano-2,3-ditolyl tetrazolium chloride staining evidence used in manual assertion
true
A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007039
plaque assay evidence
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.
PMID:25407402
A type of plaque assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007040
plaque assay evidence used in manual assertion
true
A type of plaque assay evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007041
epifluorescence microscopy evidence
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.
URL:http://www.rsc.org/publishing/journals/prospect/ontology.asp?id=CMO:0001096|URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4713126/
A type of epifluorescence microscopy evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007042
epifluorescence microscopy evidence used in manual assertion
true
A type of epifluorescence microscopy evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
TEM
conventional transmission electron microscopy(CTEM)
ECO:0007043
transmission electron microscopy evidence
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.
ERO:0000329|URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907272/
A type of transmission electron microscopy evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
TEM
conventional transmission electron microscopy(CTEM)
ECO:0007044
transmission electron microscopy evidence used in manual assertion
true
A type of transmission electron microscopy evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007045
scanning electron microscopy evidence
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.
URL:https://serc.carleton.edu/research_education/geochemsheets/techniques/SEM.html
A type of scanning electron microscopy evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007046
scanning electron microscopy evidence used in manual assertion
true
A type of scanning electron microscopy evidence that is used in a manual assertion.
ECO:RCT
A type of microscopy evidence where a serial images are taken at regular time points to capture the dynamics of what is being observed.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007047
time-lapsed microscopy evidence
A type of microscopy evidence where a serial images are taken at regular time points to capture the dynamics of what is being observed.
URL:https://www.nature.com/subjects/time-lapse-imaging
A type of time-lapsed microscopy evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007048
time-lapsed microscopy evidence used in manual assertion
true
A type of time-lapsed microscopy evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007049
phase contrast microscopy evidence
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.
CHMO:0000110
A type of phase contrast microscopy evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007050
phase contrast microscopy evidence used in manual assertion
true
A type of phase contrast microscopy evidence that is used in a manual assertion.
ECO:RCT
A type of microscopy evidence where a sample is illuminated with transmitted white light from below and observed from above.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007051
transmitted light brightfied mircoscopy evidence
A type of microscopy evidence where a sample is illuminated with transmitted white light from below and observed from above.
BAO:0000457
A type of transmitted light brightfied mircoscopy evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007052
transmitted light brightfied mircoscopy evidence used in manual assertion
true
A type of transmitted light brightfied mircoscopy evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007053
koehler illumination microscopy evidence
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.
URL:http://www.gonda.ucla.edu/bri_core/kohler.htm
A type of koehler illumination microscopy evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007054
koehler illumination microscopy evidence used in manual assertion
true
A type of koehler illumination microscopy evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
DIC microscopy
NIC microscopy
Nomarski interference contrast microscopy
Nomarski microscopy
ECO:0007055
differential interference contrast microscopy evidence
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.
URL:http://www.microscopemaster.com/differential-interference-contrast.html
A type of differential interference contrast microscopy evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
DIC microscopy
NIC microscopy
Nomarski interference contrast microscopy
Nomarski microscopy
ECO:0007056
differential interference contrast microscopy evidence used in manual assertion
true
A type of differential interference contrast microscopy evidence that is used in a manual assertion.
ECO:RCT
A type of confocal microscopy evidence that results in creation of a continuous confocal multi-colour mosaic from thousands of individually captured images.
OMP
snadendla
2018-03-14T12:44:11Z
EFLCM
ECO:0007057
extended field laser confocal microscopy evidence
A type of confocal microscopy evidence that results in creation of a continuous confocal multi-colour mosaic from thousands of individually captured images.
PMID:18627634
A type of extended field laser confocal microscopy evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
EFLCM
ECO:0007058
extended field laser confocal microscopy evidence used in manual assertion
true
A type of extended field laser confocal microscopy evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
CLSM
LSCM
confocal laser scanning fluorescence microscopy
confocal-laser scanning microscopy
fluorescence confocal scanning laser microscopy
scanning confocal fluorescence microscopy
ECO:0007059
confocal laser scanning microscopy evidence
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.
URL:http://bitesizebio.com/19958/what-is-confocal-laser-scanning-microscopy/
A type of confocal laser scanning microscopy evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
CLSM
LSCM
confocal laser scanning fluorescence microscopy
confocal-laser scanning microscopy
fluorescence confocal scanning laser microscopy
scanning confocal fluorescence microscopy
ECO:0007060
confocal laser scanning microscopy evidence used in manual assertion
true
A type of confocal laser scanning microscopy evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007061
light scattering assay evidence
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.
PMID:9013660
url:http://www.lsinstruments.ch/technology/dynamic_light_scattering_dls/
url:http://www.soft-matter.uni-tuebingen.de/index.html?dls.html
A type of light scattering assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007062
light scattering assay evidence used in manual assertion
true
A type of light scattering assay evidence that is used in a manual assertion.
ECO:RCT
A type of light scattering assay evidence derived by analyzing the fluctuations in the internsity of the scattered light by the particles in motion.
OMP
snadendla
2018-03-14T12:44:11Z
Photon Correlation Spectroscopy
Quasi-Elastic Light Scattering
ECO:0007063
dynamic light scattering assay evidence
A type of light scattering assay evidence derived by analyzing the fluctuations in the internsity of the scattered light by the particles in motion.
PMID:9013660
url:http://www.soft-matter.uni-tuebingen.de/index.html?dls.html
A type of dynamic light scattering assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
Photon Correlation Spectroscopy
Quasi-Elastic Light Scattering
ECO:0007064
dynamic light scattering assay evidence used in manual assertion
true
A type of dynamic light scattering assay evidence that is used in a manual assertion.
ECO:RCT
A type of light scattering assay evidence derived by measuring the average intensity of scattered light by the particles at multiple angles.
OMP
snadendla
2018-03-14T12:44:11Z
Rayleigh scattering
ECO:0007065
static light scattering assay evidence
A type of light scattering assay evidence derived by measuring the average intensity of scattered light by the particles at multiple angles.
PMID:9013660
A type of static light scattering assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
Rayleigh scattering
ECO:0007066
static light scattering assay evidence used in manual assertion
true
A type of static light scattering assay evidence that is used in a manual assertion.
ECO:RCT
A type of mutant phenotype evidence derived from formation of papillae that protrude outwards from the main colony by mutant cells.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007067
colony papillation assay evidence
A type of mutant phenotype evidence derived from formation of papillae that protrude outwards from the main colony by mutant cells.
PMID:27447898
A type of colony papillation assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007068
colony papillation assay evidence used in manual assertion
true
A type of colony papillation assay evidence that is used in a manual assertion.
ECO:RCT
A type of staining evidence that is derived from the use of gentian violet as a general biological stain and an acid-base indicator.
OMP
snadendla
2018-03-14T12:44:11Z
gentian violet
hexamethyl pararosaniline chloride
methyl violet 10B
ECO:0007069
crystal violet staining evidence
A type of staining evidence that is derived from the use of gentian violet as a general biological stain and an acid-base indicator.
BAO:0002468
A type of crystal violet staining evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
gentian violet
hexamethyl pararosaniline chloride
methyl violet 10B
ECO:0007070
crystal violet staining evidence used in manual assertion
true
A type of crystal violet staining evidence that is used in a manual assertion.
ECO:RCT
A type of biofilm formation assay evidence derived from in vitro cultivation and evaluation of bacterial biofilms under hydrodynamic conditions of flow.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007071
flow cell biofilm assay evidence
A type of biofilm formation assay evidence derived from in vitro cultivation and evaluation of bacterial biofilms under hydrodynamic conditions of flow.
URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438488/
A type of flow cell biofilm assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007072
flow cell biofilm assay evidence used in manual assertion
true
A type of flow cell biofilm assay evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007073
bacterial 2-hybrid assay evidence
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.
URL:http://www.pnas.org/content/97/13/7382.full.pdf
A type of bacterial 2-hybrid assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007074
bacterial 2-hybrid assay evidence used in manual assertion
true
A type of bacterial 2-hybrid assay evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007075
phenomic profiling assay evidence
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.
EDAM:topic:3298
A type of phenomic profiling assay evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007076
phenomic profiling assay evidence used in manual assertion
true
A type of phenomic profiling assay evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007077
colony morphology evidence
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.
OMP:0000100
A type of colony morphology evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007078
colony morphology evidence used in manual assertion
true
A type of colony morphology evidence that is used in a manual assertion.
ECO:RCT
A type of colony morphology evidence that results from studying the colony pigmentation.
OMP
snadendla
2018-03-14T12:44:11Z
colony pigmentation
ECO:0007079
colony color evidence
A type of colony morphology evidence that results from studying the colony pigmentation.
URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671912/
A type of colony color evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
colony pigmentation
ECO:0007080
colony color evidence used in manual assertion
true
A type of colony color evidence that is used in a manual assertion.
ECO:RCT
A type of colony morphology evidence that results from studying the size of the colony.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007081
colony size evidence
A type of colony morphology evidence that results from studying the size of the colony.
URL:http://www.nature.com/nrmicro/journal/v4/n4/full/nrmicro1384.html
A type of colony size evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007082
colony size evidence used in manual assertion
true
A type of colony size evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
ECO:0007083
zone of inhibition evidence
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.
URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC153338/
A type of zone of inhibition evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
ECO:0007084
zone of inhibition evidence used in manual assertion
true
A type of zone of inhibition evidence that is used in a manual assertion.
ECO:RCT
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.
OMP
snadendla
2018-03-14T12:44:11Z
epsilometer test
ECO:0007085
Etest evidence
true
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.
URL:http://www.joponline.org/doi/pdf/10.1902/jop.1992.63.7.576
A type of Etest evidence that is used in a manual assertion.
OMP
rctauber
2018-03-14T12:44:11Z
epsilometer test
ECO:0007086
Etest evidence used in manual assertion
true
A type of Etest evidence that is used in a manual assertion.
ECO:RCT
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.
GOC:VW
rctauber
2018-03-28T10:27:09Z
ribo-seq evidence
ribosome footprinting evidence
eco
ECO:0007087
ribosome profiling evidence
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.
PMID:27015305
A type of ribosome profiling evidence that is used in a manual assertion.
rctauber
2018-03-28T10:33:26Z
ribo-seq evidence
ribosome footprinting evidence
eco
ECO:0007087
ribosome profiling evidence used in manual assertion
true
A type of ribosome profiling evidence that is used in a manual assertion.
ECO:RCT
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.
DNA breakdown, endonucleolytic
DNA degradation, endonucleolytic
endonucleolytic DNA catabolism
endonucleolytic degradation of DNA
biological_process
GO:0000737
DNA catabolic process, endonucleolytic
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.
GOC:elh
GOC:mah
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.
biological_process
necrosis
GO:0001906
cell killing
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.
GOC:add
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.
GO:0008372
NIF_Subcellular:sao-1337158144
NIF_Subcellular:sao1337158144
cell or subcellular entity
cellular component
cellular_component
subcellular entity
GO:0005575
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.
cellular_component
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.
GOC:go_curators
NIF_Subcellular:sao-1337158144
subcellular entity
NIF_Subcellular:nlx_subcell_100315
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.
cell and encapsulating structures
NIF_Subcellular:sao1813327414
Wikipedia:Cell_(biology)
cellular_component
GO:0005623
cell
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.
GOC:go_curators
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
GO:0055134
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
biological_process
nucleobase, nucleoside and nucleotide metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
GO:0006139
nucleobase-containing compound metabolic process
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
GOC:ai
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
GOC:dph
GOC:tb
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.
GO:0055132
DNA metabolism
cellular DNA metabolism
biological_process
GO:0006259
DNA 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.
ISBN:0198506732
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.
DNA breakdown
DNA catabolism
DNA degradation
biological_process
GO:0006308
DNA catabolic process
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.
GOC:go_curators
ISBN:0198506732
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.
GO:0008178
DNA fragmentation
chromatinolysis
Reactome:REACT_102783
Reactome:REACT_105342
Reactome:REACT_110358
Reactome:REACT_113418
Reactome:REACT_1213
Reactome:REACT_28808
Reactome:REACT_33113
Reactome:REACT_92967
Reactome:REACT_94135
Reactome:REACT_98713
Reactome:REACT_99275
Reactome:REACT_99925
DNA catabolic process during apoptosis
DNA catabolism during apoptosis
DNA fragmentation involved in apoptotic nuclear change
endonucleolytic DNA catabolic process involved in apoptosis
biological_process
GO:0006309
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).
apoptotic DNA fragmentation
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.
GOC:dph
GOC:mah
GOC:mtg_apoptosis
GOC:tb
ISBN:0721639976
PMID:15723341
PMID:23379520
chromatinolysis
GOC:mtg_apoptosis
Reactome:REACT_102783
Apoptosis induced DNA fragmentation, Bos taurus
Reactome:REACT_105342
Apoptosis induced DNA fragmentation, Sus scrofa
Reactome:REACT_110358
Apoptosis induced DNA fragmentation, Xenopus tropicalis
Reactome:REACT_113418
Apoptosis induced DNA fragmentation, Plasmodium falciparum
Reactome:REACT_1213
Apoptosis induced DNA fragmentation, Homo sapiens
Reactome:REACT_28808
Apoptosis induced DNA fragmentation, Rattus norvegicus
Reactome:REACT_33113
Apoptosis induced DNA fragmentation, Mus musculus
Reactome:REACT_92967
Apoptosis induced DNA fragmentation, Drosophila melanogaster
Reactome:REACT_94135
Apoptosis induced DNA fragmentation, Taeniopygia guttata
Reactome:REACT_98713
Apoptosis induced DNA fragmentation, Canis familiaris
Reactome:REACT_99275
Apoptosis induced DNA fragmentation, Gallus gallus
Reactome:REACT_99925
Apoptosis induced DNA fragmentation, Danio rerio
DNA fragmentation involved in apoptotic nuclear change
GOC:cjm
GOC:dph
GOC:tb
The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
aromatic compound metabolism
aromatic hydrocarbon metabolic process
aromatic hydrocarbon metabolism
biological_process
GO:0006725
cellular aromatic compound metabolic process
The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
GOC:ai
ISBN:0198506732
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
nitrogen compound metabolism
biological_process
GO:0006807
nitrogen compound metabolic process
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
CHEBI:51143
GOC:go_curators
GOC:jl
ISBN:0198506732
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.
janelomax
2012-12-13T16:25:32Z
GO:0015457
GO:0015460
GO:0044765
small molecule transport
solute:solute exchange
biological_process
single-organism transport
GO:0006810
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.
transport
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.
GOC:dos
GOC:dph
GOC:jl
GOC:mah
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.
Reactome:REACT_102356
Reactome:REACT_102895
Reactome:REACT_106972
Reactome:REACT_109067
Reactome:REACT_110862
Reactome:REACT_19397
Reactome:REACT_29110
Reactome:REACT_31978
Reactome:REACT_33992
Reactome:REACT_34201
Reactome:REACT_79109
Reactome:REACT_82618
Reactome:REACT_87822
Reactome:REACT_91472
Reactome:REACT_91958
Reactome:REACT_92903
Reactome:REACT_93485
Reactome:REACT_94357
Reactome:REACT_96078
Reactome:REACT_96919
Reactome:REACT_98077
biological_process
GO:0006811
ion 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.
GOC:ai
Reactome:REACT_102356
Transport of inorganic cations/anions and amino acids/oligopeptides, Xenopus tropicalis
Reactome:REACT_102895
Transport of inorganic cations/anions and amino acids/oligopeptides, Staphylococcus aureus N315
Reactome:REACT_106972
Transport of inorganic cations/anions and amino acids/oligopeptides, Sus scrofa
Reactome:REACT_109067
Transport of inorganic cations/anions and amino acids/oligopeptides, Saccharomyces cerevisiae
Reactome:REACT_110862
Transport of inorganic cations/anions and amino acids/oligopeptides, Arabidopsis thaliana
Reactome:REACT_19397
Transport of inorganic cations/anions and amino acids/oligopeptides, Homo sapiens
Reactome:REACT_29110
Transport of inorganic cations/anions and amino acids/oligopeptides, Oryza sativa
Reactome:REACT_31978
Transport of inorganic cations/anions and amino acids/oligopeptides, Mus musculus
Reactome:REACT_33992
Transport of inorganic cations/anions and amino acids/oligopeptides, Danio rerio
Reactome:REACT_34201
Transport of inorganic cations/anions and amino acids/oligopeptides, Gallus gallus
Reactome:REACT_79109
Transport of inorganic cations/anions and amino acids/oligopeptides, Caenorhabditis elegans
Reactome:REACT_82618
Transport of inorganic cations/anions and amino acids/oligopeptides, Escherichia coli
Reactome:REACT_87822
Transport of inorganic cations/anions and amino acids/oligopeptides, Bos taurus
Reactome:REACT_91472
Transport of inorganic cations/anions and amino acids/oligopeptides, Dictyostelium discoideum
Reactome:REACT_91958
Transport of inorganic cations/anions and amino acids/oligopeptides, Drosophila melanogaster
Reactome:REACT_92903
Transport of inorganic cations/anions and amino acids/oligopeptides, Mycobacterium tuberculosis
Reactome:REACT_93485
Transport of inorganic cations/anions and amino acids/oligopeptides, Canis familiaris
Reactome:REACT_94357
Transport of inorganic cations/anions and amino acids/oligopeptides, Rattus norvegicus
Reactome:REACT_96078
Transport of inorganic cations/anions and amino acids/oligopeptides, Plasmodium falciparum
Reactome:REACT_96919
Transport of inorganic cations/anions and amino acids/oligopeptides, Taeniopygia guttata
Reactome:REACT_98077
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.
GO:0006822
biological_process
GO:0006820
anion transport
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.
GOC:ai
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.
biological_process
GO:0006869
lipid transport
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.
ISBN:0198506732
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.
GO:0006917
GO:0008632
cell suicide
cellular suicide
Reactome:REACT_100045
Reactome:REACT_100962
Reactome:REACT_101249
Reactome:REACT_104187
Reactome:REACT_105149
Reactome:REACT_106405
Reactome:REACT_106672
Reactome:REACT_107264
Reactome:REACT_108651
Reactome:REACT_109165
Reactome:REACT_110081
Reactome:REACT_111964
Reactome:REACT_13526
Reactome:REACT_13638
Reactome:REACT_13643
Reactome:REACT_28087
Reactome:REACT_28795
Reactome:REACT_28816
Reactome:REACT_30266
Reactome:REACT_30361
Reactome:REACT_30371
Reactome:REACT_30548
Reactome:REACT_30763
Reactome:REACT_31349
Reactome:REACT_34139
Reactome:REACT_578
Reactome:REACT_77132
Reactome:REACT_77313
Reactome:REACT_77415
Reactome:REACT_78287
Reactome:REACT_78802
Reactome:REACT_79809
Reactome:REACT_82724
Reactome:REACT_83328
Reactome:REACT_85877
Reactome:REACT_86749
Reactome:REACT_86873
Reactome:REACT_87570
Reactome:REACT_88740
Reactome:REACT_88784
Reactome:REACT_89196
Reactome:REACT_90267
Reactome:REACT_91011
Reactome:REACT_91243
Reactome:REACT_93937
Reactome:REACT_94099
Reactome:REACT_95069
Reactome:REACT_95675
Reactome:REACT_97627
Reactome:REACT_99784
Reactome:REACT_99799
Wikipedia:Apoptosis
apoptotic cell death
apoptotic programmed cell death
programmed cell death by apoptosis
activation of apoptosis
apoptosis
apoptosis signaling
apoptotic program
type I programmed cell death
biological_process
apoptosis activator activity
caspase-dependent programmed cell death
commitment to apoptosis
induction of apoptosis
induction of apoptosis by p53
signaling (initiator) caspase activity
GO:0006915
apoptotic process
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.
GOC:cjm
GOC:dhl
GOC:ecd
GOC:go_curators
GOC:mtg_apoptosis
GOC:tb
ISBN:0198506732
PMID:18846107
PMID:21494263
Reactome:REACT_100045
Apoptosis, Drosophila melanogaster
Reactome:REACT_100962
Apoptosis, Mus musculus
Reactome:REACT_101249
NRIF signals cell death from the nucleus, Danio rerio
Reactome:REACT_104187
NRAGE signals death through JNK, Taeniopygia guttata
Reactome:REACT_105149
NADE modulates death signalling, Rattus norvegicus
Reactome:REACT_106405
NRAGE signals death through JNK, Xenopus tropicalis
Reactome:REACT_106672
NADE modulates death signalling, Sus scrofa
Reactome:REACT_107264
NRIF signals cell death from the nucleus, Xenopus tropicalis
Reactome:REACT_108651
NRAGE signals death through JNK, Mus musculus
Reactome:REACT_109165
NRAGE signals death through JNK, Arabidopsis thaliana
Reactome:REACT_110081
NRAGE signals death through JNK, Schizosaccharomyces pombe
Reactome:REACT_111964
NRAGE signals death through JNK, Dictyostelium discoideum
Reactome:REACT_13526
NADE modulates death signalling, Homo sapiens
Reactome:REACT_13638
NRAGE signals death through JNK, Homo sapiens
Reactome:REACT_13643
NRIF signals cell death from the nucleus, Homo sapiens
Reactome:REACT_28087
Apoptosis, Saccharomyces cerevisiae
Reactome:REACT_28795
Apoptosis, Oryza sativa
Reactome:REACT_28816
Apoptosis, Danio rerio
Reactome:REACT_30266
Apoptosis, Arabidopsis thaliana
Reactome:REACT_30361
Apoptosis, Canis familiaris
Reactome:REACT_30371
NRAGE signals death through JNK, Saccharomyces cerevisiae
Reactome:REACT_30548
NRAGE signals death through JNK, Caenorhabditis elegans
Reactome:REACT_30763
NRAGE signals death through JNK, Oryza sativa
Reactome:REACT_31349
NRAGE signals death through JNK, Canis familiaris
Reactome:REACT_34139
NRAGE signals death through JNK, Gallus gallus
Reactome:REACT_578
Apoptosis, Homo sapiens
Reactome:REACT_77132
NRAGE signals death through JNK, Drosophila melanogaster
Reactome:REACT_77313
NADE modulates death signalling, Bos taurus
Reactome:REACT_77415
NRIF signals cell death from the nucleus, Canis familiaris
Reactome:REACT_78287
Apoptosis, Gallus gallus
Reactome:REACT_78802
NADE modulates death signalling, Canis familiaris
Reactome:REACT_79809
Apoptosis, Schizosaccharomyces pombe
Reactome:REACT_82724
Apoptosis, Taeniopygia guttata
Reactome:REACT_83328
Apoptosis, Sus scrofa
Reactome:REACT_85877
NRAGE signals death through JNK, Rattus norvegicus
Reactome:REACT_86749
Apoptosis, Rattus norvegicus
Reactome:REACT_86873
NRIF signals cell death from the nucleus, Gallus gallus
Reactome:REACT_87570
NRIF signals cell death from the nucleus, Rattus norvegicus
Reactome:REACT_88740
NRIF signals cell death from the nucleus, Sus scrofa
Reactome:REACT_88784
NRIF signals cell death from the nucleus, Mus musculus
Reactome:REACT_89196
Apoptosis, Dictyostelium discoideum
Reactome:REACT_90267
NRIF signals cell death from the nucleus, Taeniopygia guttata
Reactome:REACT_91011
Apoptosis, Caenorhabditis elegans
Reactome:REACT_91243
NADE modulates death signalling, Mus musculus
Reactome:REACT_93937
Apoptosis, Bos taurus
Reactome:REACT_94099
NRAGE signals death through JNK, Danio rerio
Reactome:REACT_95069
Apoptosis, Xenopus tropicalis
Reactome:REACT_95675
Apoptosis, Plasmodium falciparum
Reactome:REACT_97627
NRIF signals cell death from the nucleus, Bos taurus
Reactome:REACT_99784
NRAGE signals death through JNK, Bos taurus
Reactome:REACT_99799
NRAGE signals death through JNK, Sus scrofa
apoptotic cell death
GOC:sl
apoptotic program
GOC:add
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.
cellular component motion
cellular component movement
biological_process
cell movement
GO:0006928
Note that in GO cellular components include whole cells (cell is_a cellular component).
movement of cell or subcellular component
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.
GOC:dgh
GOC:dph
GOC:jl
GOC:mlg
cellular component motion
GOC:dph
GOC:jl
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).
Wikipedia:Chemotaxis
taxis in response to chemical stimulus
biological_process
GO:0006935
chemotaxis
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).
ISBN:0198506732
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).
biological_process
response to abiotic stress
response to biotic stress
GO:0006950
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.
response to stress
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).
GOC:mah
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.
jl
2013-12-19T15:25:51Z
GO:1902589
organelle organisation
single organism organelle organization
biological_process
organelle organization and biogenesis
single-organism organelle organization
GO:0006996
organelle organization
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.
GOC:mah
organelle organisation
GOC:curators
single organism organelle organization
GOC:TermGenie
organelle organization and biogenesis
GOC:dph
GOC:jl
GOC:mah
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
GO:0048287
nuclear organisation
nuclear organization
biological_process
nuclear morphology
nuclear organization and biogenesis
nucleus organization and biogenesis
GO:0006997
nucleus organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
GOC:dph
GOC:ems
GOC:jl
GOC:mah
nuclear organisation
GOC:curators
nuclear organization
GOC:curators
nuclear organization and biogenesis
GOC:mah
nucleus organization and biogenesis
GOC:mah
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus.
nucleolus organisation
biological_process
nucleolus organization and biogenesis
GO:0007000
nucleolus organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus.
GOC:dph
GOC:jid
GOC:jl
GOC:mah
nucleolus organisation
GOC:curators
nucleolus organization and biogenesis
GOC:mah
The cell aging process that results in the nucleolus breaking down into fragments.
GO:0046616
biological_process
nucleolar size increase
GO:0007576
nucleolar fragmentation
The cell aging process that results in the nucleolus breaking down into fragments.
GOC:mah
PMID:9271578
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.
janelomax
2012-09-19T15:05:24Z
GO:0000004
GO:0007582
GO:0044699
Wikipedia:Biological_process
biological process
physiological process
biological_process
single organism process
single-organism process
GO:0008150
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.
biological_process
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
GOC:go_curators
GOC:isa_complete
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.
janelomax
2012-10-17T15:46:40Z
GO:0044710
Wikipedia:Metabolism
metabolism
metabolic process resulting in cell growth
metabolism resulting in cell growth
biological_process
single-organism metabolic process
GO:0008152
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
metabolic process
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
GOC:go_curators
ISBN:0198547684
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).
biological_process
accidental cell death
necrosis
GO:0008219
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.
cell death
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).
GOC:mah
GOC:mtg_apoptosis
PMID:25236395
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
biological_process
GO:0008283
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.
cell proliferation
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
GOC:mah
GOC:mb
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.
janelomax
2012-10-17T15:52:35Z
GO:0044712
Wikipedia:Catabolism
breakdown
catabolism
degradation
biological_process
single-organism catabolic process
GO:0009056
catabolic process
The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
ISBN:0198547684
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.
GO:0043285
biopolymer catabolic process
macromolecule breakdown
macromolecule catabolism
macromolecule degradation
biological_process
GO:0009057
macromolecule catabolic process
The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
CHEBI:33694
GOC:mah
biopolymer catabolic process
GOC:mtg_chebi_dec09
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.
janelomax
2012-10-17T15:52:18Z
GO:0044711
Wikipedia:Anabolism
anabolism
biosynthesis
synthesis
biological_process
formation
single-organism biosynthetic process
GO:0009058
biosynthetic process
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
GOC:curators
ISBN:0198547684
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.
GO:0043284
biopolymer biosynthetic process
macromolecule anabolism
macromolecule biosynthesis
macromolecule formation
macromolecule synthesis
biological_process
GO:0009059
macromolecule biosynthetic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
CHEBI:33694
GOC:mah
biopolymer biosynthetic process
GOC:mtg_chebi_dec09
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.
response to biotic stress
biological_process
GO:0009607
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.
response to biotic stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.
GOC:hb
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.
GO:0002245
physiological response to wounding
biological_process
GO:0009611
response to wounding
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.
GOC:go_curators
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.
detoxification response
biological_process
toxin resistance
toxin susceptibility/resistance
GO:0009636
response to toxic substance
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
GOC:lr
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.
janelomax
2012-12-11T16:56:55Z
GO:0008151
GO:0044763
GO:0050875
cell physiology
cellular physiological process
cell growth and/or maintenance
biological_process
single-organism cellular process
GO:0009987
cellular process
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
GOC:go_curators
GOC:isa_complete
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.
Reactome:REACT_100537
Reactome:REACT_101147
Reactome:REACT_101952
Reactome:REACT_105649
Reactome:REACT_108313
Reactome:REACT_29068
Reactome:REACT_34240
Reactome:REACT_71
Reactome:REACT_78136
Reactome:REACT_78959
Reactome:REACT_79662
Reactome:REACT_85241
Reactome:REACT_85359
Reactome:REACT_86357
Reactome:REACT_89816
Reactome:REACT_91657
Reactome:REACT_91965
Reactome:REACT_93586
Reactome:REACT_93968
Reactome:REACT_94814
Reactome:REACT_98256
Wikipedia:Gene_expression
biological_process
GO:0010467
gene expression
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.
GOC:dph
GOC:tb
Reactome:REACT_100537
Gene Expression, Xenopus tropicalis
Reactome:REACT_101147
Gene Expression, Danio rerio
Reactome:REACT_101952
Gene Expression, Sus scrofa
Reactome:REACT_105649
Gene Expression, Drosophila melanogaster
Reactome:REACT_108313
Gene Expression, Caenorhabditis elegans
Reactome:REACT_29068
Gene Expression, Escherichia coli
Reactome:REACT_34240
Gene Expression, Staphylococcus aureus N315
Reactome:REACT_71
Gene Expression, Homo sapiens
Reactome:REACT_78136
Gene Expression, Mus musculus
Reactome:REACT_78959
Gene Expression, Taeniopygia guttata
Reactome:REACT_79662
Gene Expression, Plasmodium falciparum
Reactome:REACT_85241
Gene Expression, Oryza sativa
Reactome:REACT_85359
Gene Expression, Gallus gallus
Reactome:REACT_86357
Gene Expression, Canis familiaris
Reactome:REACT_89816
Gene Expression, Mycobacterium tuberculosis
Reactome:REACT_91657
Gene Expression, Arabidopsis thaliana
Reactome:REACT_91965
Gene Expression, Rattus norvegicus
Reactome:REACT_93586
Gene Expression, Dictyostelium discoideum
Reactome:REACT_93968
Gene Expression, Bos taurus
Reactome:REACT_94814
Gene Expression, Schizosaccharomyces pombe
Reactome:REACT_98256
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.
GO:0016244
regulated cell death
Wikipedia:Programmed_cell_death
caspase-independent cell death
non-apoptotic programmed cell death
nonapoptotic programmed cell death
biological_process
PCD
RCD
caspase-independent apoptosis
GO:0012501
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'.
programmed cell death
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.
GOC:lr
GOC:mtg_apoptosis
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.
biological_process
GO:0015711
organic anion transport
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.
GOC:ai
GOC:krc
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.
biological_process
GO:0015718
monocarboxylic acid transport
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.
GOC:krc
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.
biological_process
GO:0015849
organic acid transport
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.
ISBN:0198506732
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.
biological_process
GO:0015908
fatty acid transport
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.
GOC:ai
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.
Reactome:REACT_23892
biological_process
GO:0015909
long-chain fatty acid transport
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.
CHEBI:15904
GOC:ai
Reactome:REACT_23892
Transport of fatty acids, Homo sapiens
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
GO:0044235
GO:0071842
cell organisation
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
biological_process
cell organization and biogenesis
GO:0016043
cellular component organization
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
GOC:ai
GOC:jl
GOC:mah
cellular component organisation at cellular level
GOC:mah
cellular component organisation in other organism
GOC:mah
cell organization and biogenesis
GOC:mah
The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
GO:0048591
cellular growth
growth of cell
biological_process
cell expansion
metabolic process resulting in cell growth
metabolism resulting in cell growth
non-developmental cell growth
non-developmental growth of a unicellular organism
GO:0016049
cell growth
The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
GOC:ai
non-developmental cell growth
GOC:mah
non-developmental growth of a unicellular organism
GOC:mah
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.
Wikipedia:Cell_migration
biological_process
GO:0016477
cell migration
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.
GOC:cjm
GOC:dph
GOC:ems
GOC:pf
http://en.wikipedia.org/wiki/Cell_migration
The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
heterocycle anabolism
heterocycle biosynthesis
heterocycle formation
heterocycle synthesis
biological_process
GO:0018130
heterocycle biosynthetic process
The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
ISBN:0198547684
The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
aromatic compound anabolism
aromatic compound biosynthesis
aromatic compound formation
aromatic compound synthesis
aromatic hydrocarbon biosynthesis
aromatic hydrocarbon biosynthetic process
biological_process
GO:0019438
aromatic compound biosynthetic process
The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
GOC:ai
The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
aromatic compound breakdown
aromatic compound catabolism
aromatic compound degradation
aromatic hydrocarbon catabolic process
aromatic hydrocarbon catabolism
biological_process
GO:0019439
aromatic compound catabolic process
The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
GOC:ai
The controlled release of icosanoids, any of a group of C20 polyunsaturated fatty acids from a cell or a tissue.
eicosanoid secretion
biological_process
GO:0032309
icosanoid secretion
The controlled release of icosanoids, any of a group of C20 polyunsaturated fatty acids from a cell or a tissue.
GOC:mah
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
Reactome:REACT_102000
Reactome:REACT_103710
Reactome:REACT_107293
Reactome:REACT_108179
Reactome:REACT_109042
Reactome:REACT_13
Reactome:REACT_28699
Reactome:REACT_29108
Reactome:REACT_32429
Reactome:REACT_33347
Reactome:REACT_34326
Reactome:REACT_55564
Reactome:REACT_77741
Reactome:REACT_82379
Reactome:REACT_86268
Reactome:REACT_90299
Reactome:REACT_91959
Reactome:REACT_93580
Reactome:REACT_95666
Reactome:REACT_98086
Reactome:REACT_99241
cellular nitrogen compound metabolism
biological_process
GO:0034641
cellular nitrogen compound metabolic process
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
GOC:mah
Reactome:REACT_102000
Metabolism of amino acids and derivatives, Mycobacterium tuberculosis
Reactome:REACT_103710
Metabolism of amino acids and derivatives, Escherichia coli
Reactome:REACT_107293
Metabolism of amino acids and derivatives, Arabidopsis thaliana
Reactome:REACT_108179
Metabolism of amino acids and derivatives, Xenopus tropicalis
Reactome:REACT_109042
Metabolism of amino acids and derivatives, Sus scrofa
Reactome:REACT_13
Metabolism of amino acids and derivatives, Homo sapiens
Reactome:REACT_28699
Metabolism of amino acids and derivatives, Saccharomyces cerevisiae
Reactome:REACT_29108
Metabolism of amino acids and derivatives, Caenorhabditis elegans
Reactome:REACT_32429
Metabolism of amino acids and derivatives, Rattus norvegicus
Reactome:REACT_33347
Metabolism of amino acids and derivatives, Mus musculus
Reactome:REACT_34326
Metabolism of amino acids and derivatives, Staphylococcus aureus N315
Reactome:REACT_55564
Metabolism of amino acids and derivatives, Gallus gallus
Reactome:REACT_77741
Metabolism of amino acids and derivatives, Taeniopygia guttata
Reactome:REACT_82379
Metabolism of amino acids and derivatives, Bos taurus
Reactome:REACT_86268
Metabolism of amino acids and derivatives, Drosophila melanogaster
Reactome:REACT_90299
Metabolism of amino acids and derivatives, Oryza sativa
Reactome:REACT_91959
Metabolism of amino acids and derivatives, Plasmodium falciparum
Reactome:REACT_93580
Metabolism of amino acids and derivatives, Danio rerio
Reactome:REACT_95666
Metabolism of amino acids and derivatives, Canis familiaris
Reactome:REACT_98086
Metabolism of amino acids and derivatives, Dictyostelium discoideum
Reactome:REACT_99241
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.
GO:0034961
cellular biopolymer biosynthetic process
cellular macromolecule anabolism
cellular macromolecule biosynthesis
cellular macromolecule formation
cellular macromolecule synthesis
biological_process
GO:0034645
cellular macromolecule biosynthetic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells.
CHEBI:33694
GOC:mah
cellular biopolymer biosynthetic process
GOC:mtg_chebi_dec09
cellular macromolecule anabolism
GOC:mah
cellular macromolecule biosynthesis
GOC:mah
cellular macromolecule formation
GOC:mah
cellular macromolecule synthesis
GOC:mah
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
biological_process
GO:0034654
nucleobase-containing compound biosynthetic process
The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids.
GOC:mah
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
biological_process
nucleobase, nucleoside, nucleotide and nucleic acid catabolic process
GO:0034655
nucleobase-containing compound catabolic process
The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids.
GOC:mah
nucleobase, nucleoside, nucleotide and nucleic acid catabolic process
GOC:dph
GOC:tb
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO:0048590
biological_process
growth pattern
non-developmental growth
GO:0040007
See also the biological process term 'cell growth ; GO:0016049'.
growth
The increase in size or mass of an entire organism, a part of an organism or a cell.
GOC:bf
GOC:ma
non-developmental growth
GOC:mah
Self-propelled movement of a cell or organism from one location to another.
biological_process
GO:0040011
locomotion
Self-propelled movement of a cell or organism from one location to another.
GOC:dgh
The series of events that restore integrity to a damaged tissue, following an injury.
Wikipedia:Wound_healing
biological_process
GO:0042060
wound healing
The series of events that restore integrity to a damaged tissue, following an injury.
GOC:bf
PMID:15269788
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
response to chemical stimulus
response to chemical substance
biological_process
GO:0042221
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.
response to chemical
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
GOC:jl
response to chemical stimulus
GOC:dos
The directed movement of a motile cell or organism in response to an external stimulus.
Wikipedia:Taxis
directed movement in response to stimulus
biological_process
GO:0042330
taxis
The directed movement of a motile cell or organism in response to an external stimulus.
GOC:jl
ISBN:0192801023
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.
biological_process
GO:0042710
biofilm formation
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.
GOC:di
PMID:11932229
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.
GO:0043283
biopolymer metabolic process
macromolecule metabolism
biological_process
GO:0043170
macromolecule metabolic process
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
CHEBI:33694
GOC:mah
biopolymer metabolic process
GOC:mtg_chebi_dec09
The chemical reactions and pathways by which individual cells transform chemical substances.
cellular metabolism
biological_process
intermediary metabolism
GO:0044237
cellular metabolic process
The chemical reactions and pathways by which individual cells transform chemical substances.
GOC:go_curators
intermediary metabolism
GOC:mah
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
primary metabolism
biological_process
GO:0044238
primary metabolic process
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
GOC:go_curators
http://www.metacyc.org
The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
cellular breakdown
cellular catabolism
cellular degradation
biological_process
GO:0044248
cellular catabolic process
The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
GOC:jl
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
cellular anabolism
cellular biosynthesis
cellular formation
cellular synthesis
biological_process
GO:0044249
cellular biosynthetic process
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
GOC:jl
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.
GO:0034960
cellular biopolymer metabolic process
cellular macromolecule metabolism
biological_process
GO:0044260
cellular macromolecule metabolic process
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
CHEBI:33694
GOC:mah
cellular biopolymer metabolic process
GOC:mtg_chebi_dec09
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.
GO:0034962
cellular biopolymer catabolic process
cellular macromolecule breakdown
cellular macromolecule catabolism
cellular macromolecule degradation
biological_process
GO:0044265
cellular macromolecule catabolic process
The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells.
CHEBI:33694
GOC:jl
cellular biopolymer catabolic process
GOC:mtg_chebi_dec09
The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds.
nitrogen compound breakdown
nitrogen compound catabolism
nitrogen compound degradation
biological_process
GO:0044270
cellular nitrogen compound catabolic process
The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds.
GOC:jl
ISBN:0198506732
The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.
nitrogen compound anabolism
nitrogen compound biosynthesis
nitrogen compound formation
nitrogen compound synthesis
biological_process
GO:0044271
cellular nitrogen compound biosynthetic process
The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.
GOC:jl
ISBN:0198506732
Any process that is carried out at the cellular level which involves another organism of the same or different species.
janelomax
2012-12-11T17:00:50Z
biological_process
GO:0044764
multi-organism cellular process
Any process that is carried out at the cellular level which involves another organism of the same or different species.
GOC:jl
The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
heterocycle metabolism
biological_process
GO:0046483
heterocycle metabolic process
The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
CHEBI:5686
ISBN:0198506732
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.
biological_process
antibiotic susceptibility/resistance
GO:0046677
response to antibiotic
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.
GOC:ai
GOC:ef
The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
heterocycle breakdown
heterocycle catabolism
heterocycle degradation
biological_process
GO:0046700
heterocycle catabolic process
The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
GOC:ai
The controlled release of acid by a cell or a tissue.
biological_process
GO:0046717
acid secretion
The controlled release of acid by a cell or a tissue.
GOC:ai
The controlled release of a substance by a cell or a tissue.
biological_process
GO:0046903
secretion
The controlled release of a substance by a cell or a tissue.
GOC:ai
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-).
biological_process
GO:0046942
carboxylic acid transport
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-).
GOC:ai
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
cell locomotion
movement of a cell
biological_process
cell movement
GO:0048870
cell motility
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
GOC:dgh
GOC:dph
GOC:isa_complete
GOC:mlg
The controlled release of arachidonic acid from a cell or a tissue.
biological_process
GO:0050482
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'.
arachidonic acid secretion
The controlled release of arachidonic acid from a cell or a tissue.
GOC:ai
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.
GO:0051869
physiological response to stimulus
biological_process
GO:0050896
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.
response to stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
GOC:ai
GOC:bf
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.
jl
2013-12-18T13:51:04Z
GO:1902578
establishment and maintenance of localization
establishment and maintenance of position
localisation
establishment and maintenance of cellular component location
establishment and maintenance of substance location
establishment and maintenance of substrate location
biological_process
single organism localization
single-organism localization
GO:0051179
localization
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.
GOC:ai
GOC:dos
localisation
GOC:mah
single organism localization
GOC:TermGenie
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
establishment of localisation
biological_process
GO:0051234
establishment of localization
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
GOC:ai
GOC:dos
establishment of localisation
GOC:mah
A biological process which involves another organism of the same or different species.
GO:0051706
interaction between organisms
physiological interaction between organisms
physiological interaction with other organism
biological_process
GO:0051704
multi-organism process
A biological process which involves another organism of the same or different species.
GOC:jl
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).
biological_process
GO:0060326
cell chemotaxis
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).
GOC:dph
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.
midori
2010-03-08T02:15:14Z
biological_process
GO:0071702
organic substance transport
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.
CHEBI:50860
GOC:mah
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
midori
2010-03-08T03:32:18Z
organic molecular entity metabolic process
organic molecular entity metabolism
organic substance metabolism
biological_process
GO:0071704
organic substance metabolic process
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
CHEBI:50860
GOC:mah
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.
midori
2010-03-10T02:47:22Z
eicosanoid transport
biological_process
GO:0071715
icosanoid transport
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.
CHEBI:23899
GOC:mah
eicosanoid transport
GOC:sl
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
midori
2010-09-10T01:39:16Z
GO:0071841
cellular component organisation or biogenesis
cellular component organisation or biogenesis at cellular level
cellular component organization or biogenesis at cellular level
biological_process
GO:0071840
cellular component organization or biogenesis
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
GOC:mah
cellular component organisation or biogenesis
GOC:mah
cellular component organisation or biogenesis at cellular level
GOC:mah
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.
midori
2010-09-15T02:14:33Z
DNA anabolism
DNA biosynthesis
DNA formation
DNA synthesis
biological_process
GO:0071897
DNA biosynthetic process
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.
GOC:mah
DNA anabolism
GOC:mah
DNA biosynthesis
GOC:mah
DNA formation
GOC:mah
DNA synthesis
GOC:mah
Any cellular metabolic process involving nucleic acids.
tanyaberardini
2010-04-07T10:18:47Z
biological_process
GO:0090304
nucleic acid metabolic process
Any cellular metabolic process involving nucleic acids.
GOC:dph
GOC:tb
The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
tanyaberardini
2010-04-07T10:26:30Z
nucleic acid cleavage
biological_process
GO:0090305
nucleic acid phosphodiester bond hydrolysis
The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
GOC:dph
GOC:tb
nucleic acid cleavage
GOC:dph
GOC:tb
Synthesis of DNA that is a part of the process of duplicating one or more molecules of DNA.
tanyaberardini
2014-06-06T13:54:36Z
biological_process
GO:0090592
DNA synthesis involved in DNA replication
Synthesis of DNA that is a part of the process of duplicating one or more molecules of DNA.
GOC:vw
The chemical reactions and pathways involving organic cyclic compound.
bf
2012-09-14T09:03:51Z
organic cyclic compound metabolism
biological_process
GO:1901360
organic cyclic compound metabolic process
The chemical reactions and pathways involving organic cyclic compound.
GOC:TermGenie
organic cyclic compound metabolism
GOC:TermGenie
The chemical reactions and pathways resulting in the breakdown of organic cyclic compound.
bf
2012-09-14T09:05:04Z
organic cyclic compound breakdown
organic cyclic compound catabolism
organic cyclic compound degradation
biological_process
GO:1901361
organic cyclic compound catabolic process
The chemical reactions and pathways resulting in the breakdown of organic cyclic compound.
GOC:TermGenie
organic cyclic compound breakdown
GOC:TermGenie
organic cyclic compound catabolism
GOC:TermGenie
organic cyclic compound degradation
GOC:TermGenie
The chemical reactions and pathways resulting in the formation of organic cyclic compound.
bf
2012-09-14T09:05:22Z
organic cyclic compound anabolism
organic cyclic compound biosynthesis
organic cyclic compound formation
organic cyclic compound synthesis
biological_process
GO:1901362
organic cyclic compound biosynthetic process
The chemical reactions and pathways resulting in the formation of organic cyclic compound.
GOC:TermGenie
organic cyclic compound anabolism
GOC:TermGenie
organic cyclic compound biosynthesis
GOC:TermGenie
organic cyclic compound formation
GOC:TermGenie
organic cyclic compound synthesis
GOC:TermGenie
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.
pr
2012-11-04T17:13:49Z
biological_process
GO:1901571
fatty acid derivative transport
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.
GOC:TermGenie
GOC:pr
The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon.
pr
2012-11-05T11:04:36Z
organic molecular entity breakdown
organic molecular entity catabolic process
organic molecular entity catabolism
organic molecular entity degradation
organic substance breakdown
organic substance catabolism
organic substance degradation
biological_process
GO:1901575
organic substance catabolic process
The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon.
GOC:TermGenie
GOC:pr
organic molecular entity breakdown
GOC:TermGenie
organic molecular entity catabolism
GOC:TermGenie
organic molecular entity degradation
GOC:TermGenie
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
pr
2012-11-05T11:04:40Z
organic molecular entity anabolism
organic molecular entity biosynthesis
organic molecular entity biosynthetic process
organic molecular entity formation
organic molecular entity synthesis
organic substance anabolism
organic substance biosynthesis
organic substance formation
organic substance synthesis
biological_process
GO:1901576
organic substance biosynthetic process
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
GOC:TermGenie
GOC:pr
organic molecular entity anabolism
GOC:TermGenie
organic molecular entity biosynthesis
GOC:TermGenie
organic molecular entity formation
GOC:TermGenie
organic molecular entity synthesis
GOC:TermGenie
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.
bhm
2015-02-25T16:06:14Z
arachidonic acid transport
biological_process
GO:1903963
arachidonate transport
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.
GOC:TermGenie
GOC:bhm
GO_REF:0000065
PMID:15642721
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: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
OBI_0000217
objective specification
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
OBI_0000142
information content entity
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
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
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
Alan Ruttenberg
OBI Plan and Planned Process branch
OBI_0000344
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
plan specification
planned process
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.
Bjoern Peters
branch derived
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)
planned process
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
PERSON: Alan Ruttenberg
processed material
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
study assay
any method
assay
material processing
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca Serra
material transformation
OBI branch derived
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
OBI branch derived
intervention design
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.
PlanAndPlannedProcess Branch
OBI branch derived
cell co-culturing
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
cDNA library
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
http://en.wikipedia.org/wiki/Microtiter_plate
microtiter plate
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.
PlanAndPlannedProcess Branch
OBI branch derived
artificially induced nucleic acid hybridization
adding a material entity into a target
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.
BP
branch derived
adding a material entity into a target
metabolite profiling
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
Philippe Rocca-Serra
metabolite assay
OBI
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
PERSON: Philippe Rocca-Serra
extracted material
GROUP: OBI Biomatrial Branch
extract
transcription profiling assay
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
Philippe Rocca-Serra
gene expression profiling
OBI
transcription profiling
transcription profiling assay
analyte 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.
2013-09-23: simplify equivalent axiom
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
material combination
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.
bp
bp
material combination
tritiated thymidine incorporation assay
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.
IEDB
IEDB
tritiated thymidine incorporation assay
survival assessment
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.
survival assessment
recombinant vector
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.
recombinant vector
presentation of stimulus
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
stimulation of organism
Helen Parkinson, Jessica Turner, Dirk Derom
presentation of stimulus
northern blot analysis
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
Person: Philippe Rocca-Serra
northern blot
northern blot analysis
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.
Person: Philippe Rocca-Serra
RNAO
single-nucleotide-resolution nucleic acid structure mapping assay
RNA extract
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
Group: UPenn Group
RNA extract
cell-cell killing assay
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.
IEDB
IEDB
cell-cell killing assay
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
Person: Philippe Rocca-Serra
Wikipedia
secondary structure of sequence macromolecule
cell proliferation assay
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.
IEDB
IEDB
cell proliferation assay
Southern blot analysis
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.
Person: Philippe Rocca-Serra
Southern blot
OBI & Wikipedia
Southern blot analysis
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.
person: Bjoern Peters
person: Melanie Courtot
Q-PCR
kinetic polymerase chain reaction
qPCR
quantitative real time polymerase chain reaction
WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
real time PCR
real time polymerase chain reaction assay
protein extract
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,
Person: Philippe Rocca-Serra
OBI & wikipedia
protein extract
total RNA extract
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.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
UPenn Group
total RNA extract
secondary structure of RNA molecule
PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA.
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
Person: Philippe Rocca-Serra
secondary structure of RNA molecule
DEPC structure mapping assay
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
Person: Philippe Rocca-Serra
RNA ontology
DEPC structure mapping assay
in vitro cell killing assay
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 cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture.
IEDB
IEDB
in vitro cell killing assay
processed specimen
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.
Bjoern Peters
Bjoern Peters
A tissue sample that has been sliced and stained for a histology study.
processed specimen
in live cell assay
An assay in which a measurement is made by observing entities located in a live cell.
in live cell assay
in live organism assay
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.
PERSON:Bjoern Peters
in vivo assay
in live organism assay
container
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?)
PERSON: Bjoern Peters
container
device
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.
PERSON: Helen Parkinson
instrument
OBI development call 2012-12-17.
device
in container assay
an assay in which a measurement is made by observing entities located in a container.
in container assay
nucleic acid extract
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
PERSON: Jie Zheng
UPenn Group
nucleic acid extract
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.
Person: Philippe Rocca-Serra
RNAO and OBI
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
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.
cell culture expansion
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.
PERSON: Chris Stoeckert, Jie Zheng
MO_564 induced_mutation
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.
Person: Chris Stoeckert, Jie Zheng
MO_454 in_vivo_design
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
Person: Chris Stoeckert, Jie Zheng
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
RNA-seq assay
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.
Person: Chris Stoeckert, Jie Zheng
MO_347 in_vitro_design
in vitro design
transcription profiling by array design
A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
Person: Chris Stoeckert, Jie Zheng
MO_533 transcript_identification_design
transcription profiling by array design
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).
Person: Chris Stoeckert, Jie Zheng
Group: ArrayExpress production team
transcription profiling by RT-PCR design
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
transcription profiling by RT-PCR assay
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.
Person: Chris Stoeckert, Jie Zheng
MO_810 cellular_process_design
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.
Person: Chris Stoeckert, Jie Zheng
MO_568 stimulus_or_stress_design
stimulus or stress design
transcription profiling design
A study design that identifies forms and abundance of transcripts in the genome.
Person: Chris Stoeckert, Jie Zheng
MO_533 transcript_identification_design
transcription profiling design
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/
Person: James Malone
RNA profiling by array assay
EFO_0002768: transcription profiling by array
transcription profiling by array assay
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
nano-cap analysis of gene expression
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
PERSON:Philippe Rocca-Serra; Marcus Chibucos
CAGE
PMID:14663149
cap analysis of gene expression
cytometry assay
An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells.
An assay that measures properties of cells.
IEDB
IEDB
cytometry assay
ATP bioluminescence assay
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.
Rebecca Tauber
ATP quantitation assay
cell viability ATP quantitation assay
ECO
ATP bioluminescence assay
suppression subtractive hybridization
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.
Rebecca Tauber
SSH
subtractive hybridization
PMID:14970460
suppression subtractive hybridization
differential screening hybridization
An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes.
Rebecca Tauber
DSH
differential screening
PMID:25472628
differential screening hybridization
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.
GROUP: OBI Biomaterial Branch
WEB: http://en.wikipedia.org/wiki/Organism
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.
PERSON: James Malone
PERSON: Philippe Rocca-Serra
GROUP: OBI Biomaterial Branch
specimen
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
differential expression analysis objective
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
James Malone
PERSON: James Malone
data transformation objective
staining
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.
Philippe Rocca-Serra
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
staining
flow cell
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
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
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.
PERSON: Chris Stoeckert
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
study design
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
adding substance to cell culture
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
OBI branch derived
genetic transformation
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
PlanAndPlannedProcess Branch
OBI branch derived
sequencing assay
experimental infection of cell culture
is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture
IEDB
IEDB
experimental infection of cell culture
chromium release assay
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.
PlanAndPlannedProcess Branch, IEDB
IEDB
chromium release assay
quality of a single physical entity
A physical object quality which inheres in a single-bearer.
quality of a single physical entity