The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain that arise from laboratory experiments, computational methods, literature curation, or other means.
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.
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.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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
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
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.
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
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
preceded by
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
precedes
A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence.
In the future we may use a more generic relation with weaker domain and range constraints taken from IAO, RO or OBI.
has measurement unit label
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
relates a process to a time-measurement-datum that represents the duration of the process
Person:Alan Ruttenberg
is duration of
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
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
Alan Ruttenberg
is_specified_input_of
has_specified_output
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.
is_manufactured_by
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
Liju Fan
has_make
has_manufacturer
is_specified_output_of
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
A relation between an information content entity and a value specification that specifies its value.
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer 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
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
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
location of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporal relation
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
has measurement value
A relation between a value specification and a number that quantifies it.
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
has specified value
A relation between a value specification and a literal.
This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the 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
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
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
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
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
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways.
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
A macromolecule is a 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.
polymer
A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase.
A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival.
Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis.
Any type of microscopy where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores.
Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image.
cell
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.
A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
A leukocyte with a single non-segmented nucleus in the mature form.
A type of information that is used to support an assertion.
A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator.
inference from background scientific knowledge
A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature.
A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology.
A type of protein assay evidence where the catalytic activity of an enzyme is determined.
A type of evidence resulting from manipulation of variables in order to discover cause and effect.
A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell.
A type of experimental evidence that is based on characterization of gene expression.
Use this evidence type when the annotation is inferred from the timing or location of expression of a gene. It may be difficult to determine whether the expression pattern truly indicates that a gene plays a role in a given process.
A type of expression pattern evidence where abundance of a transcript is analyzed.
A type of expression pattern evidence resulting from protein abundance quantification techniques.
A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products.
A type of genetic interaction evidence where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background.
A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
A type of experimental phenotypic evidence derived from the difference in two alleles of a corresponding gene that result from one or more changes in the genome.
A type of mutant phenotype evidence where a phenotype is associated with altered gene product which lacks the molecular function of the wild-type gene.
loss-of-function mutant phenotype evidence
A type of experimental phenotypic evidence where a transgenic strain carrying the construct of a promoter cDNA fusion in which a gene of interest is driven by a defined promoter or enhancer is ectopically expressed in the defined pattern to characterize potential cellular properties and functions of a protein of interest.
IMP: analysis of overexpression/ectopic expression phenotype
A type of mutant phenotype evidence where a phenotype is observed while expressing an anti-sense version of a gene product in a wild-type (for that gene product) background.
A type of mutant phenotype evidence where an RNA construct is introduced into a cell and the expression of the gene bearing its complementary sequence is suppressed.
A type of protein assay evidence based on the inhibition of the molecular function of a protein.
A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
Molecules interacted with might include protein, nucleic acid, ion, or complex.
A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
A type of physical interaction evidence that depends on the strength of the interaction between two entities.
A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex.
A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein.
Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode.
A type of experimental genomic evidence resulting from a process in which single stranded nucleic acids are allowed to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences.
This term has been made obsolete with the clean up of experimental genomic evidence branch.
A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
For GO annotation, in the case of a single gene, an accession for the related gene's sequence is entered in the evidence_with field.
A type of match to sequence model evidence that is based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence.
A type of match to sequence model evidence resulting from a positive match of a protein, or set of proteins to a predictive model (signature) in the InterPro database.
match to InterPro member signature evidence
A type of BLAST evidence that is used in a manual assertion.
A type of protein BLAST evidence that is used in a manual assertion.
protein BLAST evidence used in manual assertion
BLAST search criteria for ISS assignment in PAMGO_GAT
A type of nucleotide BLAST evidence that is used in a manual assertion.
nucleotide BLAST evidence used in manual assertion
A type of author statement in which the author makes a statement that is not supported by information in that particular publication, but rather can be traced to a reference cited by that publication.
author statement supported by traceable reference
A type of author statement that is not associated with results presented or a cited reference.
author statement without traceable support
A curator inference that results from research where no information about a biological feature was found in the scientific literature, at biological databases, or within other resources.
An assertion of "no biological data found" carries the assumption that a more-or-less exhaustive search has been conducted.
The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations.
A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins.
A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
A type of evidence resulting from comparing likeness of distinct biological entities.
A type of mutant phenotype evidence resulting from a phenotype that is associated with the altered gene product which possesses a new molecular function or a new pattern of gene expression.
gain-of-function mutant phenotype evidence
A type of similarity based on biomolecular sequence.
A sequence similarity analysis may involve a gene or a gene product, and it could be based on similarity to a single other gene or to a group of other genes.
spatial pattern of protein expression evidence
A type of protein expression evidence resulting from the quantification of protein production in a sample.
spatial pattern of transcript expression evidence
A type of experimental phenotypic evidence that is based on the expression pattern of a reporter gene.
A type of phenotypic evidence based on an author's phenotypic description of a species or higher level group explicitly referencing an observation of a voucher specimen, a specimen with a permanent museum catalog.
A type of similarity based on genotype without respect to expression.
A genetic similarity analysis might consider genetic markers, polymorphisms, alleles, or other characteristics sometimes considered as part of the field of traditional genetics. Although an attempt has been made to treat as distinct the concepts of "genetic", "genotypic", "genomic", and "sequence", there is considerable overlap in usage throughout the field of biology.
A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)
suppressor/enhancer interaction evidence
A type of combinatorial analysis where data are combined and evaluated by an algorithm.
Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
A type of genetic interaction evidence that is based on the phenotypic outcome of two mutations in unrelated genetic loci.
This general 'array experiment' term should not be used - replace with the specific type of array (e.g. ECO:0000097, ECO:0000062, ECO:0000104, etc.)
A type of genetic interaction evidence that is based on the suppression of one allelic effect by an allele at another genetic locus.
Epistasis' can be used in different contexts in different areas of genetics. It is sometimes used to mean 'genetic interaction', whereas other times it may be specific to mutations that block the effects of other mutations.
A type of similarity based on the expression of a genotype in an environment.
Phenotype is defined as the outcome of the expression of a genotype in a given environment. A comparison might involve whole organisms or sub-parts of organisms.
A type of transcript expression evidence resulting from simultaneous profiling of the expression levels of thousands of genes in a single experiment allowing analysis of genes and their networks.
differential gene expression evidence from microarray experiment
A type of experimental evidence that is based on the expression of a genotype in an environment.
A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements.
A type of phenotypic evidence that is based on a gene product that is associated with a quantitative trait locus, but has not been cloned.
A type of expression microarray evidence where expression level is quantified by sample biotin-labeled cRNA (transcribed from an unknown RNA sample) hybridized to DNA oligonuclotides immoblized on a solid surface.
cRNA to DNA expression microarray evidence
A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures.
A type of functional complementation evidence that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene.
IGI: functional complementation in heterologous system
functional complementation in heterologous system evidence
A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
The assay involves screening a library of candidate proteins for the ability bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to a yeast reporter gene (TAIR:TED).
A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures.
A type of hybrid interaction evidence that is based on detection of protein-protein interaction by activation of a yeast reporter gene after a bait protein fused to a DNA-binding domain (which has been transfected into a yeast cell) is used to screen a cDNA library of clones fused to an activation domain.
A type of in vitro methylation assay evidence where methylation-sensitive restriction enzymes are utilized to compare differential methylation between two samples by first shearing DNA, followed by end-blunting, ligation of linkers, methylation sensitive restriction, PCR using linker primers, dye labeling and relative quantification of methylated DNA fragments by two-colored array hybridization to a CpG island microarray for visual assessment.
Color is indicative of methylation status - be it hypo- (pseudo-green), hyper- (pseudo-red), or equal methylation (pseudo-yellow).
differential methylation hybridization evidence
A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification.
If performing GO annotation, the interacting protein is referenced in the evidence_with column.
A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures.
A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product.
A type of physical interaction evidence that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein.
The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquitin (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough to reconstitute.TAIR:TED
A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles.
A type of physical interaction evidence that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes.
The interacting protein is referenced in the evidence_with column.
A type of in vitro methylation assay 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.
The product is the amplification of existing sequences - i.e. more DNA that can be further processed e.g. sequenced, DNA fingerprinting.
methylation-specific polymerase chain reaction evidence
A type of DNA detection assay evidence that is based on detection of a specific DNA sequence by hybridization of labeled probes to any immobilized DNA fragment with sequence similarity.
The DNA fragments are prepared through gel electrophoresis then transferred to a filter membrane.
A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound.
"Used when an annotation is made based on affinity chromatography, which is a selective separation technique by which a compound (e.g., an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components, the bound compound is displaced by changing the concentration of protons, salts, or cofactors in the eluent" (from original definition by TAIR:TED). Types of highly specific interaction might include those of antigen and antibody, enzyme and substrate, or receptor and ligand.
A type of similarity that indicates common ancestry.
A type of motif similarity evidence that is based on detection of a targeting sequence in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand.
This term has been made obsolete because PCR is not evidence. The children have been appropriately placed under other parents.
A type of motif similarity evidence that is based on detection of one, or more, transmembrane domains in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
transmembrane domain prediction evidence
A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes.
Genomic cluster analyses include synteny and operon structure.
A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding.
A type of in vitro methylation assay 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 sequences methylated at both ends and resolving the PCR products in a denaturing polyacrylamide-sequencing gel to generate fingerprints that consist of multiple anonymous bands that represent the DNA methylome of the cell.
The bands can be individually isolated and characterized which leads to the identification of hypo- and hypermethylation events.
amplification of intermethylated sites evidence
A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues.
A type of evidence that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system.
The biological system in question might be a multi-step process or pathway or a physical complex comprising several components. The components in the experimental evidence can come from the same species or a mix of species. The experimental evidences may be only partial or weak.
biological system reconstruction evidence
A type of DNA detection assay evidence resulting from the use of restriction enzymes for direct end-labeling of DNA (creating landmarks), followed by high-resolution two-dimensional electrophoresis to visualize the landmarks.
restriction landmark genome scanning evidence
restriction landmark genomic scanning evidence
A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy.
A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies.
IDA: immunolocalization of epitope-tagged protein
epitope-tagged protein immunolocalization evidence
A type of DNA detection assay evidence evidence where gene sequence or variation is determined or detected by fluorescently-labeled DNA fragments hybridized to sequence-specific oligonucleotides immobilized on an array.
single nucleotide polymorphism array evidence
The children of 'biological assay evidence' have been moved under 'direct assay evidence', and this term has been deprecated with no children left.
A type of cell growth assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect.
Cell growth aspects can include growth rate and extent of growth. A cell growth curve acts as a natural reporter.
A type of direct assay evidence based on an electrophoretic mobility shift of macromolecules, compounds, and proteins where solutions of protein and nucleic acid are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect protein-nucleic acid interactions.
EMSA: electrophoretic mobility shift assay
IDA: electrophoretic mobility shift assay
EMSA is often used for assessing TF-binding with fluorophore labelling. Protein-nucleic acid complexes generally migrate at a slower rate than the corresponding non-bonded nucleic acid.
electrophoretic mobility shift assay evidence
A type of expression microarray evidence where expression level is quantified by fluroescently-labeled cDNA (reverse transcribed from an unknown RNA sample) hybridized to DNA immobilized on a solid surface.
cDNA to DNA expression microarray evidence
A type of nucleic acid hybridization evidence based on localization of a specific segment of DNA or RNA by the application of a complementary strand of nucleic acid to which a reporter molecule is attached.
A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions.
A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information.
A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules.
A type of expression microarray evidence where expression levels are quantified by hybridization of fluorescently-labeled DNA to cDNA (reverse transcribed from an unknown RNA sample) immobilized on a solid surface.
microarray RNA expression level evidence
IEP: transcript levels (e.g. microarray data)
REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that.
DNA to cDNA expression microarray evidence
A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels.
A type of transcript expression evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples.
A type of RNA detection assay evidence where an RNA transcript is reverse transcribed into cDNA and amplified to qualitatively detect gene expression.
reverse transcription polymerase chain reaction transcription evidence
The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate.
reverse transcription polymerase chain reaction evidence
A type of nuclease protection assay evidence where mRNA is hybridized with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions, later the remaining probe target hybrids are purified and resolved on denaturing polyacrylamide gel, and quantified by autoradiography.
A type of gel electrophoresis evidence where proteins are separated using gel electrophoresis and then they are blotted on a nitrocellulose or polyvinylidene difluoride (PVDF) membrane, later an antibody with a dye or an enzyme is added to the solution which is able to bind to its specific protein and this product is detected either by chemiluminescent detection technique or fluorescence imaging technique.
IEP: protein levels (e.g. Western blots)
Western blot is used for protein detection and analysis. A mixed protein sample is separated through polyacrylamide gel electrophoresis then transferred to a membrane, such as polyvinylidene fluoride (PVDF), and labeled with protein-specific antibodies.
A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein.
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue is compared to another cell type or tissue when mRNA from each sample is reverse transcribed, labeled, and hybridized to a cDNA library to compare hybridization patterns.
Differential hybridization identifies differentially expressed cloned genes. Two different mRNA-derived probes are used to demonstrate RNA expression under a specific condition.
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue are compared to another cell type or tissue when denatured ds-cDNA from the two samples are hybridized, and the common sequences are 'subtracted'.
Subtractive hybridization is used for isolation and identification of transcripts involving the removal of any sequences present in the control from the test probe to detect only transcripts present in the sample. The method is PCR-based for the comparison of two cDNA libraries.
A type of experimental phenotypic evidence in which a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product.
A type of localization evidence where sub-cellular localization of a protein is determined.
A type of protein localization evidence resulting from the fusion of a protein of interest to a labeling protein which has enzymatic activity or fluorescence properties.
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with green fluorescent protein (GFP) from the jellyfish Aequorea victoria.
GFP fusion protein localization evidence
IDA: localization of GFP/YFP fusion protein
green fluorescent protein fusion protein localization evidence
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with yellow fluorescent protein (YFP), which was created by mutating green fluorescent protein (GFP) of the Aequorea victoria.
YFP fusion protein localization evidence
yellow fluorescent protein fusion protein localization evidence
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-glucuronidase (GUS) coding gene as a reporter gene for the localization of a particular gene product.
GUS fusion protein localization evidence
beta-glucuronidase fusion protein localization evidence
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-galactosidase coding gene (lacZ) into a specific gene to create a beta-galactosidase-tagged fusion protein.
LacZ fusion protein localization evidence
beta-galactosidase fusion protein localization evidence
A type of direct assay evidence resulting from the activity assessment of transport proteins.
A type of affinity evidence resulting from the binding of a molecule to a nucleic acid.
A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer.
A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site.
A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis.
IDA: in vitro reconstitution assay with recombinant protein
in vitro transcription reconstitution assay evidence
A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system.
in vitro recombinant protein transcription reconstitution assay evidence
A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed.
IDA: protein expression in heterologous system
heterologous protein expression evidence
A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture.
IDA: protein separation and direct sequencing
protein separation followed by direct sequencing evidence
IDA: protein separation and fragment identification
protein separation followed by fragment identification evidence
A type of transport assay evidence in which the uptake mechanism of a transporter is investigated in a cell that does not normally express that protein.
IDA: uptake assay in heterologous system
The transporter is a recombinant protein.
A type of direct assay evidence where electrical properties of cells or tissues are studied.
The scale of electrophysiology assays can range from small, e.g. a single ion channel, to large, e.g. an entire organ such as a heart.
A type of voltage clamp recording evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current.
IDA: two-electrode voltage clamp technique
two-electrode voltage clamp recording evidence
A type of direct assay evidence resulting from the detection and quantification of transcribed RNA.
A type of transcription assay evidence in which sequence-specific binding proteins that increase transcription of a specific target gene or genes are identified, quantified, and/or analyzed.
transcriptional activation assay evidence
A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed.
For example, the accumulation of a biosynthetic intermediate.
A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined.
Examples include: abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions.
A type of mutant phenotype evidence in which traits arising from a mutation are visually examined.
A type of evidence in which the location of the gene within the genome provides insight into its function, or provides evolutionary insight.
This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis.
A type of direct assay evidence resulting from a sample of microorganisms or living tissue grown in a medium.
A type of experimental evidence arising from the investigation of an animal model system.
A type of experimental evidence arising from a controlled investigation that uses human subjects.
A type of direct assay evidence resulting from a process performed outside the living organism, where the components of an organism have been isolated from their usual biological context, to permit a more detailed or more convenient analysis in an artificial setting.
Use ECO:0001563 (cell growth assay evidence) in place of this term.
A type of direct assay evidence resulting from studies in which cytoplasmic and/or nuclear cellular components from resting, nonstimulated cells, are isolated by ultracentrifugation to provide molecular machinery that can be used in reactions in the absence of many of the other cellular components for the purpose of in vitro protein synthesis, transcription, DNA replication, etc.
A type of specific protein inhibition evidence where the protein under study is an enzyme.
A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment
Such alignments may be pairwise alignments or multiple alignments.
A type of sequence similarity evidence in which orthology is established by multiple criteria, including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors.
Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor.
A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model.
Used when evidence from any kind of statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Examples of relevant evidence are: Hidden Markov Models, PROSITE motifs, and tools such as tRNASCAN.
An assertion method that does not involve human review.
An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically.
An evidence type that is based on an assertion by the author of a paper, which is read by a curator.
A type of inferential evidence that is based on a conclusion drawn by a curator.
A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST).
A type of BLAST evidence in which nucleotide sequences are aligned.
A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned.
A type of BLAST evidence that is used in an automatic assertion.
BLAST evidence used in automatic assertion
A type of nucleotide BLAST evidence that is used in an automatic assertion.
nucleotide BLAST evidence used in automatic assertion
A type of protein BLAST evidence that is used in an automatic assertion.
protein BLAST evidence used in automatic assertion
A type of evidence that arises out of the integration of more than one line of evidence.
A key aspect of this type of evidence is that two or more pieces of information are combined to generate an emergent type of evidence not possible with the constituent pieces of evidence alone. A combinatorial analysis typically involves incorporation of different types of evidence.
A type of combinatorial analysis that is used in an automatic assertion.
combinatorial evidence used in automatic assertion
A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
This type of evidence can be used in support of both positive and "not" GO annotations. It should be used to annotate ancestral genes but not extant ones.
biological aspect of descendant evidence
A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence.
rapid divergence from ancestral sequence evidence
A type of phylogenetic evidence characterized by the absence of key sequence residues.
The loss of certain residues important for function can indicate that a sequence lacks a particular function.
phylogenetic determination of loss of key residues evidence
A means by which a statement is made about an entity.
An assertion method that involves human review.
A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information.
A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides.
A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique.
Typically thousands to millions of reads are produced in parallel.
high throughput nucleotide sequencing assay evidence
A type of high throughput nucleotide sequencing evidence in which sequence is determined through hybridization of adaptor-ligated DNA to a glass slide on which each fragment is simultaneously clonally amplified, followed by progressive rounds of base incorporation with fluorescently-tagged nucleotides, washing, imaging, and cleavage.
In Illumina sequencing technology, adapters are ligated onto the ends of randomly fragmented DNA. After single-stranded fragments are bound to the inside surface of a flow cell channel, they undergo in-place bridge PCR amplification. To begin the sequencing cycle, labeled reversible terminators, primers and DNA polymerase are added, followed by laser excitation of the fluorescent label and high resolution scanning. After non-incorporated nucleotides are washed away and the dye is chemically removed, the next cycle repeats with four labeled reversible terminators, primers and DNA polymerase, again followed by imaging.
A type of high throughput nucleotide sequencing evidence in which the sequence for a ssDNA is determined by addition of primers and then nucleotides, one base pair at a time (which generate a specific fluorescence), to the target strand.
454 pyrosequencing technology amplifies individual DNA fragments inside water droplets within an oil solution (emulsion PCR). Within each droplet, a single DNA template is attached to a single primer-coated bead. Each bead is subsequently captured in a picolitre well within the sequencing machine. A luciferase-based readout system is used to identify individual nucleotides added to the nascent DNA. The target strand is usually prepared by fragmentation, adaptor ligation, and amplification by emulsion PCR.
A type of high throughput nucleotide sequencing evidence in which sequence is determined through rounds of ligation-based sequencing with fluorescently-labeled Di-base probes and cleavage, after which the template is reset, with a primer offset by one base, for subsequent rounds of ligation.
SOLiD sequencing technology is based on sequencing by ligation. After library preparation, emulsion PCR and bead enrichment are performed, including 3' modification of templates on selected beads to allow covalent bonding to a slide. 3' modified beads are attached to a glass slide and primers are added. Four fluorescently labeled di-base probes are added and multiple cycles of ligation, detection and cleavage are performed. The number of cycles determines read length. After a number of ligation cycles, the extension product is removed and another round of ligation cycles is performed with a new primer complimentary to the n-1 position of the template. Five rounds of primer reset are performed for each sequence tag. Samples are prepared by fragmentation of a sample library, adaptor ligation, emulsion PCR, and attachment of resultant beads to glass slides.
A type of nucleotide sequencing assay in which DNA sequence is determined by addition of a primed DNA template to a reaction mixture, followed by addition of DNA polymerase, deoxynucleosidetriphosphates (dNTPs - one of which may be radiolabeled), and one of four di-deoxynucleotidetriphosphates (ddNTPs), after which DNA elongation is terminated and the DNA is separated by size and imaged.
Chain termination sequencing, also called Sanger sequencing after its developer, uses dideoxynucleotide triphosphates (ddNTPs) as DNA chain terminators. Single-stranded DNA template, DNA primer, DNA polymerase, fluorescently or radioactively labeled nucleotides, and one of four ddNTPs are added together in each of four separate sequencing reactions. The synthesized and labeled DNA fragments from each of the four reactions are denatured, separated by size by gel electrophoresis, and visualized by autoradiography or UV light. The ddNTPs lack an OH group so the next dNTP cannot be attached, causing chain termination.
A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
Chromatin immunoprecipitation (ChIP) is used to investigate protein-DNA interactions in vivo. DNA and proteins are chemically cross-linked in vivo to form chromatin complexes, followed by cell lysis and DNA shearing. Fragmented DNA-protein complexes are selectively enriched for a protein of interest using a specific antibody (immunoprecipitation). Protein digestion and DNA purification are performed prior to DNA detection via molecular cloning and sequencing, polymerase chain reaction (PCR), microarray analysis (ChIP-on-chip), or direct high-throughput sequencing (ChIP-seq).
A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection.
ChIP-PCR is often used to validate ChIP-chip results and less frequently,ChIP-Seq results.
chromatin immunoprecipitation-PCR evidence
A type of chromatin immunoprecipitation evidence in which protein-DNA interactions are investigated at known genomic binding sites through a process of ChIP, DNA purification, and finally quantitative polymerase chain reaction (qPCR) for DNA detection.
chromatin immunoprecipitation-qPCR evidence
A type of chromatin immunoprecipitation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins.
ChIP-Seq experiments often use the input as a control to eliminate biases. To obtain similar results, ChIP-chip with high-density tiling arrays can be used.
chromatin immunoprecipitation-seq evidence
A type of chromatin immunoprecipitation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions.
A fixating agent such as formaldehyde is used to cross link proteins and DNA. Sonication is applied for DNA shearing. For transcription factor tagging, an antibody or epitope is employed. After cross-linking is reversed, the DNA is amplified and labeled with a flourophore for microarray which produces a resolution of aproximately 500 bp.
chromatin immunoprecipitation-chip evidence
A type of DNA detection assay evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes or fluorescent probes for detection and quantification of specific sequences in a DNA sample.
real time polymerase chain reaction evidence
Quantitative PCR enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. The dye is activated upon binding double-stranded DNA. Although qRT-PCR is commonly found in literature synonymous to qPCR, it is preferable not to use this synonym as it is the accepted abbreviation for reverse transcription PCR. qPCR should be used instead (ISBN 978-0-470-68386-6 page 173). qPCR can be used to quantitatively determine levels of gene expression.
quantitative polymerase chain reaction evidence
A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, DNA processing, and quantitation that serves to analyze the spatial organization of chromatin in a cell and quantify the number of interactions between genomic loci that are nearby in 3-D space.
chromosome conformation capture-based evidence
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.
A type of chromosome conformation-based evidence that is derived by 1) quantifying interactions between a single pair of genomic loci and not multiple interactions and 2) performing polymerase chain reaction (PCR) in the final product quantitation step.
chromosome conformation capture evidence
chromosome conformation capture-PCR evidence
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.
A type of chromosome conformation-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.
circularized chromosome conformation capture evidence
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.
A type of chromosome conformation-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
carbon-copy chromosome conformation capture evidence
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.
A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
See 3C evidence. 3C evidence was initially developed using PCR.
A type of 3C evidence evidence that 1) quantifies interactions between a single pair of genomic loci (not multiple interactions) and 2) performs quantitative polymerase chain reaction (qPCR) in the quantitation step.
chromosome conformation capture-qPCR evidence
A type of chromosome conformation-based evidence that is derived by performing immunoprecipitation enrichment of the biotin labelled ligated fragments events prior to sequencing of the library and mapping it to the genome.
Hi-C is used to study the structural properties and spatial organization of chromosomes inside cells. Hi-C is similar to other types of chromosome conformation capture technology, but involves the addition of biotinylated nucleotides during the second or fourth step and enrichment for ligated fragments using immunoprecipitation after the fourth step.
A type of chromosome conformation-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with multiplexed high-throughput (HT) sequencing.
chromosome conformation capture sequencing evidence
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.
A type of experimental phenotypic evidence in which the phenotype of an organism is observed after the disruption of a structural feature.
A type of experimental phenotypic evidence in which the phenotype of an organism is observed after modification of the extra-organismal context.
Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth.
A type of anatomical perturbation that is based on disruption of tissue.
A tissue ablation experiment involves observing the phenotype of an entity whose tissues have been disrupted through genetic or biochemical manipulation, physical destruction, or some other means.
A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure.
A type of combinatorial analysis that is used in a manual assertion.
combinatorial evidence used in manual assertion
A type of computational combinatorial analysis that is used in a manual assertion.
inferred from reviewed computational analysis
computational combinatorial evidence used in manual assertion
A type of computational combinatorial analysis that is used in an automatic assertion.
computational combinatorial evidence used in automatic assertion
A type of sequence alignment evidence that is used in a manual assertion.
sequence alignment evidence used in manual assertion
A type of sequence alignment evidence that is used in an automatic assertion.
sequence alignment evidence used in automatic assertion
A type of sequence similarity evidence that is used in an automatic assertion.
sequence similarity evidence used in automatic assertion
A type of sequence similarity evidence that is used in a manual assertion.
inferred from sequence or structural similarity
sequence similarity evidence used in manual assertion
A type of similarity evidence that is used in an automatic assertion.
similarity evidence used in automatic assertion
A type of similarity evidence that is used in a manual assertion.
similarity evidence used in manual assertion
A type of genetic similarity evidence that is used in a manual assertion.
genetic similarity evidence used in manual assertion
A type of genetic similarity evidence that is used in an automatic assertion.
genetic similarity evidence used in automatic assertion
A type of match to sequence model evidence that is used in a manual assertion.
match to sequence model evidence used in manual assertion
A type of match to sequence model evidence that is used in an automatic assertion.
match to sequence model evidence used in automatic assertion
Gene Ontology annotation through association of InterPro records with GO terms.
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl
A type of motif similarity evidence that is used in a manual assertion.
motif similarity evidence used in manual assertion
A type of motif similarity evidence that is used in an automatic assertion.
motif similarity evidence used in automatic assertion
A type of match to InterPro member signature evidence that is used in an automatic assertion.
match to InterPro member signature evidence used in automatic assertion
A type of match to InterPro member signature evidence that is used in a manual assertion.
match to InterPro member signature evidence used in manual assertion
A type of targeting sequence prediction that is used in an automatic assertion.
targeting sequence prediction evidence used in automatic assertion
A type of targeting sequence prediction that is used in a manual assertion.
targeting sequence prediction evidence used in manual assertion
A type of transmembrane domain prediction that is used in an automatic assertion.
transmembrane domain prediction evidence used in automatic assertion
A type of transmembrane domain prediction that is used in a manual assertion.
transmembrane domain prediction evidence used in manual assertion
A type of sequence orthology evidence that is used in an automatic assertion.
sequence orthology evidence used in automatic assertion
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins.
Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara
Automatic transfer of experimentally verified manual GO annotation data to fungal orthologs using Ensembl Compara
A type of sequence orthology evidence that is used in a manual assertion.
sequence orthology evidence used in manual assertion
A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate.
ELISA is sometimes used in the study of transcriptional regulation to identify a produced protein, especially secreted protein.
enzyme-linked immunoabsorbent assay evidence
A type of direct assay evidence in which cells or particles are characterized by passing them through a light source and monitoring the resultant light scatter or fluorochrome excitation.
A type of experimental evidence that is used in a manual assertion.
experimental evidence used in manual assertion
A type of expression pattern evidence that is used in a manual assertion.
expression evidence used in manual assertion
This general 'array experiment' term should not be used - replace with the specific type of array (e.g. ECO:0000273, ECO:0000276, ECO:0000285, etc.)
array experiment evidence used in manual assertion
A type of Affymetrix GeneChip evidence that is used in a manual assertion.
Affymetrix GeneChip evidence used in manual assertion
A type of cDNA to DNA expression microarray evidence that is used in a manual assertion.
cDNA to DNA expression microarray evidence used in manual assertion
A type of differential methylation hybridization evidence that is used in a manual assertion.
CpG island microarray evidence used in manual assertion
differential methylation hybridization evidence used in manual assertion
A type of expression microarray evidence that is used in a manual assertion.
expression microarray evidence used in manual assertion
A type of cRNA to DNA expression microarray evidence that is used in a manual assertion.
genomic microarray evidence used in manual assertion
cRNA to DNA expression microarray evidence used in manual assertion
A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
Nimblegen array evidence used in manual assertion
A type of array-based sequence capture evidence that is used in a manual assertion.
oligonucleotide microarray evidence used in manual assertion
array-based sequence capture evidence used in manual assertion
A type of Western blot assay that is used in a manual assertion.
western blot evidence used in manual assertion
A type of protein expression level analysis that is used in a manual assertion.
protein expression level evidence used in manual assertion
A type of expression library screen evidence that is used in a manual assertion.
expression library screen evidence used in manual assertion
A type of heterologous protein expression analysis that is used in a manual assertion.
heterologous protein expression evidence used in manual assertion
A type of protein expression spatial pattern analysis that is used in a manual assertion.
spatial pattern of protein expression evidence used in manual assertion
A type of protein expression analysis that is used in a manual assertion.
protein expression evidence used in manual assertion
A type of DNA to cDNA expression microarray evidence that is used in a manual assertion.
DNA to cDNA expression microarray evidence used in manual assertion
A type of differential hybridization experiment that is used in a manual assertion.
differential hybridization evidence used in manual assertion
A type of RNA protection assay that is used in a manual assertion.
RNA protection assay evidence used in manual assertion
A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
spatial pattern of transcript expression evidence used in manual assertion
A type of subtractive hybridization experiment that is used in a manual assertion.
subtractive hybridization evidence used in manual assertion
A type of transcript expression evidence that is used in a manual assertion.
transcript expression evidence used in manual assertion
A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
Morpholino oligonucleotides modify gene expression by blocking access of other molecules to specific, approximately 25-base-long regions of the base-pairing surfaces of ribonucleic acid (RNA). To achieve this anti-sense knockdown technique, delivery of the morpholino can be achieved via microinjection, electroporation, or another method.
A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
SELEX begins with the synthesis of a large oligonucleotide library, either single-stranded DNA or RNA, which consists of random fixed-length sequences flanked by constant 5' and 3' ends that serve as primers. The library is exposed to a target ligand, typically a protein or small organic compound. Unbound sequences are removed, typically with affinity chromatography. Bound sequences are eluted and the nucleic acid is extracted, followed by PCR amplification (RNA is first reverse transcribed). PCR product is converted to single stranded (DNA) or transcribed (RNA). Oligonucleotides are bound to the ligand again and the process is repeated with increasing elution stringency. After several rounds of the process, recovered oligonucleotides are sequenced and analyzed to reveal the binding specificity of the protein.
systematic evolution of ligands by exponential amplification evidence
systematic evolution of ligands by exponential enrichment
A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
Bacterial one-hybrid assay is a method for screening a library of candidate proteins (prey plasmid) for the ability to bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to reporter genes (bait plasmid). Transformation of a bacterial host with two different plasmids is required: One is designed to express the "bait". The other plasmid contains a "prey" which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes.
A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
differential gene expression evidence from RNA-seq experiment
Total RNA is isolated from cells and mRNA is purified by targeting the 3' polyadenylated (poly(A)) tail with poly(T) oligos covalently attached to a substrate. Next, cDNA fragments are generated either by hydrolysis of RNA into 200-300 base oligonucleotides, preceded by reverse transcription, or by reverse transcription initiated by random primers. The cDNA second strand is synthesized, fragments are adapter ligated and high-throughput sequencing is performed by Roche 454, Illumina, ABI-SOLiD, or another HT sequencing technology. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
In the embryos of some organisms, inhibition of cytokinesis blocks neither the cell cycle nor the unfolding of the developmental program. As such, embryonic morphology can be frozen, allowing analysis of the developmental fate of each cell present at the time of cleavage arrest.
A type of cleavage arrested development that arises after treatment with cytochalasin.
Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments.
A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript".
green fluorescent protein immunolocalization evidence
A type of immunolocalization evidence that was generated using LacZ protein as a marker.
LacZ protein immunolocalization evidence
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript".
beta-galactosidase protein immunolocalization evidence
A type of author statement that is used in a manual assertion.
author statement used in manual assertion
A type of author statement without traceable support that is used in a manual assertion.
author statement without traceable support used in manual assertion
A type of author statement supported by traceable reference that is used in a manual assertion.
author statement supported by traceable reference used in manual assertion
A type of curator inference that is used in a manual assertion.
curator inference used in manual assertion
A type of inference from background scientific knowledge that is used in a manual assertion.
inference from background scientific knowledge used in manual assertion
A type of no biological data found that is used in a manual assertion.
no biological data found used in manual assertion
A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
First, a characteristic of the most recent common ancestor (MRCA) is inferred from experimental evidence in descendants; this is followed by inferring a characteristic of a descendant of the MRCA. This type of evidence can be used in support of both positive and "not" GO annotations.
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system.
Complementary DNA (cDNA) is synthesized from microgram quantities of mRNA using first-strand cDNA primer (oligo dT12-18) and reverse transcriptase in the presence of trehalose and sorbitol, followed by selection of full-length cDNA with biotinylated cap-trapper. Linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI, which creates a two base overhang. After amplification, sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
cap analysis of gene expression evidence
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching.
NanoCAGE captures the 5' ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5' full length cDNAs is extended upon hybridization of the riboguanosine-tailed template switching oligonucleotides to these extra cytosines. In semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers, which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template switching, semisuppressive PCR, and EcoP151 cleavage, 25-bp tags are ligated to bar code-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. NanoCAGE requires as little as 10 nanograms of total RNA.
nano-cap analysis of gene expression evidence
A type of evidence that is based on work performed by a person or group prior to a use by a different person or group.
A type of imported information that is used in a manual assertion.
imported information used in manual assertion
A type of imported information that is used in an automatic assertion.
imported information used in automatic assertion
A type of direct assay evidence that is used in a manual assertion.
direct assay evidence used in manual assertion
A type of mutant phenotype evidence that is used in a manual assertion.
mutant phenotype evidence used in manual assertion
A type of genetic interaction experiment evidence that is used in a manual assertion.
genetic interaction evidence used in manual assertion
A type of genomic context evidence that is used in a manual assertion.
genomic context evidence used in manual assertion
A type of biological aspect of ancestor evidence that is used in a manual assertion.
inferred from biological aspect of ancestor
biological aspect of ancestor evidence used in manual assertion
A type of biological aspect of descendant evidence that is used in a manual assertion.
inferred from biological aspect of descendant
biological aspect of descendant evidence used in manual assertion
A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
phylogenetic determination of loss of key residues evidence used in manual assertion
A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
rapid divergence from ancestral sequence evidence used in manual assertion
Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
imported manually asserted information used in automatic assertion
Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.
Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.
A type of imported information used in automatic assertion that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
imported automatically asserted information used in automatic assertion
Gene Ontology annotation based on automatic assignment of UniProtKB keywords in UniProtKB/TrEMBL entries.
Gene Ontology annotation based on the automatic assignment of UniProtKB Subcellular Location terms in UniProtKB/TrEMBL entries.
A type of direct assay evidence in which an image is created and analyzed.
A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase.
A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript.
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child.
whole transcript splice pattern evidence
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript.
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child.
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion.
whole transcript splice pattern evidence used in manual assertion
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion.
coding sequence splice pattern evidence used in manual assertion
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion.
coding sequence splice pattern evidence used in automatic assertion
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion.
whole transcript splice pattern evidence used in automatic assertion
A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
Electrophoretic mobility is a function of both the length and charge of a protein. The protein sample is linearized with sodium dodecyl sulfate (SDS), an anionic detergent. Typically, polypeptides bound with SDS possess an even distribution of charge per unit mass, and subsequent fractionation is by size.
sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence
A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined.
An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system.
A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
Two examples of substance quantification assay are (i) measuring how much of a radiolabelled compound is taken up by a cell and (ii) measuring how much of a substrate is turned over by a given enzyme.
A type of cell proliferation assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed usually by means of a fluorescent marker and flow cytometric analysis.
A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field.
Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch.
A type of gel electrophoresis evidence in which large DNA molecules are separated on agarose gel by alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous.
pulsed-field gel electrophoresis evidence
A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide.
The first dimension gel is intentionally run at low voltage in low percentage agarose to separate DNA molecules in proportion to their mass. The second dimension is run at high voltage in a gel of higher agarose concentration in the presence of ethidium bromide so that the mobility of a non-linear molecule is drastically influenced by its shape.
two-dimensional agarose gel electrophoresis evidence
A type of experimental evidence in which retention of an introduced plasmid is determined when a mitotically stable plasmid (or minichromosome) is introduced into cells, which are grown without selection for several generations.
minichromosome maintenance assay evidence
Loss per generation is determined by comparing colony numbers on selective and non-selective media.
A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
specific protein inhibition by antibody evidence
A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
RNA-seq alignment intron location evidence is used by NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq). Exon-exon boundaries (or intron locations) of a RefSeq transcript, as determined by aligning the transcript to a reference chromosome, are compared to intron locations supported by RNAseq data.
Support of intron position by RNA-seq alignment evidence
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
Full support entails that all exon pairs represented in the transcript are supported. For example, for a transcript containing five exons, if liver RNA-seq reads support all four introns but brain RNA-seq supports only three introns, then the liver data fully support the transcript exons whereas the brain data do not.
Full support of intron position by RNA-seq alignment evidence
A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript.
Partial support can occur in two ways. First, one or more exon-exon pair (intron) is not supported by any RNA-seq sample included in the analysis. Second, no single RNA-seq sample provides support for all exon-exon pairs (introns) represented in a transcript, but all represented exons are supported by at least one sample.
Partial support of intron position by RNA-seq alignment evidence
single exon transcript confirmation via alignment evidence
A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
Support of intron position by RNA-seq alignment evidence used in manual assertion
A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
Support of intron position by RNA-seq alignment evidence used in automatic assertion
A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
Full support of intron position by RNA-seq alignment evidence used in automatic assertion
A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
Full support of intron position by RNA-seq alignment evidence used in manual assertion
A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion.
Partial support of intron position by RNA-seq alignment evidence used in automatic assertion
A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion.
Partial support of intron position by RNA-seq alignment evidence used in manual assertion
A type of evidence that is used in an manual assertion.
A type of physical interaction evidence that is used in a manual assertion.
physical interaction evidence used in manual assertion
A type of gene neighbors evidence that is used in a manual assertion.
gene neighbors evidence used in manual assertion
A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
Example of use: "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor." PMID: 7013637. Northcutt RG. (1981) Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci.
A type of transcript expression evidence resulting from a microarray analysis with the use of the Gene Set Enrichment Analysis (GSEA) method or the Fisher's-Exact (FE) method to assess the differential expression.
differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact)
A type of transcript expression evidence resulting from the use of the Gene Set Enrichment Analysis (GSEA) method or Fisher's-Exact (FE) method to assess an RNA-seq dataset for differential gene expression.
differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact)
biological target-disease association via drug
A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
Inference is the process of deriving logical conclusions from premises known or assumed to be true, or alternatively, arriving at conclusions via some non-logical means of observation of patterns of facts, which can result in identifying new meanings and contexts for understanding. Given the evidence provided by a set of premises, deductive reasoning involves drawing conclusions that necessarily follow, i.e. are certain, whereas inductive reasoning generates conclusions that are likely to be, but are not necessarily, true.
A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is computationally derived.
evidence based on computational logical inference
A type of evidence based on computational logical inference that is used in automatic assertion.
evidence based on computational logical inference used in automatic assertion
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
evidence based on logical inference from manual annotation used in automatic assertion
A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
evidence based on logical inference from automatic annotation used in automatic assertion
A type of evidence that is used in an automatic assertion.
Gene Ontology annotation based on Enzyme Commission mapping.
Gene Ontology annotation based on Swiss-Prot keyword mapping.
Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.
A type of cell proliferation assay evidence resulting from the growth of cells in a micro-environment that mimics real tissue and establishes physiological cell-cell and cell-substrate interactions that regulate proliferation and differentiation.
A type of cell-based assay evidence resulting from labeling cells with [3H]arachidonic acid and subsequently determining the release of the arachidonic acid by the cells.
[3H]arachidonic acid release assay evidence
A type of DNA synthesis cell proliferation assay evidence resulting from the measurement of cell proliferation rate by determining the incorporation of [3H]-thymidine into cellular nucleic acids.
[3H]-thymidine incorporation assay evidence
A type of cytotoxicity assay evidence resulting from the measurement of the amount of radioactive 51Cr released in the supernatant of a sample of 51Cr pre-labeled cells via cytolysis by effector cells (cytotoxic T-cells).
A type of apoptotic assay evidence resulting from the use of 7-aminoactinomycin D (7-AAD) to distinguish viable, apoptotic, and dead cells, using the fact that permeability of the cell membrane, and fluorescence intensity, is low in early apoptotic cells and high in late apoptotic and dead cells.
A type of cell-based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells.
A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host.
A type of cell viability assay evidence resulting from the continuous measurement of fluorescence intensity from the viable cells, where a cell permeable compound, resazurin (the active ingredient of alamarBlue), is reduced to fluorescent resorufin.
A type of anatomical perturbation evidence where an organ or tissue is transplanted from one individual to another of the same species with a different genotype.
allograft transplantation experiment evidence
A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules.
A type of apoptotic assay evidence resulting from the addition and subsequent binding of Annexin V to phosphatidylserine in cells to detect if they are viable, apoptotic, or necrotic.
A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning.
A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies.
A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets.
A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the number of cells that migrate from the upper compartment of a chamber (separated by a micro-porous membrane) to the lower compartment, in which chemotactic agents are present.
A type of nucleotide analog incorporation evidence resulting from the incorporation of bromodeoxyuridine (BrdU) as a thymidine analog into nuclear DNA, resulting in a label that can be tracked using antibody probes.
cell proliferation marker detection assay evidence
5-bromo-2'-deoxyuridine incorporation assay evidence
bromodeoxyuridine incorporation assay evidence
A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis.
A type of cell-based assay evidence resulting from the quantification of a sample of cells.
A type of cell-based assay evidence resulting from the quantification of cell permeability.
A type of staining evidence resulting from monitoring division by the use of carboxyfluorescein diacetate succinimidyl ester (CFSE) to label intracellular molecules with carboxyfluorescein; when a labeled cell divides, the number of carboxyfluorescein-tagged molecules is split.
carboxyfluorescein diacetate succinimidyl ester staining evidence
A type of protein detection assay evidence resulting from a complex (a chemiluminescent compound, protein and a steroidal hapten) utilized as a labeled antigen, which emits light when treated with hydrogen peroxide and copper acetate at a high pH.
chemiluminescence-linked immunoassay evidence
A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product.
A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions.
A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location.
A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish.
A type of physical interaction evidence resulting from the separation of a mixture of molecules under the influence of a force such as artificial gravity, where molecules sedimenting together are assumed to interact.
A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration.
A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal.
A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation.
A type of experimental phenotypic evidence resulting from a constitutively active mutant (CAM), resulting in mutant proteins that remain active in the absence of upstream signals.
A type of protein binding evidence resulting from the identification of two interacting proteins (that exist in close proximity) by linking through covalent bonds followed by identification
A type of structure determination evidence resulting from the use of a narrow beam of x-rays to identify molecular structures by creating a diffraction pattern.
A type of histochemistry evidence resulting from localizing chemical components of cells and organelles on histological sections.
A type of apoptotic assay evidence resulting from the identification of an accumulation of cytochrome C in the cytoplasm after its release from the mitochondria, an early event in apoptosis.
A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence.
4',6-diamidino-2-phenylindole staining evidence
A type of experimental phenotypic evidence resulting from a mutation in which there is a removal of one or more contiguous nucleotides.
A type of apoptotic assay evidence resulting from the visualization via gel electrophoresis of the fragmented DNA (DNA ladder) which is the result of apoptotic DNA fragmentation.
A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments.
A type of experimental phenotypic evidence resulting from the analysis of a mutated gene producing mutant polypeptides that disrupt the activity of the wild-type genes.
A type of Edman degradation evidence that is used in a manual assertion.
Edman degradation evidence used in manual assertion
A type of protein detection assay evidence resulting from labeling a termonal amino acid residue and cleaving it from a peptide by sequentially removing one residue at a time from the amino end of the peptide, without disrupting the bonds.
A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters.
A type of physical interaction evidence resulting from a mixture of two molecules passed through a nitrocellulose filter, where one may be immobilized on the filter, and if the immobilized molecule is capable of binding to the other, it will be retained on the filter as well.
A type of nucleic acid localization evidence and in situ hybridization evidence resulting from the use of fluorescent probes to detect complementary sequences of nucleic acids.
fluorescence in situ hybridization evidence
A type of physical interaction evidence resulting from the measurement of the proximity of two fluorophores, where the energy from an excited molecular fluorophore to another fluorophore can only occur within ~10nm.
fluorescence resonance energy transfer evidence
A type of chromatography evidence resulting from the exclusion of proteins based on molecular size by filtration through a porous matrix (swollen gel), from which larger molecules are excluded.
A type of histology evidence resulting from the identification of chemical components in cells and tissues.
A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues.
A type of chromatography evidence resulting from the separation of molecules in a solute by forcing the solvent containing the sample through a column packed with nonporous particles at high pressure.
high-performance liquid chromatography evidence
A type of protein detection assay evidence resulting from the use of antibodies linked to coloring agents to localize structures in cell cultures to identify proteins.
A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample.
A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections.
A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation.
A type of acetylation assay evidence used in an in vitro experiment.
A type of cleavage assay evidence used in an in vitro experiment.
A type of deubiquitination assay evidence used in an in vitro experiment.
in vitro deubiquitination assay evidence
A type of deacetylation assay evidence used in an in vitro experiment.
A type of defarnesylation assay evidence used in an in vitro experiment.
A type of demethylation assay evidence used in an in vitro experiment.
A type of desumoylation assay evidence used in an in vitro experiment.
A type of farnesylation assay evidence used in an in vitro experiment.
A type of methylation assay evidence used in an in vitro experiment.
A type of palmitoylation assay evidence used in an in vitro experiment.
A type of phosphatase assay evidence used in an in vitro experiment.
A type of protein kinase assay evidence used in an in vitro experiment.
A type of polyADP-ribosylation assay evidence used in an in vitro experiment.
in vitro polyADP-ribosylation assay evidence
A type of sumoylation assay evidence used in an in vitro experiment.
A type of transcription assay evidence used in an in vitro experiment.
A type of translation assay evidence used in an in vitro experiment.
A type of ubiquitination assay evidenceused in an in vitro experiment.
A type of acetylation assay evidence used in an in vivo experiment.
A type of cleavage assay evidence used in an in vivo experiment.
A type of deacetylation assay evidence used in an in vivo experiment.
A type of defarnesylation assay evidence used in an in vivo experiment.
A type of demethylation assay evidence used in an in vivo experiment.
A type of deubiquitination assay evidence used in an in vivo experiment.
A type of desumoylation assay evidence used in an in vivo experiment.
A type of farnesylation assay evidence used in an in vivo experiment.
A type of methylation assay evidence used in an in vivo experiment.
A type of palmitoylation assay evidence used in an in vivo experiment.
A type of phosphatase assay evidence used in an in vivo experiment.
A type of protein kinase assay evidence used in an in vivo experiment.
A type of sumoylation assay evidence used in an in vivo experiment.
A type of transcription assay evidence used in an in vivo experiment.
A type of translation assay evidence used in an in vivo experiment.
A type of ubiquitination assay evidence used in an in vivo experiment.
A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence.
A type of genetic transformation evidence resulting from the removal of a particular gene (or genes), disrupting the function and allowing for functional analysis.
A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid.
A type of physical interaction evidence resulting from the analysis of protein-protein interactions by use of a luciferase enzyme fused to a particular protein (or proteins), which are coexpressed with epitope-tagged partners in mammalian cells.
luminescence-based mammalian interactome mapping assay evidence
A type of hybrid interaction evidence resulting from the analysis of proteins of interest attached to two portions of the transcriptional activator, and in interaction bring the two portions together to increase expression of the reporter gene.
A type of spectrometry evidence resulting from identifying the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles.
A type of imaging assay evidence resulting from the use of technology to visualize and provide information about the body to diagnose, treat, or monitor medical conditions.
A type of direct assay evidence where a microscope was used to view a sample.
A type of cell-based assay evidence to measure cell motility in which a "wound" is created in a cell monolayer and the migration of the cells is captured by imaging at regular intervals during cell migration to close the wound.
A type of apoptotic assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) in combination with phenazine methyl sulfate (PMS) as an intermediate electron acceptor reagent to produce a soluble formazan dye in viable cells.
A type of apoptotic assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to its insoluble purple formazan dye in viable cells and measures cell viability / metabolic activity.
3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
A type of protein detection assay evidence resulting from determination of analyte concentration by fluorescent bead sets attached to an antibody (to a specific analyte) with a fluorescent reporter dye label attached to a second antibody (to a specific analyte).
multiplex bead-based immunoassay evidence
A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits.
A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death.
A type of structure determination evidence resulting from the use of an MRI to provide chemical information about tissue metabolites.
nuclear magnetic resonance spectroscopy evidence
A type of RNA detection assay evidence resulting from the detection and quantitation of specific RNAs (from a sample of total cellular RNA) that are bound by antisense RNA or DNA probes and therefore protected from nucleases.
A type of DNA synthesis cell proliferation assay evidence resulting from the analysis and measurement of the incorporation of fluorescently labeled nucleotide analog(s) into the DNA.
nucleotide analog incorporation assay evidence
A type of protein binding evidence resulting from the panning of a phage library where the individual phage displayed a different peptide or protein by fusion to coat proteins on the capsid.
A type of protein assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis.
phosphopeptide affinity enrichment evidence
A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample.
A type of protein assay evidence resulting from protein-bound peptides detected from a collection of peptides arranged as an array and incubated with the partner protein in order to map protein-protein interaction sites.
A type of experimental phenotypic evidence resulting from the change in a single nucleotide.
A type of staining evidence resulting from the binding and labeling of DNA (during apoptosis, when there is a loss of nuclear DNA content) with propidium iodide (PI) to identify the cells from which it originated.
A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore.
A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged.
A type of protein detection assay evidence resulting from proteins immobilized to prepare protein chips, or microwells, that can be utilized to determine presence of proteins, monitor differential expression profiles, and/or study protein interactions.
A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein.
A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes.
A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant.
A type of protein detection assay evidence resulting from the use of a radioligand to measure the binding of a substance to a specific antibody or other receptor system.
A type of direct assay evidence from the analysis of the real-time interaction between an analyte in solution and its interactant linked to the surface of the resonant mirror.
A type of DNA detection assay evidence resulting from homologous DNA fragments digested by restriction enzymes, and the resulting restriction fragments are sorted by length to illustrate differences.
A type of spectrometry evidence resulting from the evaluation of a molecule in a fluid by its ability to alter the transmission of light at specific wavelengths.
A type of physical interaction evidence based on real-time, rapid plasmon generation on the interface between a planar surface and vacuum that measures changes in refractive index close to the sensor surface when an analyte and its immobilized ligand bind to observe and characterize molecular interaction.
Plasmons are generated by an incident light beam.
A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin.
syngeneic transplantation experiment evidence
A type of enzyme assay evidence resulting from the analysis of tumor necrosis factor (TNF)-a converting enzyme (TACE), which releases a soluble TNF-a from the membrane-bound precursor protein.
Tumor necrosis factor - alpha converting enzyme activity assay
A type of cytochemistry evidence resulting from the analysis of section(s) of a paraffin block containing embedded tissues cores arranged in an array pattern.
A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification.
A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate.
tryptic phosphopeptide mapping assay evidence
A type of apoptotic assay evidence resulting from the visualization of DNA fragmentation by detection of exposed 3'-OH ends, localized by terminal deoxynucleotidyl transferase (TdT) which then catalyzes the addition of labeled dUTPs.
TdT-mediated dUTP-biotin nick end labeling assay
terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence
A type of direct assay evidence resulting from the analysis of a urine sample.
A type of cell proliferation assay evidence resulting from the assessment of metabolic activity from a water-soluble tetrazolium salt WST-1 being reduced outside the cell (by reacting with mitochondrial succinate-tetrazolium reductase) to form a formazan dye.
metabolic cell proliferation assay evidence
A type of anatomical perturbation evidence where live cells, tissues, or organs from a non-human animal source are transplanted, implanted or infused into a human recipient.
A type of 3D cell culture evidence that is used in a manual assertion.
3D cell culture evidence used in manual assertion
A type of 51Cr release assay evidence that is used in a manual assertion.
51Cr release assay evidence used in manual assertion
A type of 7-aminoactinomycin staining evidence that is used in a manual assertion.
7-aminoactinomycin staining evidence used in manual assertion
A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion.
[3H]-thymidine incorporation assay evidence used in manual assertion
A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion.
[3H]arachidonic acid release assay evidence used in manual assertion
A type of adhesion assay evidence that is used in a manual assertion.
adhesion assay evidence used in manual assertion
A type of adoptive cell transfer evidence that is used in a manual assertion.
adoptive cell transfer evidence used in manual assertion
A type of alamarBlue assay evidence that is used in a manual assertion.
alamarBlue assay evidence used in manual assertion
A type of allograft transplantation experiment evidence that is used in a manual assertion.
allograft transplantation experiment evidence used in manual assertion
A type of anion-exchange chromatography evidence that is used in a manual assertion.
anion-exchange chromatography evidence used in manual assertion
A type of annexin-V staining evidence that is used in a manual assertion.
annexin-V staining evidence used in manual assertion
A type of behavioral assay evidence used that is used in a manual assertion.
behavioral assay evidence used in manual assertion
A type of blocking monoclonal antibody evidence that is used in a manual assertion.
blocking monoclonal antibody evidence used in manual assertion
A type of blocking peptide evidence that is used in a manual assertion.
blocking peptide evidence used in manual assertion
A type of blocking polyclonal antibody evidence tthat is used in a manual assertion.
blocking polyclonal antibody evidence used in manual assertion
A type of blood test evidence that is used in a manual assertion.
blood test evidence used in manual assertion
A type of Boyden chamber assay evidence that is used in a manual assertion.
Boyden chamber assay evidence used in manual assertion
A type of bromodeoxyuridine incorporation assay evidence used in manual assertion.
bromodeoxyuridine incorporation assay evidence used in manual assertion
A type of caspase assay evidence that is used in a manual assertion.
caspase assay evidence used in manual assertion
A type of cell counting evidence that is used in a manual assertion.
cell counting evidence used in manual assertion
A type of cell permeability assay evidence that is used in a manual assertion.
cell permeability assay evidence used in manual assertion
A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion.
carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion
A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion.
chemiluminescence-linked immunoassay evidence used in manual assertion
A type of chimeric protein evidence that is used in a manual assertion.
chimeric protein evidence used in manual assertion
A type of co-electrophoresis evidence that is used in a manual assertion.
co-electrophoresis evidence used in manual assertion
A type of co-localization evidence that is used in a manual assertion.
co-localization evidence used in manual assertion
A type of co-sedimentation assay evidence that is used in a manual assertion.
co-sedimentation assay evidence used in manual assertion
A type of colony counting evidence that is used in a manual assertion.
colony counting evidence used in manual assertion
A type of comet assay evidence that is used in a manual assertion.
comet assay evidence used in manual assertion
A type of conditional knockin evidence that is used in a manual assertion.
conditional knockin evidence used in manual assertion
A type of conditional knockout evidence that is used in a manual assertion.
conditional knockout evidence used in manual assertion
A type of constitutively active mutant evidence that is used a in manual assertion.
constitutively active mutant evidence used in manual assertion
A type of cross-linking evidence that is used in a manual assertion.
cross-linking evidence used in manual assertion
A type of crystallography evidence that is used in a manual assertion.
crystallography evidence used in manual assertion
A type of cytochemistry evidence that is used in a manual assertion.
cytochemistry evidence used in manual assertion
A type of cytochrome C release assay evidence that is used in a manual assertion.
cytochrome C release assay evidence used in manual assertion
A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion.
4',6-diamidino-2-phenylindole staining evidence used in manual assertion
A type of deletion evidence that is used in a manual assertion.
deletion mutation evidence used in manual assertion
A type of DNA laddering assay evidence that is used in a manual assertion.
DNA laddering assay evidence used in manual assertion
A type of RNA dot blot assay evidence that is used in a manual assertion.
RNA dot blot assay evidence used in manual assertion
A type of dominant-negative mutant evidence that is used in a manual assertion.
dominant-negative mutant evidence used in manual assertion
A type of eTag assay evidence that is used in a manual assertion.
eTag assay evidence used in manual assertion
A type of filter binding assay evidence that is used in a manual assertion.
filter binding assay evidence used in manual assertion
A type of fluorescence in situ hybridization evidence that is used in a manual assertion.
fluorescence in situ hybridization evidence used in manual assertion
A type of fluorescence resonance energy transfer evidence that is used in a manual assertion.
fluorescence resonance energy transfer evidence used in manual assertion
A type of gel-filtration evidence that is used in a manual assertion.
gel-filtration evidence used in manual assertion
A type of histochemistry evidence that is used in a manual assertion.
histochemistry evidence used in manual assertion
A type of immunocytochemistry evidence that is used in a manual assertion.
immunocytochemistry evidence used in manual assertion
A type of histology evidence that is used in a manual assertion.
histology evidence used in manual assertion
A type of immunodepletion evidence that is used in a manual assertion.
immunodepletion evidence used in manual assertion
A type of immunohistochemistry evidence that is used in a manual assertion.
immunohistochemistry evidence used in manual assertion
A type of in vitro acetylation assay evidence that is used in a manual assertion.
in vitro acetylation assay evidence used in manual assertion
A type of in vitro cleavage assay evidence that is used in a manual assertion.
in vitro cleavage assay evidence used in manual assertion
A type of in vitro deacetylation assay evidence that is used in a manual assertion.
in vitro deacetylation assay evidence used in manual assertion
A type of in vitro defarnesylation assay evidence that is used in a manual assertion.
in vitro defarnesylation assay evidence used in manual assertion
A type of in vitro demethylation assay evidence that is used in a manual assertion.
in vitro demethylation assay evidence used in manual assertion
A type of in vitro desumoylation assay evidence that is used in a manual assertion.
in vitro desumoylation assay evidence used in manual assertion
A type of in vitro deubiquitination assay evidence that is used in a manual assertion.
in vitro deubiquitination assay evidence used in manual assertion
A type of in vitro farnesylation assay evidence that is used in a manual assertion.
in vitro farnesylation assay evidence used in manual assertion
A type of in vitro methylation assay evidence that is used in a manual assertion.
in vitro methylation assay evidence used in manual assertion
A type of in vitro palmitoylation assay evidence that is used in a manual assertion.
in vitro palmitoylation assay evidence used in manual assertion
A type of in vitro phosphatase assay evidence that is used in a manual assertion.
in vitro phosphatase assay evidence used in manual assertion
A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion.
in vitro polyADP-ribosylation assay evidence used in manual assertion
A type of in vitro protein kinase assay evidence that is used in a manual assertion.
in vitro protein kinase assay evidence used in manual assertion
A type of in vitro sumoylation assay evidence that is used in a manual assertion.
in vitro sumoylation assay evidence used in manual assertion
A type of in vitro transcription assay evidence that is used in a manual assertion.
in vitro transcription assay evidence used in manual assertion
A type of in vitro translation assay evidence that is used in a manual assertion.
in vitro translation assay evidence used in manual assertion
A type of in vitro ubiquitination assay evidence that is used in a manual assertion.
in vitro ubiquitination assay evidence used in manual assertion
A type of in vivo acetylation assay evidence that is used in manual assertion.
in vivo acetylation assay evidence used in manual assertion
A type of in vivo cleavage assay evidence that is used in a manual assertion.
in vivo cleavage assay evidence used in manual assertion
A type of in vivo deacetylation assay evidence that is used in a manual assertion.
in vivo deacetylation assay evidence used in manual assertion
A type of in vivo defarnesylation assay evidence that is used in a manual assertion.
in vivo defarnesylation assay evidence used in manual assertion
A type of in vivo demethylation assay evidence that is used in a manual assertion.
in vivo demethylation assay evidence used in manual assertion
A type of in vivo desumoylation assay evidence that is used in a manual assertion.
in vivo desumoylation assay evidence used in manual assertion
A type of in vivo deubiquitination assay evidence that is used in a manual assertion.
in vivo deubiquitination assay evidence used in manual assertion
A type of in vivo farnesylation assay evidence that is used in a manual assertion.
in vivo farnesylation assay evidence used in manual assertion
A type of in vivo methylation assay evidence that is used in a manual assertion.
in vivo methylation assay evidence used in manual assertion
A type of in vivo palmitoylation assay evidence that is used in a manual assertion.
in vivo palmitoylation assay evidence used in manual assertion
A type of in vivo phosphatase assay evidence that is used in a manual assertion.
in vivo phosphatase assay evidence used in manual assertion
A type of in vivo protein kinase assay evidence that is used in a manual assertion.
in vivo protein kinase assay evidence used in manual assertion
A type of in vivo sumoylation assay evidence that is used in a manual assertion.
in vivo sumoylation assay evidence used in manual assertion
A type of in vivo transcription assay evidence that is used in a manual assertion.
in vivo transcription assay evidence used in manual assertion
A type of in vivo translation assay evidence that is used in a manual assertion.
in vivo translation assay evidence used in manual assertion
A type of in vivo ubiquitination assay evidence that is used in a manual assertion.
in vivo ubiquitination assay evidence used in manual assertion
A type of induced mutation evidence that is used in a manual assertion.
induced mutation evidence used in manual assertion
A type of knockin evidence that is used in a manual assertion.
knockin evidence used in manual assertion
A type of knockout evidence that is used in a manual assertion.
knockout evidence used in manual assertion
A type of lipid binding assay evidence that is used in a manual assertion.
lipid binding assay evidence used in manual assertion
A type of LUMIER assay evidence that is used in a manual assertion.
luminescence-based mammalian interactome mapping assay evidence used in manual assertion
A type of macroscopy evidence that is used in a manual assertion.
macroscopy evidence used in manual assertion
A type of mammalian 2-hybrid assay evidence that is used in a manual assertion.
mammalian 2-hybrid assay evidence used in manual assertion
A type of mass spectrometry evidence that is used in a manual assertion.
mass spectrometry evidence used in manual assertion
A type of medical imaging evidence that is used in a manual assertion.
medical imaging evidence used in manual assertion
A type of microscopy evidence that is used in a manual assertion.
microscopy evidence used in manual assertion
A type of motility wound healing assay evidence that is used in a manual assertion.
wound healing assay evidence used in manual assertion
motility wound healing assay evidence used in manual assertion
A type of MTS assay evidence that is used in a manual assertion.
MTS assay evidence used in manual assertion
A type of MTT assay evidence that is used in a manual assertion.
MTT assay evidence used in manual assertion
A type of multiplex bead-based immunoassay evidence that is used in a manual assertion.
multiplex bead-based immunoassay evidence used in manual assertion
A type of natural variation mutant evidence that is used in a manual assertion.
natural variation mutant evidence used in manual assertion
A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion.
nuclear magnetic resonance spectroscopy evidence used in manual assertion
A type of nuclear fragmentation evidence that is used in a manual assertion.
nuclear fragmentation evidence used in manual assertion
A type of nuclease protection assay evidence that is used in a manual assertion.
nuclease protection assay evidence used in manual assertion
A type of nucleotide analog incorporation assay evidence that is used in a manual assertion.
nucleotide analog incorporation assay evidence used in manual assertion
A type of phage display evidence that is used in a manual assertion.
phage display evidence used in manual assertion
A type of phosphoamino acid analysis evidence that is used in a manual assertion.
phosphoamino acid analysis evidence used in manual assertion
A type of peptide affinity enrichment evidence that is used in a manual assertion.
peptide affinity enrichment evidence used in manual assertion
A type of peptide array evidence that is used in a manual assertion.
peptide array evidence used in manual assertion
A type of physical examination evidence that is used in a manual assertion.
physical examination evidence used in manual assertion
A type of point mutation evidence that is used in a manual assertion.
point mutation evidence used in manual assertion
A type of propidium iodide staining evidence that is used in a manual assertion.
propidium iodide staining evidence used in manual assertion
A type of protein detection by fluorescence evidence that is used in a manual assertion.
fluorescence evidence used in manual assertion
A type of protein dot blot assay evidence that is used in a manual assertion.
protein dot blot assay evidence used in manual assertion
A type of protein microarray evidence that is used in a manual assertion.
protein microarray evidence used in manual assertion
A type of protein sequencing assay evidence that is used in a manual assertion.
protein sequencing assay evidence used in manual assertion
A type of quantitative mass spectrometry evidence that is used in a manual assertion.
quantitative mass spectrometry evidence used in manual assertion
A type of radioisotope assay evidence that is used in a manual assertion.
radioisotope assay evidence used in manual assertion
A type of radioimmunoassay evidence that is used in a manual assertion.
radioimmunoassay evidence used in manual assertion
A type of imaging assay evidence that is used in a manual assertion.
imaging assay evidence used in manual assertion
A type of restriction fragment detection evidence that is used in a manual assertion.
restriction fragment detection evidence used in manual assertion
A type of spectrophotometry evidence that is used in a manual assertion.
spectrophotometry evidence used in manual assertion
A type of syngeneic transplantation experiment evidence that is used in a manual assertion.
syngeneic transplantation experiment evidence used in manual assertion
A type of xenotransplantation experiment evidence that is used in a manual assertion.
xenotransplantation experiment evidence used in manual assertion
A type of WST-1 assay evidence that is used in a manual assertion.
WST-1 assay evidence used in manual assertion
A type of urine test evidence that is used in a manual assertion.
urine test evidence used in manual assertion
A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence assay evidence that is used in a manual assertion.
TdT-mediated dUTP-biotin nick end labeling assay evidence
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion
A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion.
tryptic phosphopeptide mapping assay evidence used in manual assertion
A type of transgenic organism evidence that is used in a manual assertion.
transgenic organism evidence used in manual assertion
A type of tissue microarray evidence that is used in a manual assertion.
tissue microarray evidence used in manual assertion
A type of TACE activity assay evidence that is used in a manual assertion.
Tumor necrosis factor - alpha converting enzyme activity assay evidence
TACE activity assay evidence used in manual assertion
A type of surface plasmon resonance evidence that is used in a manual assertion.
surface plasmon resonance evidence used in manual assertion
A type of restriction landmark genome scanning evidence that is used in a manual assertion.
restriction landmark genomic scanning evidence used in manual assertion
A type of resonant mirror biosensor evidence that is used in a manual assertion.
resonant mirror biosensor evidence used in manual assertion
A type of high-performance liquid chromatography evidence that is used in a manual assertion.
high-performance liquid chromatography evidence used in manual assertion
A type of ectopic expression evidence that is used in a manual assertion.
ectopic expression evidence used in manual assertion
A type of direct assay evidence in which the sub-cellular location of a protein or nucleic acid sequence is determined.
A type of localization evidence based on localization of a specific segment of DNA or RNA within tissue by the application of a complementary strand of nucleic acid to which a reporter molecule (i.e. either radio-, fluorescent- or antigen-labeled probe) is attached and quantified using either autoradiography, fluorescence microscopy, or immunohistochemistry.
A type of direct assay evidence where acetylated residues are detected in a protein.
A type of direct assay evidence where the cleavage of a protein into protein fragments by a protease is detected.
A type of direct assay evidence where the removal of acetyl groups are detected in a protein.
A type of direct assay evidence where the removal of farnesyl groups from a protein is detected.
A type of direct assay evidence where the removal of methyl groups from a substrate (RNA/DNA or protein) is detected.
A type of direct assay evidence where the removal of sumo groups from a protein is detected.
A type of direct assay evidence where the removal of ubiquitin groups from a protein is detected.
A type of direct assay evidence where farnesylated residues in proteins are detected.
A type of direct assay evidence where methylated residues of a substarte (RNA/DNA or protein) are detected.
A type of direct assay evidence where palmitoylated residues in a protein are detected.
A type of direct assay evidence where the removal of phosphatase groups from a protein is detected.
A type of direct assay evidence where ADP-ribosylated residues in proteins are detected.
A type of direct assay evidence where phosphorylated residues in proteins are detected.
A type of direct assay evidence where sumoylated residues on a protein are detected.
A type of direct assay evidence where de novo protein synthesis is detected.
A type of direct assay evidence where ubiquitinated residues on a protein are detected.
A type of direct assay evidence where biological cell development, i.e. an increase in cell mass and size are measured.
A type of direct assay evidence resulting from the study of cells.
A type of protein-binding evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
A type of cell-based assay evidence in which living cells are stained with a vital stain, i.e. dye that can be used on living cells without causing cell death.
A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing.
Secreted Embryonic Alkaline Phosphatase reporter assay
Alkaline phosphatase reporter assay produces a hybrid protein with alkaline phosphatase activity following transportation across the cellular membrane.
alkaline phosphatase reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium.
The assay is often performed using a plasmid borne construction on a lacZ strain.
beta-galactosidase reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic.
The amount of acetylated chloramphenicol is directly proportional to the amount of CAT enzyme present.
chloramphenicol acetyltransferase reporter gene assay evidence
A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection.
beta-glucuronidase reporter gene assay evidence
A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence.
A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data.
chromatin immunoprecipitation- exonuclease evidence
A type of electrophoretic mobility shift that is used in a manual assertion.
electrophoretic mobility shift assay evidence used in manual assertion
A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion.
reverse transcription polymerase chain reaction evidence used in manual assertion
A type of chromatography evidence where immobilized promoter DNA is labeled and bound to a matrix through which a protein mixture is poured and then eluted to purify specific DNA binding proteins.
Biotinylation is commonly used for labeling and beads are commonly used as the matrix. Bound protein will remain attached to the beads. Results can be detected through gel electrophoresis and then sequenced by mass-spectrometry. This technique can be used to demonstrate binding of a purified protein, or to purify the binding protein from crude extract or protein mixture.
A type of nucleic acid binding evidence where proteins that have been bound to DNA protect a binding site from enzymatic cleavage with DNAse, thereby detecting protein-DNA interactions.
In DNAse footingprinting amplified DNA combined with TF and DNAse is electrophoresed for fragment comparison with a non-TF control sample. TF-bound fragments do not appear in the gel. Such fragments can be isolated, purified, and sequenced. This technique is often used to identify the binding motif of a TF resolving the protected region to 50-100 bp which can be further examined for TF-binding sites.
A type of fluorescence evidence based on rapid and quantitative analysis of diverse molecular interactions, enzyme activities, and nucleic acid hybridization which uses a fluorophore to measure the binding constants and kinetics of reactions that cause a change in the rotational time of the molecules.
The degree of polarization of a fluorophore is inversely related to its molecular rotation. When the fluorophore is bound to a small molecule, the rate at which it tumbles can decrease significantly from when it is bound tightly to a large protein. If the fluorophore is attached to the larger protein in a binding pair, the difference in polarization between bound and unbound states will be smaller and less accurate. The degree of binding is calculated by using the difference in anisotropy of the partially bound, free, and fully bound states measured by titrating the two binding partners. Fluorescence polarixation assays are homogeneous.
A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing.
The reported sequences should always be verified for presence in the genome sequence.
genomic systematic evolution of ligands by exponential amplification evidence
A type of nuclear magnetic resonance spectroscopy evidence based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum.
Chemical shifts in the spectrum indicating binding can be detected from analysis of a protein spectrum in the presence or absence of its cognate DNA binding site.
heteronuclear single quantum coherence spectroscopy evidence
A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA.
Methidiumpropyl-EDTA Fe(II) footprinting
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
A type of nucleic acid binding evidence where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts.
copper-phenanthroline footprinting evidence
A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light.
green fluorescent protein transcript localization evidence
green fluorescent protein promoter fusion
green fluorescent protein reporter gene assay evidence
A type of protein binding evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions.
The recombinant protein can also be eluted following the pull-down and analyzed further with qPCR or sequencing.
glutathione S-transferase pull-down assay evidence
A type of nucleic acid binding evidence used to identify protein-binding sites on the DNA molecule where DNA that has been bound to protein is digested with hydroxyl radical produced by reduction of hydrogen peroxide with iron (II), followed by separating the cleavage products on a denaturing electrophoresis gel.
A type of transcript expression evidence used to determine expression levels of mRNA where a radiolabeled synthetic oligonucleotide primer is annealed to mRNA at the transcription start site of a gene and the mRNA is extended with reverse transcriptase producing cDNA which is electrophoresed on a polyacrylamide gel and autoradiographed, and the band size is proportional to the initial RNA.
The most commonly used radiolabel is 32P.
A type of nucleotide sequencing assay evidence in which RT-PCR (cDNA synthesis) is first used to produce a cDNA copy of a region of the RNA transcript being investigated followed by PCR to capture either the unknown 5' or 3' end of the transcript for sequencing, depending on whether 5' RACE-PCR or 3' RACE-PCR are being undertaken.
5' and 3' RACE-PCR utilize different protocols to amplify an unknown end using the known sequence of the center of the transcript. For cDNA synthesis, 5' RACE-PCR uses an anti-sense oligonucleotide primer (gene specific primer (GSP)) that recognizes a known sequence in the middle of the gene of interest and the reverse transcriptase to add base pairs to the 3' end of the primer. Next, terminal deoxynucleotidyl transferase (TdT) is used to add a string of identical nucleotides to the 3' end of the cDNA. A PCR reaction is then carried out, using a second anti-sense gene specific primer (GSP2) that binds to the known sequence, and a sense (forward) universal primer (UP) that binds the homopolymeric tail added to the 3' ends of the cDNAs to amplify a cDNA product from the 5' end. In contrast, 3' RACE-PCR utilizes the naturally occurring 3' polyA tail of the transcript and uses an Oligo-dT-adaptor primer (a primer with a short sequence of deoxy-thymine nucleotides) that complements the polyA tail and adds a special adaptor sequence to the 5' end of each cDNA. PCR is then used to amplify 3' cDNA from a known region using a sense GSP, and an anti-sense primer complementary to the adaptor sequence.
RACE PCR is frequently used to verify transcription start sites relevant to the function of transcription factor binding sites such as repression.
rapid amplification of cDNA ends polymerase chain reaction evidence
Use ECO:0000295 (RNA-seq evidence) in place of this term.
A type of knockout evidence based on the survival of an organism in a particular environment where a gene for an enzyme or regulator is knocked out and results are used as a natural reporter.
A type of crystallography evidence where a purified sample at high concentration is crystallised and the crystals are exposed to an x ray beam to obtain three dimensional molecular structure of proteins and biological macromolecules.
X-ray crystallography can be used for a crystal used to probe at the tridimensional structure of proteins. In some cases, it is possible to co-crystallize the protein bound to its DNA binding site, providing detail on the particular arrangement of the two components.
A type of affinity evidence used to identify DNA binding sites in eukaryotes where Escherichia coli DNA adenine methyltransferase (Dam) is fused to a transcription factor, co-factor, chromatin-associated protein, or nuclear-associated protein, followed by a methyl-dependent PCR to localize methyltransferase in the region of the binding site.
The methylation tag is detected with methylation-sensitive restriction enzymes, DpnI and DpnII.
DNA adenine methyltransferase identification evidence
A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction.
When ITC is used to study TF, the temperature of two identical cells containing a known concentration of TF is monitored. After the ligand is added to the cells in precisely measured aliquots, the temperature difference in each cell is observed to determine target binding. This value can be used to compute the energetics of the reaction and hence, binding affinity of the TF for the DNA fragment. The thermodynamic profile that is measured includes the values of binding constant (K(a)), stoichiometry (n), and the enthalpy of binding (DeltaH(b)).
isothermal titration calorimetry evidence
A type of nucleic acid binding evidence where DNA is non-specifically fragmented with ultraviolet light while protein-bound regions are protected from UV damage and strand breakage patterns are analyzed by PAGE and sequenced to detect protein-DNA contacts.
A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel.
methylation interference footprinting evidence
A type of inference from background scientific knowledge used in manual assertion where a visual inspection of promoter region is made to identify putative binding sites.
A type of reporter gene assay evidence used to locate and isolate Fur sites where a plasmid library is created and cloned into a cell line with a ferric uptake regulator (Fur)-repressed reporter and the Fur protein is titrated away from its binding site on the reporter, after which the cell is isolated and plasmid extracted for further sequence analysis.
ferric uptake regulator titration assay evidence
A type of cell-based assay evidence resulting from analyzing the ability of cells to survive or live successfully.
A type of cell-based assay evidence resulting from the measurement of the number of cells, which is a reflection of the balance between cell division and cell loss through cell differentiation or cell death.
A type of cell proliferation assay evidence resulting from the measure of DNA synthesis in the presece of a label.
DNA synthesis cell proliferation assay evidence
A type of cell viability assay evidence resulting from the analysis of ATP concentration (by measuring light intensity) when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions and molecular oxygen.
A type of cell-based assay evidence resulting from the ability of an agent to induce cellular necrosis or apoptosis and the subsequent analysis of cell death mechanism.
Use children of ECO:0001565 (cell-based assay evidence) in place of this term.
A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image.
A type of cell-based assay evidence resulting from the evaluation of chemotactic ability (i.e. the movement, or lack of movement, in response to a chemical stimulus) of prokaryotic or eukaryotic cells.
A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA.
A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures.
A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image.
A type of cell-based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis.
A type of polyADP-ribosylation assay evidence used in an in vivo experiment.
in vivo polyADP-ribosylation assay evidence
A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion.
in vivo polyADP-ribosylation assay evidence used in manual assertion
A type of direct assay evidence derived by studying an organ, tissues, or cells taken from an organism and studied in an external environment with the minimum alteration of natural conditions.
A type of gel electrophoresis evidence that involves one dimension electrophoresis where biomolecules are electrophoresed on a low percentage polyacrylamide gel to be separated in proportion to their mass or isoelectric point, followed by high voltage electrophoresis on a higher percentage gel in the presence of ethidium bromide to alter non-linear molecular shape.
Two-dimensional polyacrylamide gel electrophoresis is commonly employed to establish a proteome for an organism and demonstrate expression changes.
two-dimensional polyacrylamide gel electrophoresis evidence
A type of experimental evidence resulting from the use of a spectrometer.
A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression.
Regular expression is a computational tool used for determining whether a given genome contains a DNA region resembling a transcription factor binding motif. For example A/T=W indicates A or T may be present in a column of the alignment. (PMID: 20708667).
regular expression motif search evidence
A type of point mutation evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another.
A type of point mutation evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon.
A type of point mutation evidence resulting from the change of a DNA nucleotide that does not cause any changes in the amino acid sequence.
A type of experimental phenotypic evidence resulting from a mutation in which there is an insertion of an additional nucleotide, or nucleotides.
A type of experimental phenotypic evidence resulting from a mutation in which inserted nucleotide(s) have a sequence identical to, or derived from, adjacent nucleotides.
A type of experimental phenotypic evidence resulting from any mutation that causes a shift in bases and therefore changes the code for the amino acids.
A type of experimental phenotypic evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated.
A type of experimental phenotypic evidence resulting from a mutation in which there is a change in nucleotides at a splice site
A type of experimental phenotypic evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome
A type of experimental evidence resulting from the detection and analysis of molecular markers.
A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins.
A type of molecule detection assay evidence resulting from the detection of specific RNAs.
A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA.
A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels.
Differences in the optical path lengths between a surface layer and a buried silica layer can be measured very precisely allowing optical height information to be converted to accumulated mass on the surface. For the purpose of TF-binding site identification, IRIS is coupled with DNA-arrays with immobilized potential binding regions exposed to the protein of interest and eluted. Protein-bound fragments exhibit changes in reflectance that can be used to gauge binding quantitatively.
interferometric reflectance imaging sensor evidence
A type of nuclease protection assay evidence where RNA is hybridized with complementary DNA probes and exposed to S1 nuclease for unbound RNA degradation after which the intact RNA is run on a gel for probe size determination and RNA identification to detect and map specific RNAs in a complex mixture of total cellular RNA.
A type of DNA detection assay evidence resulting from evaluation of the relative abundance of target sequences hybridizing to DNA samples that are immobilized on a nitrocellulose or nylon membrane.
A type of DNA dot blot assay evidence that is used in a manual assertion.
DNA dot blot assay evidence used in manual assertion
A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology.
MALDI-TOF MS is commonly used for protein identification in constructing a proteome where protein fingerprints obtained by microbial cells are compared with a database of reference spectra by means of various algorithms integrated in systems recently made commercially available.
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion.
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
A type of experimental phenotypic evidence based on target-specified mutagenesis for the characterization of various gene and protein interactions, structures, and functions where oligonucleotide primers are used to alter a nucleotide sequence.
Site-directed mutagenesis is often performed in tandem with EMSA. It is often implemented only in conserved motif positions or serially through all positions of a site.
A type of experimental phenotypic evidence where radiation or a DNA-damaging agent in vivo, or PCR with degenerate primers in vitro are used for non-targeted mutagenesis.
Random mutagenesis is not often used in TF-binding site determination; however, it is sometimes used to investigate the effect of mutations in TF binding domains in conjunction with expression assays. Random mutations can also be introduced via chemicals, error-prone PCR (EP-PCR), degenerate oligonucleotides-Pfu(DOP), UV irradiation, mutator strains, nucleotide analogs, or DNA recombination.
A type of random mutagenesis evidence that is used in a manual assertion.
random mutagenesis evidence used in manual assertion
A type of multiple sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs.
Relationship type between sequences (e.g. orthologs from multiple genomes or co-expressed genes in the same genome) is not necessarily assumed. The local multiple sequence alignment is typically ungapped. A common application of motif discovery is to infer the binding motif of a given transcription factor (TF). This can be based on the results of a whole-genome expression analysis, assuming that co-expressed genes are co-regulated by the same TF, from peaks in ChIP-seq experiments with the TF, or from the comparative genomics analysis of the promoter regions of orthologs.
A type of motif similarity evidence where the motif is represented by a consensus sequence which incorporates the most frequent nucleotide at each position acting as a generic representative for the sequences in the alignment, and is compared to the genetic sequence for a perfect or imperfect match.
This technique is used to identify transcription factor binding sites by searching a bacterial genome for DNA regions resembling a given TF-binding motif. PMID: 17085555.
A type of motif discovery evidence based on a set of algorithms that infer motifs in non-coding DNA sequences from the conservation of functional regulatory sites through evolution at a higher rate than their local surroundings for the identification of an evolutionary 'footprint'.
The name derives to experimental footprinting techniques where transcription factor (TF)-binding sites are identified by sequencing the region of DNA protected from biochemical agents by the bound TF. This technique is used to identify or verify transcription factor-binding motifs, most commonly in the Eukaryota (PMID: 11997340).
A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes.
This technique is used to predict transcription factor binding sites in gene promoter regions by identifying conserved DNA regions across multiple genomes. PMID: 22305460. Orthology is a typical comparative criterion used.
comparative genomics motif search evidence
A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences.
Machine learning algorithms include, but are not limited to artificial neural networks, random-forest, k-means clustering, hidden Markov models. This suite of methods can be used to identify or verify transcription factor-binding sites in genomic sequences (PMID: 15703297).
machine learning prediction of motif instance evidence
A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis.
This technique is used to predict transcription factor binding sites in gene promoter regions by using a position weight matrix approach. (PMID: 15604457).
position-specific scoring matrix motif search evidence
A type of reporter gene assay evidence based on the fusion of the xylE gene to a specific promoter for the expression of catechol 2,3-dioxygenase that converts the colorless catechol substrate to yellow 2-hydroxymuconic semialdehyde for identification of the expression of a particular gene.
computationally derived logical inference
computationally derived logical inference used in automatic assertion
computationally derived logical inference from automatic assertion used in automatic assertion
computationally derived logical inference from manual assertion used in automatic assertion
A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion.
Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof.
biological system reconstruction evidence by experimental evidence from single species used in manual assertion
A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion.
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. The evidence may originate from a combination of several experiments.
biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion
A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion.
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments.
biological system reconstruction evidence based on orthology evidence used in manual assertion
A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by orthology from an existing experimentally supported model to a process, pathway or complex in another species.
biological system reconstruction evidence based on orthology evidence
A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion.
biological system reconstruction evidence based on paralogy evidence used in manual assertion
A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion.
Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components.
biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion
A type of biological system reconstruction based solely on background scientific knowledge of that biological system.
The available knowledge is usually a combination of partial or weak experimental evidence where either some components are missing or no physical interaction evidence can be found but the system is inferred by similarity to related systems in taxonomically-disparate organisms with experimental evidence. Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components.
biological system reconstruction evidence based on inference from background scientific knowledge
A type of biological system reconstruction where the evidence is inferred by homology based on conservation of sequence, function, and composition from an existing experimentally supported model to a process, pathway, or complex.
Inference may be based on paralogy and/or orthology of the genome-encoded components and is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments in the same or another species.
biological system reconstruction evidence based on homology evidence
A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by paralogy from an existing experimentally supported model to a process, pathway, or complex in the same species.
biological system reconstruction evidence based on paralogy evidence
A type of biological system reconstruction evidence that uses experimental evidence as support.
biological system reconstruction evidence by experimental evidence
A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment.
biological system reconstruction evidence by experimental evidence from mixed species
A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species.
biological system reconstruction evidence by experimental evidence from single species
A type of sequence alignment evidence where two sequences are aligned to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).
A type of sequence alignment evidence where three or more biological sequences (protein or nucleic acid) of similar length are aligned to infer homology and the evolutionary relationships between the sequences studied.
A type of multiple sequence alignment evidence that is used in a manual assertion.
multiple sequence alignment evidence used in manual assertion
A type of multiple sequence alignment evidence that is used in an automatic assertion.
multiple sequence alignment evidence used in automatic assertion
A type of motif discovery evidence that is used in a manual assertion.
motif discovery evidence used in manual assertion
A type of motif discovery evidence that is used in an automatic assertion.
motif discovery evidence used in automatic assertion
A type of pairwise sequence alignment evidence that is used in a manual assertion.
pairwise sequence alignment evidence used in manual assertion
A type of pairwise sequence alignment evidence that is used in an automatic evidence.
pairwise sequence alignment evidence used in automatic assertion
A type of protein kinase assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated kinase substrate.
A type of voltage clamp recording evidence that involves recording trace of the current (pA) going through the analyzed ion channels determined from voltage clamp current recording.
A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane.
A type of electrophysiology assay evidence that involves the measurement of the current that persists after the fast and slow inactivation of the analyzed channels.
steady state inactivation curve evidence
A type of electrophysiology assay evidence in which the amount of current remaining after a series of depolarization at different frequencies described as the normalized current related to the time course.
A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell.
current clamp voltage recording evidence
current clamp voltage recording protocol
A type of voltage clamp recording evidence that involves direct measurement of ionic current across a membrane while controlling the membrane potential by maintaining the voltage.
whole-cell voltage clamp recording evidence
whole-cell voltage clamp recording protocol
A type of patch-clamp recording evidence that involves isolation of a patch of membrane electrically from the external solution and to record current flowing into the patch and this is achieved by pressing a fire-polished glass pipette, which has been filled with a suitable electrolyte solution, against the surface of a cell and applying light suction.
cell-attached patch-clamp recording evidence
cell-attached single-channel recording evidence
cell-attached single-channel recording protocol
A type of patch-clamp recording evidence that involves study of individual ion channels by gently pulling the patch of membrane away from the cell, and the patch remains attached to the pipette with its cytoplasmic surface exposed to the bathing solution.
cell-detached inside-out patch-clamp recording evidence
cell-detached inside-out single-channel recording evidence
cell-detached inside-out single-channel recording protocol
A type of patch-clamp reocrding evidence that involves ion channel analysis by incorporating the ion channels into liposomes suitable for patch-clamping which allows isolation and study of a specific population of channels into that bilayer membrane.
reconstituted bilayer single-channel patch recording evidence
reconstituted bilayer single-channel patch recording protocol
A type of electrophysiology assay evidence that involves recording membrane potential by controlling the membrane voltage and measuring the transmembrane current required to maintain that voltage.
voltage clamp current recording evidence
voltage clamp current recording protocol
A type of electrophysiology assay evidence that involves recording the electrical activity of the brain by means of electrodes placed on the surface of the head.
electroencephalography recording evidence
electroencephalography recording protocol
A type of microscopy evidence where the images are taken with a higher resolution than the diffraction limit that help in studying nanoscopic sub-cellular structures.
A type of immunogold labelling evidence that is used in a manual assertion.
immunogold labelling evidence used in manual assertion
A type of flow cytometry evidence that is used in a manual assertion.
flow cytometry evidence used in manual assertion
A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion.
ELISA evidence|enzyme-linked immunosorbent assay evidence
enzyme-linked immunoabsorbent assay evidence used in manual assertion
A type of patch-clamp recording evidence where a part of cellular membrane is detached from the cell and whose external face is exposed to the extracellular medium which allows isolating and studying a single or at least a small number of channels into that fragment (patch).
cell-detached outside-out patch-clamp evidence
cell-detached outside-out single-channel recording evidence
A type of voltage clamp recording evidence that involves inserting the oocyte in a chamber that separates the surface into 3 regions where the top portion of the oocyte membrane is the region that is clamped from which currents are actually recorded while the bottom portion is the region of the oocyte that is cut-open, making it possible to inject current intracellularly through a low resistance pathway.
cut-open oocyte voltage clamp recording evidence
A type of voltage clamp recording evidence where recording is done on a fragment of the cell membrane (attached to or detached from the cell) using a large tip diameter pipette that allows isolating and studying a small number of channels into that fragment (patch).
macropatch voltage clamp recording evidence
A type of mass spectrometry evidence where mass-to-charge ratio (m/z) of gas-phase ions is measured which is used to identify and quantify molecules in complex solutions within the framework of high throughput studies.
There are significant differences in data analysis and data evaluation if to compare a HTP mass-spec and a regular mass-spec. The regular mass spec method is quite a reliable technique for identifying a protein molecular weight and analysing its post-modifications, other mass-spec applications might require the additional quality controls and more stringent data evaluation. More complex sample mixture is processed, more quality questions should be addressed, such as a sample contamination and sensitivity of the mass spectrometer while using HTP mass-spec. For HTP mass-spec, the analysis of the small data sets allows to manually assign the spectra to proteins or peptides, but for large data sets only the statistical tools can be used instead.
high throughput mass spectrometry evidence
A type of high throughput mass spectrometry evidence that is used in a manual assertion.
high throughput mass spectrometry evidence used in manual assertion
A type of microscopy evidence where sharp images are taken by excluding most of the light from the specimen that is not from the microscope's focal plane, thus allowing better contrast and less haze, which makes it possible to build three-dimensional reconstructions of a volume of the specimen by assembling a series of thin slices taken along the vertical axis.
A type of microscopy evidence where imaging of a thin cell or a tissue specimen is performed by full aperture emission of light gathered by the microscope's objective, which maximizes the recorded signal and simultaneously minimizes the required exposure times.
A type confocal microscopy evidence that is used in a manual assertion.
confocal microscopy evidence used in manual assertion
A type of wide-field microscopy evidence that is used in a manual assertion.
wide-field microscopy evidence used in manual assertion
A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles.
immunogold labelling electron microscopy assay evidence
A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion.
immunogold labelling electron microscopy assay evidence used in manual assertion
A type of direct assay evidence that involves the use of antibodies to detect biomolecules.
A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody.
immunoperoxidase immunolocalization evidence
A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion.
immunoperoxidase immunolocalization evidence used in manual assertion
A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody.
Immunoperoxidase labelling electron microscopy
immunoperoxidase immunolocalization electron microscopy evidence
A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion.
immunoperoxidase labelling electron microscopy evidence
immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion
A type of wide-field microscopy evidence where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter.
The optical filter is used to select the wavelength of excitation light. The detection camera is typically a CCD camera. Both topographical and dynamic information of a sample are obtained.
wide-field fluorescence microscopy evidence
A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
immunofluorescence wide-field microscopy evidence
A type of confocal microscopy evidence where light passes through immunofluorescent-stained tissue sections or cells and then the emitted light passes through the dichroic mirror and is focused onto the pinhole for subsequent detection.
This allows visualization of sub cellular distribution of biomolecules of interest.
immunofluorescence confocal microscopy evidence
A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion.
immunofluorescence confocal microscopy evidence used in manual assertion
A type of protein expression level evidence where the level of expression of a protein is determined in a cell or tissue extract by western blot technique.
protein expression level evidence based on western blot
A type of mass spectrometry evidence where one or more protein analyses are performed.
A type of cell proliferation assay evidence where the investigated organism or a potential antagonist is inoculated so as to grow along the diameter line of the agar medium in a Petri dish, then, potentially susceptible microbes (usually bacteria) are streaked perpendicularly to the growth line and inhibition of growth of a test microbe in the vicinity of that line suggests that the antagonist secretes one or more diffusible antibiotics.
A type of zone of inhibition evidence where sensitivity/resistance to an antimicrobial agent is tested by impregnating small filter disks with a known concentration of antimicrobial agent which is then placed on a Mueller-Hinton agar plate inoculated with the test organism.
A type of experimental evidence where a foreign genetic material is introduced into the cell for study of gene function and regulation and protein function.
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by observing the rotational behavior of the cells tethered to a coverslip by their flagella.
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by measuring chemotaxis in response to sudden concentration changes from one uniform spatial environment to another.
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the rate of accumulation of the cells into a capillary.
To determine the presence of negative chemotaxis, a repellent is added to the organismal suspension (but not in the capillary) and the organisms that fled into the capillary are measured.
To determine the presence of positive chemotaxis, an attractant is placed in the capillary and the presence of positive chemotaxis is determined based on the amount of organism that accumulated in the capillary.
A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion.
biological system reconstruction evidence based on homology evidence used in manual assertion
A type of direct assay evidence used in manual assertion where phenotype or disease association is made with the gene because of involvement in the molecular mechanism of disease or involvement in a pathway known to contribute to a disease.
inference from experimental data evidence
A type of mutant phenotype evidence used in manual assertion where variations or changes, such as mutations or abnormal levels of the product(s) of a single gene of interest, including non-mutational changes such as inhibition with antibodies or other inhibitors are determined.
Changes can include any gene mutation/knockout, over-expression or ectopic expression of wild-type or mutant genes, anti-sense experiments, RNAi experiments, specific protein inhibitors.
inference from phenotype manipulation evidence
A type of natural variation mutant evidence used in manual assertion where alleles are directly linked to phenotype and Mendelian diseases as a result of various experiments.
inferred by association of genotype from phenotype
Used for 1) polymorphism or segregation of genetic markers (SNPs, mutations, RFLPs, microsatellites); 2) polymorphism or segregation of physical markers (FISH, centromeric or heterochromatic regions, chromosomal banding patterns); 3) detection of polymorphisms in inbred stock.
inference by association of genotype from phenotype
A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion.
two-dimensional polyacrylamide gel electrophoresis evidence used in manual assertion
A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion.
alkaline phosphatase reporter gene assay evidence used in manual assertion
A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion.
LacZ transcript localization evidence used in manual assertion
beta-galactosidase reporter gene assay evidence used in manual assertion
A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion.
chloramphenicol acetyltransferase reporter gene assay evidence used in manual assertion
A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion.
chromatin immunoprecipitation-chip evidence used in automatic assertion
A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion.
chromatin immunoprecipitation- exonuclease evidence used in automatic assertion
A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion.
chromatin immunoprecipitation-PCR evidence used in manual assertion
A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion.
chromatin immunoprecipitation-seq evidence used in automatic assertion
A type of comparative genomics motif search evidence that is used in a manual assertion.
comparative genomics motif search evidence used in manual assertion
A type of comparative genomics motif search evidence that is used in an automatic assertion.
comparative genomics motif search evidence used in automatic assertion
A type of consensus search evidence that is used in a manual assertion.
consensus search evidence used in manual assertion
A type of consensus search evidence that is used in an automatic assertion.
consensus search evidence used in automatic assertion
A type of copper-phenanthroline footprinting evidence that is used in a manual assertion.
1,10-phenanthroline-copper footprinting evidence
copper-phenanthroline footprinting evidence used in manual assertion
A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion.
DNA adenine methyltransferase identification evidence used in manual assertion
A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion.
DNA adenine methyltransferase identification evidence used in automatic assertion
A type of DNA affinity chromatography evidence that is used in a manual assertion.
DNA affinity chromatography evidence used in manual assertion
A type of cDNA to DNA expression microarray evidence that is used in an automatic assertion.
cDNA to DNA expression microarray evidence used in automatic assertion
A type of DNAse footprinting evidence that is used in a manual assertion.
DNAse footprinting evidence used in manual assertion
A type of fluorescence anisotropy evidence that is used in a manual assertion.
fluorescence anisotropy evidence used in manual assertion
A type of ferric uptake regulator titration assay evidence that is used in a manual assertion.
ferric uptake regulator titration assay evidence used in manual assertion
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion.
genomic systematic evolution of ligands by exponential amplification evidence used in manual assertion
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion.
genomic systematic evolution of ligands by exponential amplification evidence used in automatic assertion
A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion.
green fluorescent protein transcript localization evidence used in manual assertion
green fluorescent protein reporter gene assay evidence used in manual assertion
A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion.
green fluorescent protein transcript localization evidence used in automatic assertion
green fluorescent protein reporter gene assay evidence used in automatic assertion
A type of cell growth regulation assay evidence that is used in a manual assertion.
cell growth regulation assay evidence used in manual assertion
A type of cell growth regulation assay evidence that is used in an automatic assertion.
cell growth regulation assay evidence used in automatic assertion
A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion.
glutathione S-transferase pull-down assay evidence used in manual assertion
A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion.
beta-glucuronidase reporter gene assay evidence used in manual assertion
A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion.
heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
A type of hydroxyl-radical footprinting evidence that is used in a manual assertion.
hydroxyl-radical footprinting evidence used in manual assertion
A type of immunoprecipitation evidence that is used in a manual assertion.
immunoprecipitation evidence used in manual assertion
A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion.
spectral reflectance imaging biosensor evidence
interferometric reflectance imaging sensor evidence used in manual assertion
A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion.
interferometric reflectance imaging sensor evidence used in automatic assertion
A type of isothermal titration calorimetry evidence that is used in a manual assertion.
isothermal titration calorimetry evidence used in manual assertion
A type of luciferase reporter gene assay evidence that is used in a manual assertion.
luciferase reporter gene assay evidence used in manual assertion
A type of machine learning prediction of motif instance evidence that is used in a manual assertion.
machine learning prediction of motif instance evidence used in manual assertion
A type of machine learning prediction of motif instance evidence that is used in an automatic assertion.
machine learning prediction of motif instance evidence used in automatic assertion
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion.
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in automatic assertion
A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion.
Methidiumpropyl-EDTA Fe(II) footprinting evidence
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in manual assertion
A type of northern assay evidence that is used in a manual assertion.
northern assay evidence used in manual assertion
A type of phylogenetic footprinting evidence that is used in a manual assertion.
phylogenetic footprinting evidence used in manual assertion
A type of phylogenetic footprinting evidence that is used in an automatic assertion.
phylogenetic footprinting evidence used in automatic assertion
A type of methylation interference footprinting evidence that is used in a manual assertion.
premethylation interference footprinting evidence used in manual assertion
methylation interference footprinting evidence used in manual assertion
A type of primer extension assay evidence that is used in a manual assertion.
primer extension assay evidence used in manual assertion
A type of position-specific scoring matrix motif search evidence that is used in a manual assertion.
position-specific scoring matrix motif search evidence used in manual assertion
A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion.
position-specific scoring matrix motif search evidence used in automatic assertion
A type of quantitative polymerase chain reaction evidence that is used in a manual assertion.
quantitative polymerase chain reaction evidence used in manual assertion
A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion.
rapid amplification of cDNA ends polymerase chain reaction evidence used in manual assertion
A type of regular expression motif search evidence that is used in a manual assertion.
regular expression motif search evidence used in manual assertion
A type of regular expression motif search evidence that is used in an automatic assertion.
regular expression motif search evidence used in automatic assertion
Use ECO:0006068 (RNA-seq evidence used in manual assertion) in place of this term.
RNA sequencing assay evidence used in manual assertion
Use ECO:0006069 (RNA-seq evidence used in automatic assertion) in place of this term.
RNA sequencing assay evidence used in automatic assertion
A type of S1 nuclease protection assay evidence that is used in a manual assertion.
S1 nuclease protection assay evidence used in manual assertion
A type of site-directed mutagenesis evidence that is used in a manual assertion.
site-directed mutagenesis evidence used in manual assertion
A type of survival rate analysis evidence that is used in a manual assertion.
survival rate analysis evidence used in manual assertion
A type of ultraviolet light footprinting evidence that is used in a manual assertion.
ultraviolet light footprinting evidence used in manual assertion
A type of x-ray crystallography evidence that is used in a manual assertion.
x-ray crystallography evidence used in manual assertion
A type of x-ray crystallography evidence that is used in an automatic assertion.
x-ray crystallography evidence used in automatic assertion
A type of xylE reporter gene assay evidence that is used in a manual assertion.
xylE reporter gene assay evidence used in manual assertion
A type of experimental phenotypic evidence where a non-standard trait (e.g. natural competence) is assessed qualitatively (e.g. presence/absence) and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor.
ad-hoc qualitative phenotype observation evidence
A type of ad-hoc qualitative phenotype observation that is used in a manual assertion.
ad-hoc qualitative phenotype observation evidence used in manual assertion
A type of experimental phenotypic evidence where a quantifiable phenotypic trait (e.g. glucose intake) is assessed in a quantitative manner after induction of the regulatory mechanism and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor.
ad-hoc quantitative phenotype observation evidence
A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion.
ad-hoc quantitative phenotype observation evidence used in manual assertion
A direct assay evidence where the activity of a solution is determined by exposing an indicator culture or organism to a series of dilutions and determining the lowest concentration that elicits a biological response.
For chemicals, bacteriocins, or phage, the indicator culture is typically present in a soft-agar layer on top of nutrient agar and a small quantity of each dilution is spotted onto the soft agar overlay.
dilution assay evidence
A type of enzyme assay evidence that is used in a manual assertion.
enzyme assay evidence used in manual assertion
A type of cell transfection experiment evidence that is used in a manual assertion.
cell transfection experiment evidence used in manual assertion
A type of direct assay evidence where the motility of a cell or cells is determined.
A type of immunofluorescence evidence that is used in a manual assertion.
immunofluorescence evidence used in manual assertion
A type of yeast 2-hybrid evidence that is used in a manual assertion.
yeast 2-hybrid evidence used in manual assertion
A type of evidence derived from exploiting the CyaA (calmodulin-activated adenylate cyclase toxin) secreted by Bordatella pertussis to synthesize cAMP and alter cellular physiology in a host cell for various biological applications.
A type of Cya fusion reporter assay evidence that is used in a manual assertion.
Cya fusion reporter assay evidence used in manual assertion
A type of electron microscopy evidence that is used in a manual assertion.
electron microscopy evidence used in manual assertion
A type of super-resolution microscopy evidence that is used in a manual assertion.
super-resolution microscopy evidence used in manual assertion
A type of fractionation evidence that is used in a manual assertion.
fractionation evidence used in manual assertion
A type of electrophysiology assay evidence that is used in a manual assertion.
electrophysiology assay evidence used in manual assertion
A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion.
chromatin immunoprecipitation-chip evidence used in manual assertion
A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion.
chromatin immunoprecipitation- exonuclease evidence used in manual assertion
A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion.
chromatin immunoprecipitation-seq evidence used in manual assertion
A type of nucleic acid binding evidence in which RNA-binding proteins are identified through cross-linking RNA and proteins by UV light, capturing RNA-protein complexes on oligo(dT) beads, and finally identifying by mass spectrometry.
ultraviolet light cross-linking RNA binding evidence
A type of mRNA interactome capture evidence that is used in a manual assertion.
mRNA interactome capture evidence used in manual assertion
A type of electrophysiology assay evidence in which a glass micropipette is sealed to the surface of a cell membrane (patch) to study ion channels.
A type of patch-clamp recording evidence that is used in a manual assertion.
patch-clamp recording evidence used in manual assertion
A type of patch-clamp recording evidence in which a glass micropipette filled with a prepared solution is used to form a seal with the cell membrane followed by rupture of membrane to provide accurate and high resolution electrical property measurements of the whole cell.
whole-cell patch-clamp recording evidence
A type of whole-cell patch-clamp recording evidence that is used in a manual assertion.
whole-cell patch-clamp recording evidence used in manual assertion
A type of traceable author statement that is based on a publication about a clinical study.
traceable author statement from published clinical study
author statement from published clinical study
A type of author statement from published clinical study that is used in a manual assertion.
Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used when evidence for an HPO annotation is information extracted from articles in the medical literature.
author statement from published clinical study used in manual assertion
A type of curator inference that is based on the individual clinical experience of a clinician
inference based on individual clinical experience
A type of inference based on individual clinical experience that is used in a manual assertion.
Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used for annotating disorders with a limited amount of published data, and is accompanied by a reference to the individual or center performing the annotation.
inference based on individual clinical experience used in manual assertion
A type of cell proliferation assay evidence in which biofilm growth is monitored and detected from attachment to development.
A type of biofilm formation assay evidence that is used in a manual assertion.
biofilm formation assay evidence used in manual assertion
A type of biofilm formation assay evidence in which microtiter dishes or tubes are inoculated and incubated to promote biofilm formation, and then biofilms are detected by staining with crystal violet or safranin to observe phenotypes.
A type of microtiter plate biofilm assay evidence that is used in a manual assertion.
microtiter plate biofilm assay evidence used in manual assertion
A type of biofilm formation assay evidence in which biofilm formation is analyzed, without staining, over 4 to 48 hours by growth on a tilted multiwell plate.
Tilting of the plate positions the air-liquid interface on a clear portion to improve visability.
A type of air-liquid interface assay evidence that is used in a manual assertion.
air-liquid interface assay evidence used in manual assertion
A type of biofilm formation assay evidence in which a colony is grown on a semipermeable membrane on an agar plate. The plate serves to supply nutrients and the semipermeable membrane can be relocated to fresh plates.
The plates commonly contain different carbon sources or antibiotic treatments to observe properties of the cells.
A type of colony biofilm assay evidence that is used in a manual assertion.
colony biofilm assay evidence used in manual assertion
A type of biofilm formation assay evidence in which mature bacterial biofilms are grown in a multiwell plate that has a growth medium continually pumped through the wells while waste is continually pumped out.
A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion.
Kadouri drip-fed biofilm assay evidence used in manual assertion
A type of co-immunoprecipitation evidence that is used in a manual assertion.
co-immunoprecipitation evidence used in manual assertion
A type of immunolocalization evidence that is used in a manual assertion.
immunolocalization evidence used in manual assertion
A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators.
A type of optogenetic evidence that is used in a manual assertion.
optogenetic evidence used in manual assertion
A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor.
Examples include sensors for ion concentration and potential difference across a membrane.
A type of fluorescent sensor evidence that is used in a manual assertion.
fluorescent sensor evidence used in manual assertion
A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor.
genetically encoded fluorescent sensor evidence
A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion.
genetically encoded fluorescent sensor evidence used in manual assertion
A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors.
electrophysiology - optical assay evidence
Examples include genetically encoded sensors that detect potential difference across plasma membrane.
genetically encoded fluorescent electrophysiology assay evidence
A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion.
genetically encoded fluorescent electrophysiology assay evidence used in manual assertion
A type of genetically encoded fluorescent electrophysiology assay evidence that is based on direct, quantitative measurement of ion concentration using a genetically encoded fluorescent sensor.
Examples include the genetically encoded calcium indicator GCaMP.
genetically encoded fluorescent ion concentration sensor assay evidence
A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion.
genetically encoded fluorescent ion concentration sensor assay evidence used in manual assertion
A type of cell fractionation evidence that is used in a manual assertion.
cell fractionation evidence used in manual assertion
A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons.
A type of extracellular recording evidence that is used in a manual assertion.
extracellular recording evidence used in manual assertion
A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron.
single-unit extracellular recording evidence
A type of single-unit extracellular recording evidence that is used in a manual assertion.
single-unit extracellular recording evidence used in manual assertion
A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes.
local field potential recording evidence
A type of field potential recording evidence that is used in a manual assertion.
field potential recording evidence used in manual assertion
A type of genetic transformation evidence that is used in a manual assertion
genetic transformation evidence used in manual assertion
A type of anti-sense experiment evidence that is used in a manual assertion.
anti-sense experiment evidence used in manual assertion
A type of morpholino experiment evidence that is used in a manual assertion.
morpholino experiment evidence used in manual assertion
A type of RNAi evidence that is used in a manual assertion.
A type of experimental phenotypic evidence that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist.
A type of experimental phenotypic evidence used in a manual assertion that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist.
pharmacological assay evidence used in manual assertion
A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
Some relevant articles include: PMID: 23340846, doi:10.1038/nmeth0607-523
A type of evidence that is used in a manual assertion where data generation is automated with equipment to allow for assaying large numbers of samples or molecules in parallel.
inferred from high throughput experiment
high throughput evidence used in manual assertion
A type of evidence that is used in an automatic assertion where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
high throughput evidence used in automatic assertion
A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
HT methodologies may incorporate techniques from optics, chemistry, biology or image analysis (https://en.wikipedia.org/wiki/High_throughput_biology)
A type of high throughput evidence used in a manual assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
high throughput cell biology evidence used in manual assertion
A type of high throughput evidence used in an automatic assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
high throughput cell biology evidence used in automatic assertion
A type of wide-field fluorescence microscopy evidence used in a manual assertion where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
wide-field epifluorescence microscopy evidence
immunofluorescence wide-field microscopy evidence used in manual assertion
A type of wide-field microscopy evidence that is used in a manual assertion where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter.
wide-field fluorescence microscopy evidence used in manual assertion
A type of experimental phenotypic evidence that is used in a manual assertion where a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product.
over expression analysis evidence used in manual assertion
A type of cell-free assay evidence that is used in a manual assertion.
cell-free assay evidence used in manual assertion
in vitro cell based assay evidence used in manual assertion
A type of fluorescence evidence where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse.
FRAP is a fluorescence microscopy-based technique.
fluorescence recovery after photobleaching evidence
A type of fluorescence evidence that is used in a manual assertion where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse.
fluorescence recovery after photobleaching evidence used in manual assertion
A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
RNA sequencing|differential gene expression evidence from RNA-seq experiment
RNA-seq evidence used in manual assertion
A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
RNA-seq evidence used in automatic assertion
A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
immunolabelling electron microscopy evidence
immuno-labelling electron microscopy evidence
A type of electron microscopy evidence used in a manual assertion resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
immuno-labelling electron microscopy evidence used in manual assertion
A type of super-resolution microscopy evidence resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue.
immunofluorescence super resolution microscopy evidence
A type of super-resolution microscopy evidence used in a manual assertion resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue.
immunofluorescence super resolution microscopy evidence used in manual assertion
A type of physical interaction evidence that is used in manual assertion where a cellular component subunit is isolated as part of purification of its larger complex.
co-purification evidence used in manual assertion
A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities.
affinity evidence used in manual assertion
A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex.
protein binding evidence used in manual assertion
A type of affinity evidence that is used in manual assertion where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein.
hybrid interaction evidence used in manual assertion
A type of affinity evidence that is used in manual assertion resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
immunological assay evidence used in manual assertion
A type of hybrid interaction evidence that is used in manual assertion that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
yeast one-hybrid evidence used in manual assertion
A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein.
split-ubiquitin assay evidence used in manual assertion
A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes.
far-Western blotting evidence used in manual assertion
A type of affinity evidence that is used in a manual assertion that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound.
affinity chromatography evidence used in manual assertion
A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid.
nucleic acid binding evidence used in manual assertion
A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer.
ribohomopolymer binding assay evidence used in manual assertion
A type of protein binding evidence that is used in a manual assertion resulting from a metal ion binding to a protein at a specific binding site.
protein:ion binding evidence used in manual assertion
A type of nucleic acid binding evidence that is used in a manual assertion in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
Southwestern blot evidence used in manual assertion
A type of nucleic acid binding evidence that is used in a manual assertion in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
Northwestern blot evidence used in manual assertion
A type of evidence that is used in a manual assertion arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
systematic evolution of ligands by exponential amplification evidence used in manual assertion
A type of hybrid interaction evidence that is used in a manual assertion that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
bacterial one-hybrid evidence used in manual assertion
A type of oligonucleotide microarray evidence that is used in a manual assertion that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
protein-binding microarray evidence used in manual assertion
A type of genetic interaction evidence that is used in a manual assertion where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background.
functional complementation evidence used in manual assertion
A type of functional complementation evidence that is used in a manual assertion that is used in manual assertion resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
transgenic rescue experiment evidence used in manual assertion
A type of transient rescue experiment evidence that is used in a manual assertion.
transient rescue experiment evidence used in manual assertion
A type of genetic interaction evidence that is used in a manual assertion resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
suppressor/enhancer interaction evidence used in manual assertion
A type of genetic interaction evidence that is used in a manual assertion that is based on the phenotypic outcome of two mutations in unrelated genetic loci.
double mutant phenotype evidence used in manual assertion
A type of genetic interaction evidence that is used in a manual assertion that is based on the suppression of one allelic effect by an allele at another genetic locus.
epistatic interaction evidence used in manual assertion
A type of functional complementation evidence that is used in a manual assertion that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene.
functional complementation in heterologous system evidence used in manual assertion
A type of mutant phenotype evidence based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures.
temperature-sensitive mutant phenotype evidence
A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures.
temperature-sensitive mutant phenotype evidence used in manual assertion
A type of mutant phenotype evidence based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself.
A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself.
recessive mutant phenotype evidence used in manual assertion
A type of high throughput evidence derived from high throughput analysis of differences in alleles of a corresponding gene.
high throughput mutant phenotype evidence
A type of high throughput evidence that is used in a manual assertion derived from high throughput analysis of differences in alleles of a corresponding gene.
inferred from high throughput mutant phenotype
When using the HMP evidence code, the guidelines for IMP should be adhered to (http://geneontology.org/page/imp-inferred-mutant-phenotype)
high throughput mutant phenotype evidence used in manual assertion
A type of high throughput evidence derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products.
high throughput genetic interaction evidence
A type of high throughput evidence that is used in a manual assertion derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products.
inferred from high throughput genetic interaction
When using the HGI evidence code, the guidelines for IGI should be adhered to (http://geneontology.org/page/igi-inferred-genetic-interaction)
high throughput genetic interaction evidence used in manual assertion
A type of high throughput evidence derived from the high throughput direct measurement of some aspect of a biological feature.
A type of high throughput evidence that is used in a manual assertion derived from the high throughput direct measurement of some aspect of a biological feature.
inferred from high throughput direct assay
When using the HDA evidence code, the guidelines for IDA should be adhered to (http://geneontology.org/page/ida-inferred-direct-assay)
high throughput direct assay evidence used in manual assertion
A type of high throughput evidence derived from the high throughput characterization of gene expression.
high throughput expression pattern evidence
A type of high throughput evidence that is used in a manual assertion derived from the high throughput characterization of gene expression.
inferred from high throughput expression pattern
When using the HEP evidence code, the guidelines for EXP should be adhered to (http://geneontology.org/page/iep-inferred-expression-pattern)
high throughput expression pattern evidence used in manual assertion
A type of protein binding evidence in which radioactive ligands are used to measure receptor-ligand interactions, such as in determining selectivity for a particular ligand.
radioactive ligand binding assay evidence
radiometric ligand-binding assay evidence
A type of radioligand binding assay evidence that is used in a manual assertion.
radioligand binding assay evidence used in manual assertion
A type of inferential evidence resulting from a conclusion drawn by the author of the publication.
A type of combinatorial evidence in which the author draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments.
combinatorial evidence from author knowledge and experimental evidence
A type of combinatorial evidence in which the curator draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments.
combinatorial evidence from curator knowledge and experimental evidence
A type of combinatorial evidence from author knowledge and experimental evidence that is used in a manual assertion.
combinatorial evidence from author knowledge and experimental evidence used in manual assertion
A type of combinatorial evidence from curator knowledge and experimental evidence that is used in a manual assertion.
combinatorial evidence from curator knowledge and experimental evidence used in manual assertion
A type of substance quantification evidence where an electrical gradient potential is applied to analyze an analyte of interest, resulting in a measurement amount of electrical current across the potential range applied.
A type of voltammetry evidence that is used in a manual assertion.
voltammetry evidence used in manual assertion
A type of fluorescence evidence where a molecule tagged with a fluorescent protein is exposed to ultraviolet or blue light to shift the spectral emission properties for visualization.
A type of photoconversion evidence that is used in a manual assertion.
photoconversion evidence used in manual assertion
A type of immunological assay evidence that involves observation of visible clumping of antibody and antigen into a complex.
A type of agglutination test evidence that is used in a manual assertion.
agglutination test evidence used in manual assertion
A type of agglutination test evidence that involves observaiton of visible clumping of antibody and antigen into a complex on a slide.
A type of slide agglutination test evidence that is used in a manual assertion.
slide agglutination test evidence used in manual assertion
A type of agglutination test evidence that results in detection of nonagglutinating antibodies or complement proteins on red blood cells in vivo.
A type of direct Coombs test evidence that is used in a manual assertion.
direct Coombs test evidence used in manual assertion
A type of agglutination test evidence that results in screening of antibodies against red blood cell antigens (other than the A and B antigens) that are unbound in a patient's serum in vitro.
A type of indirect Coombs test evidence that is used in a manual assertion.
indirect Coombs test evidence used in manual assertion
A type of agglutination test evidence where some bacteria and viruses cross-link red blood cells and clump together.
A type of direct hemagglutination assay evidence that is used in a manual assertion.
direct hemagglutination assay evidence used in manual assertion
A type of agglutination test evidence where antiviral antibodies in a patient's serum or in a lab-produced antiserum neutralize the virus and block it from agglutinating the red blood cells.
viral hemagglutination inhibition assay evidence
A type of viral hemagglutination inhibition assay evidence that is used in a manual assertion.
viral hemagglutination inhibition assay evidence used in manual assertion
A type of immunological assay evidence that results in the detection of presence of specific antibodies in the patient's serum based on the use of complement, a biologically labile serum factor.
A type of compement fixation assay evidence that is used in a manual assertion.
compement fixation assay evidence used in manual assertion
A type of immunogical assay evidence that results in detection of specific neutralizing antibodies in a sample.
A type of neutralization test assay evidence that is used in a manual assertion.
neutralization test assay evidence used in manual assertion
A type of transport assay evidence where the rate of copper transport is estimated.
A type of copper transport assay evidence that is used in a manual assertion.
copper transport assay evidence used in manual assertion
A type of staining evidence that involves the use of the redox dye 5-cyano-2,3-ditolyl tetrazolium chloride to evaluate the respiratory activity of cells.
5-cyano-2,3-ditolyl tetrazolium chloride staining evidence
A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in a manual assertion.
5-cyano-2,3-ditolyl tetrazolium chloride staining evidence used in manual assertion
A type of cell growth assay evidence resulting in direct quantification of infectious virons and antiviral substances through the counting of discrete plaques (infectious units and cellular dead zones) in cell culture.
A type of plaque assay evidence that is used in a manual assertion.
plaque assay evidence used in manual assertion
A type of microscopy evidence where the light source is mounted above the specimen and the excitation light passes through the microscope objective lens on its way toward the specimen.
A type of epifluorescence microscopy evidence that is used in a manual assertion.
epifluorescence microscopy evidence used in manual assertion
A type of electron microscopy evidence where a beam of electrons are transmitted through an ultra thin specimen forming an image which is magnified and focused onto an imaging device, such as a fluorescent screen, on a layer of photographic film, or to be detected by a sensor such as a CCD camera.
conventional transmission electron microscopy(CTEM)
transmission electron microscopy evidence
A type of transmission electron microscopy evidence that is used in a manual assertion.
transmission electron microscopy evidence used in manual assertion
A type of electron microscopy evidence where a focused beam of high-energy electrons is used to generate a variety of signals at the surface of solid specimens.
A type of scanning electron microscopy evidence that is used in a manual assertion.
scanning electron microscopy evidence used in manual assertion
A type of microscopy evidence where a serial images are taken at regular time points to capture the dynamics of what is being observed.
A type of time-lapsed microscopy evidence that is used in a manual assertion.
time-lapsed microscopy evidence used in manual assertion
A type of microscopy evidence where a transparent specimen is illuminated with visible light and small phase shifts in the light passing through the specimen are used to produce an image.
A type of phase contrast microscopy evidence that is used in a manual assertion.
phase contrast microscopy evidence used in manual assertion
A type of microscopy evidence where a sample is illuminated with transmitted white light from below and observed from above.
transmitted light brightfied mircoscopy evidence
A type of transmitted light brightfied mircoscopy evidence that is used in a manual assertion.
transmitted light brightfied mircoscopy evidence used in manual assertion
A type of microscopy evidence that results in a bright image without glare and minimum heating of the specimen by employing both field and an aperture iris diaphragm for illumination.
koehler illumination microscopy evidence
A type of koehler illumination microscopy evidence that is used in a manual assertion.
koehler illumination microscopy evidence used in manual assertion
A type of microscopy evidence that results in visualization of living cells and transparent specimens by taking advantage of differences in the light refraction of different parts of the specimen.
Nomarski interference contrast microscopy
differential interference contrast microscopy evidence
A type of differential interference contrast microscopy evidence that is used in a manual assertion.
differential interference contrast microscopy evidence used in manual assertion
A type of confocal microscopy evidence that results in creation of a continuous confocal multi-colour mosaic from thousands of individually captured images.
extended field laser confocal microscopy evidence
A type of extended field laser confocal microscopy evidence that is used in a manual assertion.
extended field laser confocal microscopy evidence used in manual assertion
A type of confocal microscopy evidence that results in an image that is built up pixel-by-pixel by collecting the emitted photons from the fluorophores in the sample by passing a laser beam through a light source aperture which is then focused by an objective lens into a small area on the surface of the sample.
confocal laser scanning fluorescence microscopy
fluorescence confocal scanning laser microscopy
scanning confocal fluorescence microscopy
confocal laser scanning microscopy evidence
A type of confocal laser scanning microscopy evidence that is used in a manual assertion.
confocal laser scanning microscopy evidence used in manual assertion
A type of direct assay evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight, diffusion and interaction strength by illuminating the sample with a laser beam and the scattered intensity is probed at a certain angle by a detector.
A type of light scattering assay evidence that is used in a manual assertion.
light scattering assay evidence used in manual assertion
A type of light scattering assay evidence derived by analyzing the fluctuations in the internsity of the scattered light by the particles in motion.
A type of dynamic light scattering assay evidence that is used in a manual assertion.
dynamic light scattering assay evidence used in manual assertion
A type of light scattering assay evidence derived by measuring the average intensity of scattered light by the particles at multiple angles.
A type of static light scattering assay evidence that is used in a manual assertion.
static light scattering assay evidence used in manual assertion
A type of mutant phenotype evidence derived from formation of papillae that protrude outwards from the main colony by mutant cells.
A type of colony papillation assay evidence that is used in a manual assertion.
colony papillation assay evidence used in manual assertion
A type of staining evidence that is derived from the use of gentian violet as a general biological stain and an acid-base indicator.
A type of crystal violet staining evidence that is used in a manual assertion.
crystal violet staining evidence used in manual assertion
A type of biofilm formation assay evidence derived from in vitro cultivation and evaluation of bacterial biofilms under hydrodynamic conditions of flow.
A type of flow cell biofilm assay evidence that is used in a manual assertion.
flow cell biofilm assay evidence used in manual assertion
A type of hybrid interaction evidence that involves the detection of protein-protein interaction by fusing the protein target (the "bait") to RNA polymerase and fusing protein or peptide library to be analyzed (the "prey") to DNA-binding domain.
A type of bacterial 2-hybrid assay evidence that is used in a manual assertion.
bacterial 2-hybrid assay evidence used in manual assertion
A type of experimental phenotypic evidence that results from the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors.
A type of phenomic profiling assay evidence that is used in a manual assertion.
phenomic profiling assay evidence used in manual assertion
A type of experimental phenotypic evidence that results from studying the physical characteristics of an assemblage of microorganisms growing on a solid surface such as the surface of an agar culture medium.
A type of colony morphology evidence that is used in a manual assertion.
colony morphology evidence used in manual assertion
A type of colony morphology evidence that results from studying the colony pigmentation.
A type of colony color evidence that is used in a manual assertion.
colony color evidence used in manual assertion
A type of colony morphology evidence that results from studying the size of the colony.
A type of colony size evidence that is used in a manual assertion.
colony size evidence used in manual assertion
A type of cell growth assay evidence resulting from assessing the sensitivity or resistance of bacteria or fungi to an antimicrobial agent or chemical by measuring the size of the zone of inhibition that results when the test organism is grown on a solid surface in the presence of the antimicrobial agent or chemical.
A type of zone of inhibition evidence that is used in a manual assertion.
zone of inhibition evidence used in manual assertion
A type of zone of inhibition evidence resulting from testing the antimicrobial susceptibility by using predefined, continuous, and exponential gradient of antibiotic concentrations immobilized along a rectangular plastic test strip.
A type of Etest evidence that is used in a manual assertion.
A type of expression pattern evidence in which translation is measured by the positions of ribosomes active in a cell, identified through deep sequencing of ribosome-protected mRNA fragments.
A type of ribosome profiling evidence that is used in a manual assertion.
ribosome profiling evidence used in manual assertion
A type of loss-of-function mutant phenotype evidence that is used in a manual assertion.
loss-of-function mutant phenotype evidence used in manual assertion
A type of structural similarity evidence that is used in a manual assertion.
structural similarity evidence used in manual assertion
A type of gain-of-function mutant phenotype evidence that is used in a manual assertion.
gain-of-function mutant phenotype evidence used in manual assertion
A type of voucher specimen analysis evidence that is used in a manual assertion.
voucher specimen analysis evidence used in manual assertion
A type of positional similarity evidence that is used in a manual assertion.
positional similarity evidence used in manual assertion
A type of quantitative trait analysis evidence that is used in a manual assertion.
quantitative trait analysis evidence used in manual assertion
A type of compositional similarity evidence that is used in a manual assertion.
compositional similarity evidence used in manual assertion
A type of developmental similarity evidence that is used in a manual assertion.
developmental similarity evidence used in manual assertion
A type of morphological similarity evidence that is used in a manual assertion.
morphological similarity evidence used in manual assertion
A type of gene expression similarity evidence that is used in a manual assertion.
gene expression similarity evidence used in manual assertion
A type of methylation-specific polymerase chain reaction evidence that is used in a manual assertion.
methylation-specific polymerase chain reaction evidence used in manual assertion
A type of southern hybridization evidence that is used in a manual assertion.
southern hybridization evidence used in manual assertion
A type of intermethylated site amplification evidence that is used in a manual assertion.
intermethylated site amplification evidence used in manual assertion
A type of epitope-tagged protein immunolocalization evidence that is used in a manual assertion.
epitope-tagged protein immunolocalization evidence used in manual assertion
A type of co-fractionation evidence that is used in a manual assertion.
co-fractionation evidence used in manual assertion
A type of green fluorescent protein fusion protein localization evidence that is used in a manual assertion.
green fluorescent protein fusion protein localization evidence used in manual assertion
A type of yellow fluorescent protein fusion protein localization evidence that is used in a manual assertion.
yellow fluorescent protein fusion protein localization evidence used in manual assertion
A type of beta-glucuronidase fusion protein localization evidence that is used in a manual assertion.
beta-glucuronidase fusion protein localization evidence used in manual assertion
A type of beta-galactosidase fusion protein localization evidence that is used in a manual assertion.
beta-galactosidase fusion protein localization evidence used in manual assertion
A type of thin layer chromatography evidence that is used in a manual assertion.
thin layer chromatography evidence used in manual assertion
A type of in vitro recombinant protein transcription reconstitution assay evidence that is used in a manual assertion.
in vitro recombinant protein transcription reconstitution assay evidence used in manual assertion
A type of protein separation followed by direct sequencing evidence that is used in a manual assertion.
protein separation followed by direct sequencing evidence used in manual assertion
A type of protein separation followed by fragment identification evidence that is used in a manual assertion.
protein separation followed by fragment identification evidence used in manual assertion
A type of heterologous system uptake evidence that is used in a manual assertion.
heterologous system uptake evidence used in manual assertion
A type of two-electrode voltage clamp recording evidence that is used in a manual assertion.
two-electrode voltage clamp recording evidence used in manual assertion
A type of biochemical trait analysis evidence that is used in a manual assertion.
biochemical trait analysis evidence used in manual assertion
A type of mutant physiological response evidence that is used in a manual assertion.
mutant physiological response evidence used in manual assertion
A type of mutant visible phenotype evidence that is used in a manual assertion.
mutant visible phenotype evidence used in manual assertion
A type of in vivo assay evidence that is used in a manual assertion.
in vivo assay evidence used in manual assertion
A type of animal model system study evidence that is used in a manual assertion.
animal model system study evidence used in manual assertion
A type of clinical study evidence that is used in a manual assertion.
clinical study evidence used in manual assertion
A type of in vitro assay evidence that is used in a manual assertion.
in vitro assay evidence used in manual assertion
A type of enzyme inhibition evidence that is used in a manual assertion.
enzyme inhibition evidence used in manual assertion
A type of Illumina sequencing evidence that is used in a manual assertion.
Illumina sequencing evidence used in manual assertion
A type of 454 pyrosequencing evidence that is used in a manual assertion.
454 pyrosequencing evidence used in manual assertion
A type of SOLiD sequencing evidence that is used in a manual assertion.
SOLiD sequencing evidence used in manual assertion
A type of chain termination sequencing evidence that is used in a manual assertion.
chain termination sequencing evidence used in manual assertion
A type of chromatin immunoprecipitation-qPCR evidence that is used in a manual assertion.
chromatin immunoprecipitation-qPCR evidence used in manual assertion
A type of 4C evidence that is used in a manual assertion.
circularized chromosome conformation capture evidence used in manual assertion
A type of 5C evidence that is used in a manual assertion.
carbon-copy chromosome conformation capture evidence used in manual assertion
A type of 3C-qPCR evidence that is used in a manual assertion.
chromosome conformation capture-qPCR evidence used in manual assertion
3C-qPCR evidence used in manual assertion
A type of Hi-C evidence that is used in a manual assertion.
A type of 3C-seq evidence that is used in a manual assertion.
chromosome conformation capture sequencing evidence used in manual assertion
3C-seq evidence used in manual assertion
A type of environmental perturbation evidence that is used in a manual assertion.
environmental perturbation evidence used in manual assertion
A type of tissue ablation evidence that is used in a manual assertion.
tissue ablation evidence used in manual assertion
A type of tissue grafting evidence that is used in a manual assertion.
tissue grafting evidence used in manual assertion
A type of cytochalasin experiment evidence that is used in a manual assertion.
cytochalasin experiment evidence used in manual assertion
A type of green fluorescent protein immunolocalization evidence that is used in a manual assertion.
green fluorescent protein immunolocalization evidence used in manual assertion
A type of beta-galactosidase protein immunolocalization evidence that is used in a manual assertion.
beta-galactosidase protein immunolocalization evidence used in manual assertion
A type of cap analysis of gene expression evidence that is used in a manual assertion.
cap analysis of gene expression evidence used in manual assertion
A type of nano-cap analysis of gene expression evidence that is used in a manual assertion.
nano-cap analysis of gene expression evidence used in manual assertion
A type of particle size and count assay evidence that is used in a manual assertion.
particle size and count assay evidence used in manual assertion
A type of competitive growth assay evidence that is used in a manual assertion.
competitive growth assay evidence used in manual assertion
A type of pulsed-field gel electrophoresis evidence that is used in a manual assertion.
pulsed-field gel electrophoresis evidence used in manual assertion
A type of two-dimensional agarose gel electrophoresis evidence that is used in a manual assertion.
two-dimensional agarose gel electrophoresis evidence used in manual assertion
A type of plasmid maintenance assay evidence that is used in a manual assertion.
plasmid maintenance assay evidence used in manual assertion
A type of specific protein inhibition by antibody evidence that is used in a manual assertion.
specific protein inhibition by antibody evidence used in manual assertion
A type of single exon transcript confirmation via alignment evidence that is used in a manual assertion.
single exon transcript confirmation via alignment evidence used in manual assertion
A type of phylogenetic distribution evidence that is used in a manual assertion.
phylogenetic distribution evidence used in manual assertion
A type of differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) that is used in a manual assertion.
differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) used in manual assertion
A type of differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) that is used in a manual assertion.
differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) used in manual assertion
A type of biological target-disease association via drug that is used in a manual assertion.
biological target-disease association via drug used in manual assertion
A type of cell staining evidence that is used in a manual assertion.
cell staining evidence used in manual assertion
A type of visual sequence inspection evidence that is used in a manual assertion.
visual sequence inspection evidence used in manual assertion
A type of ATP bioluminescence assay evidence that is used in a manual assertion.
ATP bioluminescence assay evidence used in manual assertion
A type of missense mutation evidence that is used in a manual assertion.
missense mutation evidence used in manual assertion
A type of nonsense mutation evidence that is used in a manual assertion.
nonsense mutation evidence used in manual assertion
A type of silent mutation evidence that is used in a manual assertion.
silent mutation evidence used in manual assertion
A type of insertion mutation evidence that is used in a manual assertion.
insertion mutation evidence used in manual assertion
A type of duplication mutation evidence that is used in a manual assertion.
duplication mutation evidence used in manual assertion
A type of frameshift mutation evidence that is used in a manual assertion.
frameshift mutation evidence used in manual assertion
A type of repeat expansion mutation evidence that is used in a manual assertion.
repeat expansion mutation evidence used in manual assertion
A type of splice site mutation evidence that is used in a manual assertion.
splice site mutation evidence used in manual assertion
A type of translocation mutation evidence that is used in a manual assertion.
translocation mutation evidence used in manual assertion
A type of in-gel protein kinase assay evidence that is used in a manual assertion.
in-gel protein kinase assay evidence used in manual assertion
A type of macroscopic current trace evidence that is used in a manual assertion.
macroscopic current trace evidence used in manual assertion
A type of current density evidence that is used in a manual assertion.
current density evidence used in manual assertion
A type of sustained current evidence that is used in a manual assertion.
sustained current evidence used in manual assertion
A type of use dependence of inactivation evidence that is used in a manual assertion.
use dependence of inactivation evidence used in manual assertion
A type of current clamp recording evidence that is used in a manual assertion.
current clamp recording evidence used in manual assertion
A type of whole-cell voltage clamp recording evidence that is used in a manual assertion.
whole-cell voltage clamp recording evidence used in manual assertion
A type of cell-attached single-channel recording evidence that is used in a manual assertion.
cell-attached single-channel recording evidence used in manual assertion
A type of cell-detached inside-out single-channel recording evidence that is used in a manual assertion.
cell-detached inside-out single-channel recording evidence used in manual assertion
A type of reconstituted bilayer single-channel patch recording evidence that is used in a manual assertion.
reconstituted bilayer single-channel patch recording evidence used in manual assertion
A type of electroencephalography recording evidence that is used in a manual assertion.
electroencephalography recording evidence used in manual assertion
A type of cell-detached outside-out single-channel recording evidence that is used in a manual assertion.
cell-detached outside-out single-channel recording evidence used in manual assertion
A type of cut-open oocyte voltage clamp recording evidence that is used in a manual assertion.
cut-open oocyte voltage clamp recording evidence used in manual assertion
A type of macropatch voltage clamp recording evidence that is used in a manual assertion.
macropatch voltage clamp recording evidence used in manual assertion
A type of protein expression level evidence based on western blot that is used in a manual assertion.
protein expression level evidence based on western blot used in manual assertion
A type of protein mass spectrometry evidence that is used in a manual assertion.
protein mass spectrometry evidence used in manual assertion
A type of cross-streak test evidence that is used in a manual assertion.
cross-streak test evidence used in manual assertion
A type of tethered cell assay evidence that is used in a manual assertion.
tethered cell assay evidence used in manual assertion
A type of tumble frequency assay evidence that is used in a manual assertion.
tumble frequency assay evidence used in manual assertion
A type of capillary assay evidence that is used in a manual assertion.
capillary assay evidence used in manual assertion
A type of inference from experimental data evidence that is used in a manual assertion.
inference from experimental data evidence used in manual assertion
A type of inference from phenotype manipulation evidence that is used in a manual assertion.
inference from phenotype manipulation evidence used in manual assertion
A type of inference by association of genotype from phenotype that is used in a manual assertion.
inference by association of genotype from phenotype used in manual assertion
A type of motility assay evidence that is used in a manual assertion.
motility assay evidence used in manual assertion
A type of loss-of-function mutant phenotype evidence that is used in an automatic assertion.
loss-of-function mutant phenotype evidence used in automatic assertion
A type of structural similarity evidence that is used in an automatic assertion.
structural similarity evidence used in automatic assertion
A type of gain-of-function mutant phenotype evidence that is used in an automatic assertion.
gain-of-function mutant phenotype evidence used in automatic assertion
A type of voucher specimen analysis evidence that is used in an automatic assertion.
voucher specimen analysis evidence used in automatic assertion
A type of positional similarity evidence that is used in an automatic assertion.
positional similarity evidence used in automatic assertion
A type of quantitative trait analysis evidence that is used in an automatic assertion.
quantitative trait analysis evidence used in automatic assertion
A type of compositional similarity evidence that is used in an automatic assertion.
compositional similarity evidence used in automatic assertion
A type of developmental similarity evidence that is used in an automatic assertion.
developmental similarity evidence used in automatic assertion
A type of morphological similarity evidence that is used in an automatic assertion.
morphological similarity evidence used in automatic assertion
A type of gene expression similarity evidence that is used in an automatic assertion.
gene expression similarity evidence used in automatic assertion
A type of methylation-specific polymerase chain reaction evidence that is used in an automatic assertion.
methylation-specific polymerase chain reaction evidence used in automatic assertion
A type of southern hybridization evidence that is used in an automatic assertion.
southern hybridization evidence used in automatic assertion
A type of intermethylated site amplification evidence that is used in an automatic assertion.
intermethylated site amplification evidence used in automatic assertion
A type of epitope-tagged protein immunolocalization evidence that is used in an automatic assertion.
epitope-tagged protein immunolocalization evidence used in automatic assertion
A type of co-fractionation evidence that is used in an automatic assertion.
co-fractionation evidence used in automatic assertion
A type of green fluorescent protein fusion protein localization evidence that is used in an automatic assertion.
green fluorescent protein fusion protein localization evidence used in automatic assertion
A type of yellow fluorescent protein fusion protein localization evidence that is used in an automatic assertion.
yellow fluorescent protein fusion protein localization evidence used in automatic assertion
A type of beta-glucuronidase fusion protein localization evidence that is used in an automatic assertion.
beta-glucuronidase fusion protein localization evidence used in automatic assertion
A type of beta-galactosidase fusion protein localization evidence that is used in an automatic assertion.
beta-galactosidase fusion protein localization evidence used in automatic assertion
A type of thin layer chromatography evidence that is used in an automatic assertion.
thin layer chromatography evidence used in automatic assertion
A type of in vitro recombinant protein transcription reconstitution assay evidence that is used in an automatic assertion.
in vitro recombinant protein transcription reconstitution assay evidence used in automatic assertion
A type of protein separation followed by direct sequencing evidence that is used in an automatic assertion.
protein separation followed by direct sequencing evidence used in automatic assertion
A type of protein separation followed by fragment identification evidence that is used in an automatic assertion.
protein separation followed by fragment identification evidence used in automatic assertion
A type of heterologous system uptake evidence that is used in an automatic assertion.
heterologous system uptake evidence used in automatic assertion
A type of two-electrode voltage clamp recording evidence that is used in an automatic assertion.
two-electrode voltage clamp recording evidence used in automatic assertion
A type of biochemical trait analysis evidence that is used in an automatic assertion.
biochemical trait analysis evidence used in automatic assertion
A type of mutant physiological response evidence that is used in an automatic assertion.
mutant physiological response evidence used in automatic assertion
A type of mutant visible phenotype evidence that is used in an automatic assertion.
mutant visible phenotype evidence used in automatic assertion
A type of in vivo assay evidence that is used in an automatic assertion.
in vivo assay evidence used in automatic assertion
A type of animal model system study evidence that is used in an automatic assertion.
animal model system study evidence used in automatic assertion
A type of clinical study evidence that is used in an automatic assertion.
clinical study evidence used in automatic assertion
A type of in vitro assay evidence that is used in an automatic assertion.
in vitro assay evidence used in automatic assertion
A type of enzyme inhibition evidence that is used in an automatic assertion.
enzyme inhibition evidence used in automatic assertion
A type of Illumina sequencing evidence that is used in an automatic assertion.
Illumina sequencing evidence used in automatic assertion
A type of 454 pyrosequencing evidence that is used in an automatic assertion.
454 pyrosequencing evidence used in automatic assertion
A type of SOLiD sequencing evidence that is used in an automatic assertion.
SOLiD sequencing evidence used in automatic assertion
A type of chain termination sequencing evidence that is used in an automatic assertion.
chain termination sequencing evidence used in automatic assertion
A type of chromatin immunoprecipitation-qPCR evidence that is used in an automatic assertion.
chromatin immunoprecipitation-qPCR evidence used in automatic assertion
A type of 4C evidence that is used in an automatic assertion.
circularized chromosome conformation capture evidence used in automatic assertion
A type of 5C evidence that is used in an automatic assertion.
carbon-copy chromosome conformation capture evidence used in automatic assertion
A type of 3C-qPCR evidence that is used in an automatic assertion.
chromosome conformation capture-qPCR evidence used in automatic assertion
3C-qPCR evidence used in automatic assertion
A type of Hi-C evidence that is used in an automatic assertion.
Hi-C evidence used in automatic assertion
A type of 3C-seq evidence that is used in an automatic assertion.
chromosome conformation capture sequencing evidence used in automatic assertion
3C-seq evidence used in automatic assertion
A type of environmental perturbation evidence that is used in an automatic assertion.
environmental perturbation evidence used in automatic assertion
A type of tissue ablation evidence that is used in an automatic assertion.
tissue ablation evidence used in automatic assertion
A type of tissue grafting evidence that is used in an automatic assertion.
tissue grafting evidence used in automatic assertion
A type of cytochalasin experiment evidence that is used in an automatic assertion.
cytochalasin experiment evidence used in automatic assertion
A type of green fluorescent protein immunolocalization evidence that is used in an automatic assertion.
green fluorescent protein immunolocalization evidence used in automatic assertion
A type of beta-galactosidase protein immunolocalization evidence that is used in an automatic assertion.
beta-galactosidase protein immunolocalization evidence used in automatic assertion
A type of cap analysis of gene expression evidence that is used in an automatic assertion.
cap analysis of gene expression evidence used in automatic assertion
A type of nano-cap analysis of gene expression evidence that is used in an automatic assertion.
nano-cap analysis of gene expression evidence used in automatic assertion
A type of particle size and count assay evidence that is used in an automatic assertion.
particle size and count assay evidence used in automatic assertion
A type of competitive growth assay evidence that is used in an automatic assertion.
competitive growth assay evidence used in automatic assertion
A type of pulsed-field gel electrophoresis evidence that is used in an automatic assertion.
pulsed-field gel electrophoresis evidence used in automatic assertion
A type of two-dimensional agarose gel electrophoresis evidence that is used in an automatic assertion.
two-dimensional agarose gel electrophoresis evidence used in automatic assertion
A type of plasmid maintenance assay evidence that is used in an automatic assertion.
plasmid maintenance assay evidence used in automatic assertion
A type of specific protein inhibition by antibody evidence that is used in an automatic assertion.
specific protein inhibition by antibody evidence used in automatic assertion
A type of single exon transcript confirmation via alignment evidence that is used in an automatic assertion.
single exon transcript confirmation via alignment evidence used in automatic assertion
A type of phylogenetic distribution evidence that is used in an automatic assertion.
phylogenetic distribution evidence used in automatic assertion
A type of differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) that is used in an automatic assertion.
differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) used in automatic assertion
A type of differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) that is used in an automatic assertion.
differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) used in automatic assertion
A type of biological target-disease association via drug that is used in an automatic assertion.
biological target-disease association via drug used in automatic assertion
A type of cell staining evidence that is used in an automatic assertion.
cell staining evidence used in automatic assertion
A type of visual sequence inspection evidence that is used in an automatic assertion.
visual sequence inspection evidence used in automatic assertion
A type of ATP bioluminescence assay evidence that is used in an automatic assertion.
ATP bioluminescence assay evidence used in automatic assertion
A type of missense mutation evidence that is used in an automatic assertion.
missense mutation evidence used in automatic assertion
A type of nonsense mutation evidence that is used in an automatic assertion.
nonsense mutation evidence used in automatic assertion
A type of silent mutation evidence that is used in an automatic assertion.
silent mutation evidence used in automatic assertion
A type of insertion mutation evidence that is used in an automatic assertion.
insertion mutation evidence used in automatic assertion
A type of duplication mutation evidence that is used in an automatic assertion.
duplication mutation evidence used in automatic assertion
A type of frameshift mutation evidence that is used in an automatic assertion.
frameshift mutation evidence used in automatic assertion
A type of repeat expansion mutation evidence that is used in an automatic assertion.
repeat expansion mutation evidence used in automatic assertion
A type of splice site mutation evidence that is used in an automatic assertion.
splice site mutation evidence used in automatic assertion
A type of translocation mutation evidence that is used in an automatic assertion.
translocation mutation evidence used in automatic assertion
A type of in-gel protein kinase assay evidence that is used in an automatic assertion.
in-gel protein kinase assay evidence used in automatic assertion
A type of macroscopic current trace evidence that is used in an automatic assertion.
macroscopic current trace evidence used in automatic assertion
A type of current density evidence that is used in an automatic assertion.
current density evidence used in automatic assertion
A type of sustained current evidence that is used in an automatic assertion.
sustained current evidence used in automatic assertion
A type of use dependence of inactivation evidence that is used in an automatic assertion.
use dependence of inactivation evidence used in automatic assertion
A type of current clamp recording evidence that is used in an automatic assertion.
current clamp recording evidence used in automatic assertion
A type of whole-cell voltage clamp recording evidence that is used in an automatic assertion.
whole-cell voltage clamp recording evidence used in automatic assertion
A type of cell-attached single-channel recording evidence that is used in an automatic assertion.
cell-attached single-channel recording evidence used in automatic assertion
A type of cell-detached inside-out single-channel recording evidence that is used in an automatic assertion.
cell-detached inside-out single-channel recording evidence used in automatic assertion
A type of reconstituted bilayer single-channel patch recording evidence that is used in an automatic assertion.
reconstituted bilayer single-channel patch recording evidence used in automatic assertion
A type of electroencephalography recording evidence that is used in an automatic assertion.
electroencephalography recording evidence used in automatic assertion
A type of cell-detached outside-out single-channel recording evidence that is used in an automatic assertion.
cell-detached outside-out single-channel recording evidence used in automatic assertion
A type of cut-open oocyte voltage clamp recording evidence that is used in an automatic assertion.
cut-open oocyte voltage clamp recording evidence used in automatic assertion
A type of macropatch voltage clamp recording evidence that is used in an automatic assertion.
macropatch voltage clamp recording evidence used in automatic assertion
A type of protein expression level evidence based on western blot that is used in an automatic assertion.
protein expression level evidence based on western blot used in automatic assertion
A type of protein mass spectrometry evidence that is used in an automatic assertion.
protein mass spectrometry evidence used in automatic assertion
A type of cross-streak test evidence that is used in an automatic assertion.
cross-streak test evidence used in automatic assertion
A type of tethered cell assay evidence that is used in an automatic assertion.
tethered cell assay evidence used in automatic assertion
A type of tumble frequency assay evidence that is used in an automatic assertion.
tumble frequency assay evidence used in automatic assertion
A type of capillary assay evidence that is used in an automatic assertion.
capillary assay evidence used in automatic assertion
A type of inference from experimental data evidence that is used in an automatic assertion.
inference from experimental data evidence used in automatic assertion
A type of inference from phenotype manipulation evidence that is used in an automatic assertion.
inference from phenotype manipulation evidence used in automatic assertion
A type of inference by association of genotype from phenotype that is used in an automatic assertion.
inference by association of genotype from phenotype used in automatic assertion
A type of motility assay evidence that is used in an automatic assertion.
motility assay evidence used in automatic assertion
A type of experimental evidence that is used in an automatic assertion.
experimental evidence used in automatic assertion
A type of expression pattern evidence that is used in an automatic assertion.
expression pattern evidence used in automatic assertion
A type of Affymetrix GeneChip evidence that is used in an automatic assertion.
Affymetrix GeneChip evidence used in automatic assertion
A type of cRNA to DNA expression microarray evidence that is used in an automatic assertion.
cRNA to DNA expression microarray evidence used in automatic assertion
A type of expression microarray evidence that is used in an automatic assertion.
expression microarray evidence used in automatic assertion
A type of differential methylation hybridization evidence that is used in an automatic assertion.
differential methylation hybridization evidence used in automatic assertion
A type of transcript expression evidence that is used in an automatic assertion.
transcript expression evidence used in automatic assertion
A type of Nimblegen array evidence that is used in an automatic assertion.
Nimblegen array evidence used in automatic assertion
A type of array-based sequence capture evidence that is used in an automatic assertion.
array-based sequence capture evidence used in automatic assertion
A type of western blot evidence that is used in an automatic assertion.
western blot evidence used in automatic assertion
A type of direct assay evidence that is used in an automatic assertion.
direct assay evidence used in automatic assertion
A type of protein expression level evidence that is used in an automatic assertion.
protein expression level evidence used in automatic assertion
A type of protein expression evidence that is used in an automatic assertion.
protein expression evidence used in automatic assertion
A type of expression library screen evidence that is used in an automatic assertion.
expression library screen evidence used in automatic assertion
A type of heterologous protein expression evidence that is used in an automatic assertion.
heterologous protein expression evidence used in automatic assertion
A type of spatial pattern of protein expression evidence that is used in an automatic assertion.
spatial pattern of protein expression evidence used in automatic assertion
A type of DNA to cDNA expression microarray evidence that is used in an automatic assertion.
DNA to cDNA expression microarray evidence used in automatic assertion
A type of differential hybridization evidence that is used in an automatic assertion.
differential hybridization evidence used in automatic assertion
A type of RNA protection assay evidence that is used in an automatic assertion.
RNA protection assay evidence used in automatic assertion
A type of nuclease protection assay evidence that is used in an automatic assertion.
nuclease protection assay evidence used in automatic assertion
A type of spatial pattern of transcript expression evidence that is used in an automatic assertion.
spatial pattern of transcript expression evidence used in automatic assertion
A type of subtractive hybridization evidence that is used in an automatic assertion.
subtractive hybridization evidence used in automatic assertion
A type of author statement that is used in an automatic assertion.
author statement used in automatic assertion
A type of author statement without traceable support that is used in an automatic assertion.
non-traceable author statement used in automatic assertion
author statement without traceable support used in automatic assertion
A type of author statement supported by traceable reference that is used in an automatic assertion.
traceable author statement used in automatic assertion
author statement supported by traceable reference used in automatic assertion
A type of curator inference that is used in an automatic assertion.
curator inference used in automatic assertion
A type of inference from background scientific knowledge that is used in an automatic assertion.
inference from background scientific knowledge used in automatic assertion
A type of no biological data found that is used in an automatic assertion.
no biological data found used in automatic assertion
A type of mutant phenotype evidence that is used in an automatic assertion.
mutant phenotype evidence used in automatic assertion
A type of genetic interaction evidence that is used in an automatic assertion.
genetic interaction evidence used in automatic assertion
A type of genomic context evidence that is used in an automatic assertion.
genomic context evidence used in automatic assertion
A type of biological aspect of ancestor evidence that is used in an automatic assertion.
biological aspect of ancestor evidence used in automatic assertion
A type of biological aspect of descendant evidence that is used in an automatic assertion.
biological aspect of descendant evidence used in automatic assertion
A type of phylogenetic determination of loss of key residues evidence that is used in an automatic assertion.
phylogenetic determination of loss of key residues evidence used in automatic assertion
A type of rapid divergence from ancestral sequence evidence that is used in an automatic assertion.
rapid divergence from ancestral sequence evidence used in automatic assertion
A type of physical interaction evidence that is used in an automatic assertion.
physical interaction evidence used in automatic assertion
A type of gene neighbors evidence that is used in an automatic assertion.
gene neighbors evidence used in automatic assertion
A type of Edman degradation evidence that is used in an automatic assertion.
Edman degradation evidence used in automatic assertion
A type of 3D cell culture evidence that is used in an automatic assertion.
3D cell culture evidence used in automatic assertion
A type of 51Cr release assay evidence that is used in an automatic assertion.
51Cr release assay evidence used in automatic assertion
A type of 7-aminoactinomycin staining evidence that is used in an automatic assertion.
7-aminoactinomycin staining evidence used in automatic assertion
A type of [3H]-thymidine incorporation assay evidence that is used in an automatic assertion.
[3H]-thymidine incorporation assay evidence used in automatic assertion
A type of [3H]arachidonic acid release assay evidence that is used in an automatic assertion.
[3H]arachidonic acid release assay evidence used in automatic assertion
A type of adhesion assay evidence that is used in an automatic assertion.
adhesion assay evidence used in automatic assertion
A type of adoptive cell transfer evidence that is used in an automatic assertion.
adoptive cell transfer evidence used in automatic assertion
A type of alamarBlue assay evidence that is used in an automatic assertion.
alamarBlue assay evidence used in automatic assertion
A type of allograft transplantation experiment evidence that is used in an automatic assertion.
allograft transplantation experiment evidence used in automatic assertion
A type of anion-exchange chromatography evidence that is used in an automatic assertion.
anion-exchange chromatography evidence used in automatic assertion
A type of annexin-V staining evidence that is used in an automatic assertion.
annexin-V staining evidence used in automatic assertion
A type of behavioral assay evidence that is used in an automatic assertion.
behavioral assay evidence used in automatic assertion
A type of blocking monoclonal antibody evidence that is used in an automatic assertion.
blocking monoclonal antibody evidence used in automatic assertion
A type of immunological assay evidence that is used in an automatic assertion.
immunological assay evidence used in automatic assertion
A type of blocking peptide evidence that is used in an automatic assertion.
blocking peptide evidence used in automatic assertion
A type of blocking polyclonal antibody evidence that is used in an automatic assertion.
blocking polyclonal antibody evidence used in automatic assertion
A type of blood test evidence that is used in an automatic assertion.
blood test evidence used in automatic assertion
A type of Boyden chamber assay evidence that is used in an automatic assertion.
Boyden chamber assay evidence used in automatic assertion
A type of bromodeoxyuridine incorporation assay evidence that is used in an automatic assertion.
bromodeoxyuridine incorporation assay evidence used in automatic assertion
A type of nucleotide analog incorporation assay evidence that is used in an automatic assertion.
nucleotide analog incorporation assay evidence used in automatic assertion
A type of caspase assay evidence that is used in an automatic assertion.
caspase assay evidence used in automatic assertion
A type of cell counting evidence that is used in an automatic assertion.
cell counting evidence used in automatic assertion
A type of cell permeability assay evidence that is used in an automatic assertion.
cell permeability assay evidence used in automatic assertion
A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in an automatic assertion.
carboxyfluorescein diacetate succinimidyl ester staining evidence used in automatic assertion
A type of chemiluminescence-linked immunoassay evidence that is used in an automatic assertion.
chemiluminescence-linked immunoassay evidence used in automatic assertion
A type of chimeric protein evidence that is used in an automatic assertion.
chimeric protein evidence used in automatic assertion
A type of co-electrophoresis evidence that is used in an automatic assertion.
co-electrophoresis evidence used in automatic assertion
A type of co-localization evidence that is used in an automatic assertion.
co-localization evidence used in automatic assertion
A type of imaging assay evidence that is used in an automatic assertion.
imaging assay evidence used in automatic assertion
A type of co-sedimentation assay evidence that is used in an automatic assertion.
co-sedimentation assay evidence used in automatic assertion
A type of colony counting evidence that is used in an automatic assertion.
colony counting evidence used in automatic assertion
A type of comet assay evidence that is used in an automatic assertion.
comet assay evidence used in automatic assertion
A type of conditional knockin evidence that is used in an automatic assertion.
conditional knockin evidence used in automatic assertion
A type of knockin evidence that is used in an automatic assertion.
knockin evidence used in automatic assertion
A type of conditional knockout evidence that is used in an automatic assertion.
conditional knockout evidence used in automatic assertion
A type of knockout evidence that is used in an automatic assertion.
knockout evidence used in automatic assertion
A type of constitutively active mutant evidence that is used in an automatic assertion.
constitutively active mutant evidence used in automatic assertion
A type of cross-linking evidence that is used in an automatic assertion.
cross-linking evidence used in automatic assertion
A type of protein binding evidence that is used in an automatic assertion.
protein binding evidence used in automatic assertion
A type of crystallography evidence that is used in an automatic assertion.
crystallography evidence used in automatic assertion
A type of cytochemistry evidence that is used in an automatic assertion.
cytochemistry evidence used in automatic assertion
A type of histochemistry evidence that is used in an automatic assertion.
histochemistry evidence used in automatic assertion
A type of cytochrome C release assay evidence that is used in an automatic assertion.
cytochrome C release assay evidence used in automatic assertion
A type of 4',6-diamidino-2-phenylindole staining evidence that is used in an automatic assertion.
4',6-diamidino-2-phenylindole staining evidence used in automatic assertion
A type of deletion mutation evidence that is used in an automatic assertion.
deletion mutation evidence used in automatic assertion
A type of DNA laddering assay evidence that is used in an automatic assertion.
DNA laddering assay evidence used in automatic assertion
A type of RNA dot blot assay evidence that is used in an automatic assertion.
RNA dot blot assay evidence used in automatic assertion
A type of dominant-negative mutant evidence that is used in an automatic assertion.
dominant-negative mutant evidence used in automatic assertion
A type of eTag assay evidence that is used in an automatic assertion.
eTag assay evidence used in automatic assertion
A type of affinity evidence that is used in an automatic assertion.
affinity evidence used in automatic assertion
A type of filter binding assay evidence that is used in an automatic assertion.
filter binding assay evidence used in automatic assertion
A type of fluorescence in situ hybridization evidence that is used in an automatic assertion.
fluorescence in situ hybridization evidence used in automatic assertion
A type of fluorescence resonance energy transfer evidence that is used in an automatic assertion.
fluorescence resonance energy transfer evidence used in automatic assertion
A type of gel-filtration evidence that is used in an automatic assertion.
gel-filtration evidence used in automatic assertion
A type of histology evidence that is used in an automatic assertion.
histology evidence used in automatic assertion
A type of immunocytochemistry evidence that is used in an automatic assertion.
immunocytochemistry evidence used in automatic assertion
A type of immunodepletion evidence that is used in an automatic assertion.
immunodepletion evidence used in automatic assertion
A type of immunohistochemistry evidence that is used in an automatic assertion.
immunohistochemistry evidence used in automatic assertion
A type of in vitro acetylation assay evidence that is used in an automatic assertion.
in vitro acetylation assay evidence used in automatic assertion
A type of in vitro cleavage assay evidence that is used in an automatic assertion.
in vitro cleavage assay evidence used in automatic assertion
A type of in vitro deacetylation assay evidence that is used in an automatic assertion.
in vitro deacetylation assay evidence used in automatic assertion
A type of in vitro defarnesylation assay evidence that is used in an automatic assertion.
in vitro defarnesylation assay evidence used in automatic assertion
A type of in vitro demethylation assay evidence that is used in an automatic assertion.
in vitro demethylation assay evidence used in automatic assertion
A type of in vitro desumoylation assay evidence that is used in an automatic assertion.
in vitro desumoylation assay evidence used in automatic assertion
A type of in vitro deubiquitination assay evidence that is used in an automatic assertion.
in vitro deubiquitination assay evidence used in automatic assertion
A type of in vitro farnesylation assay evidence that is used in an automatic assertion.
in vitro farnesylation assay evidence used in automatic assertion
A type of in vitro methylation assay evidence that is used in an automatic assertion.
in vitro methylation assay evidence used in automatic assertion
A type of in vitro palmitoylation assay evidence that is used in an automatic assertion.
in vitro palmitoylation assay evidence used in automatic assertion
A type of in vitro phosphatase assay evidence that is used in an automatic assertion.
in vitro phosphatase assay evidence used in automatic assertion
A type of in vitro polyADP-ribosylation assay evidence that is used in an automatic assertion.
in vitro polyADP-ribosylation assay evidence used in automatic assertion
A type of in vitro protein kinase assay evidence that is used in an automatic assertion.
in vitro protein kinase assay evidence used in automatic assertion
A type of in vitro sumoylation assay evidence that is used in an automatic assertion.
in vitro sumoylation assay evidence used in automatic assertion
A type of in vitro transcription assay evidence that is used in an automatic assertion.
in vitro transcription assay evidence used in automatic assertion
A type of in vitro translation assay evidence that is used in an automatic assertion.
in vitro translation assay evidence used in automatic assertion
A type of in vitro ubiquitination assay evidence that is used in an automatic assertion.
in vitro ubiquitination assay evidence used in automatic assertion
A type of in vivo acetylation assay evidence that is used in an automatic assertion.
in vivo acetylation assay evidence used in automatic assertion
A type of in vivo cleavage assay evidence that is used in an automatic assertion.
in vivo cleavage assay evidence used in automatic assertion
A type of in vivo deacetylation assay evidence that is used in an automatic assertion.
in vivo deacetylation assay evidence used in automatic assertion
A type of in vivo defarnesylation assay evidence that is used in an automatic assertion.
in vivo defarnesylation assay evidence used in automatic assertion
A type of in vivo demethylation assay evidence that is used in an automatic assertion.
in vivo demethylation assay evidence used in automatic assertion
A type of in vivo desumoylation assay evidence that is used in an automatic assertion.
in vivo desumoylation assay evidence used in automatic assertion
A type of in vivo deubiquitination assay evidence that is used in an automatic assertion.
in vivo deubiquitination assay evidence used in automatic assertion
A type of in vivo farnesylation assay evidence that is used in an automatic assertion.
in vivo farnesylation assay evidence used in automatic assertion
A type of in vivo methylation assay evidence that is used in an automatic assertion.
in vivo methylation assay evidence used in automatic assertion
A type of in vivo palmitoylation assay evidence that is used in an automatic assertion.
in vivo palmitoylation assay evidence used in automatic assertion
A type of in vivo phosphatase assay evidence that is used in an automatic assertion.
in vivo phosphatase assay evidence used in automatic assertion
A type of in vivo protein kinase assay evidence that is used in an automatic assertion.
in vivo protein kinase assay evidence used in automatic assertion
A type of in vivo sumoylation assay evidence that is used in an automatic assertion.
in vivo sumoylation assay evidence used in automatic assertion
A type of in vivo transcription assay evidence that is used in an automatic assertion.
in vivo transcription assay evidence used in automatic assertion
A type of in vivo translation assay evidence that is used in an automatic assertion.
in vivo translation assay evidence used in automatic assertion
A type of in vivo ubiquitination assay evidence that is used in an automatic assertion.
in vivo ubiquitination assay evidence used in automatic assertion
A type of induced mutation evidence that is used in an automatic assertion.
induced mutation evidence used in automatic assertion
A type of genetic transformation evidence that is used in an automatic assertion.
genetic transformation evidence used in automatic assertion
A type of lipid binding assay evidence that is used in an automatic assertion.
lipid binding assay evidence used in automatic assertion
A type of luminescence-based mammalian interactome mapping assay evidence that is used in an automatic assertion.
luminescence-based mammalian interactome mapping assay evidence used in automatic assertion
A type of macroscopy evidence that is used in an automatic assertion.
macroscopy evidence used in automatic assertion
A type of mammalian 2-hybrid assay evidence that is used in an automatic assertion.
mammalian 2-hybrid assay evidence used in automatic assertion
A type of hybrid interaction evidence that is used in an automatic assertion.
hybrid interaction evidence used in automatic assertion
A type of mass spectrometry evidence that is used in an automatic assertion.
mass spectrometry evidence used in automatic assertion
A type of medical imaging evidence that is used in an automatic assertion.
medical imaging evidence used in automatic assertion
A type of microscopy evidence that is used in an automatic assertion.
microscopy evidence used in automatic assertion
A type of motility wound healing assay evidence that is used in an automatic assertion.
motility wound healing assay evidence used in automatic assertion
A type of MTS assay evidence that is used in an automatic assertion.
MTS assay evidence used in automatic assertion
A type of MTT assay evidence that is used in an automatic assertion.
MTT assay evidence used in automatic assertion
A type of multiplex bead-based immunoassay evidence that is used in an automatic assertion.
multiplex bead-based immunoassay evidence used in automatic assertion
A type of natural variation mutant evidence that is used in an automatic assertion.
natural variation mutant evidence used in automatic assertion
A type of nuclear magnetic resonance spectroscopy evidence that is used in an automatic assertion.
nuclear magnetic resonance spectroscopy evidence used in automatic assertion
A type of nuclear fragmentation evidence that is used in an automatic assertion.
nuclear fragmentation evidence used in automatic assertion
A type of phage display evidence that is used in an automatic assertion.
phage display evidence used in automatic assertion
A type of phosphoamino acid analysis evidence that is used in an automatic assertion.
phosphoamino acid analysis evidence used in automatic assertion
A type of peptide affinity enrichment evidence that is used in an automatic assertion.
peptide affinity enrichment evidence used in automatic assertion
A type of peptide array evidence that is used in an automatic assertion.
peptide array evidence used in automatic assertion
A type of physical examination evidence that is used in an automatic assertion.
physical examination evidence used in automatic assertion
A type of point mutation evidence that is used in an automatic assertion.
point mutation evidence used in automatic assertion
A type of propidium iodide staining evidence that is used in an automatic assertion.
propidium iodide staining evidence used in automatic assertion
A type of fluorescence evidence that is used in an automatic assertion.
fluorescence evidence used in automatic assertion
A type of protein dot blot assay evidence that is used in an automatic assertion.
protein dot blot assay evidence used in automatic assertion
A type of protein microarray evidence that is used in an automatic assertion.
protein microarray evidence used in automatic assertion
A type of protein sequencing assay evidence that is used in an automatic assertion.
protein sequencing assay evidence used in automatic assertion
A type of quantitative mass spectrometry evidence that is used in an automatic assertion.
quantitative mass spectrometry evidence used in automatic assertion
A type of radioisotope assay evidence that is used in an automatic assertion.
radioisotope assay evidence used in automatic assertion
A type of radioimmunoassay evidence that is used in an automatic assertion.
radioimmunoassay evidence used in automatic assertion
A type of restriction fragment detection evidence that is used in an automatic assertion.
restriction fragment detection evidence used in automatic assertion
A type of spectrophotometry evidence that is used in an automatic assertion.
spectrophotometry evidence used in automatic assertion
A type of syngeneic transplantation experiment evidence that is used in an automatic assertion.
syngeneic transplantation experiment evidence used in automatic assertion
A type of xenotransplantation experiment evidence that is used in an automatic assertion.
xenotransplantation experiment evidence used in automatic assertion
A type of WST-1 assay evidence that is used in an automatic assertion.
WST-1 assay evidence used in automatic assertion
A type of urine test evidence that is used in an automatic assertion.
urine test evidence used in automatic assertion
A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence that is used in an automatic assertion.
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in automatic assertion
A type of tryptic phosphopeptide mapping assay evidence that is used in an automatic assertion.
tryptic phosphopeptide mapping assay evidence used in automatic assertion
A type of transgenic organism evidence that is used in an automatic assertion.
transgenic organism evidence used in automatic assertion
A type of tissue microarray evidence that is used in an automatic assertion.
tissue microarray evidence used in automatic assertion
A type of TACE activity assay evidence that is used in an automatic assertion.
TACE activity assay evidence used in automatic assertion
A type of enzyme assay evidence that is used in an automatic assertion.
enzyme assay evidence used in automatic assertion
A type of surface plasmon resonance evidence that is used in an automatic assertion.
surface plasmon resonance evidence used in automatic assertion
A type of restriction landmark genomic scanning evidence that is used in an automatic assertion.
restriction landmark genomic scanning evidence used in automatic assertion
A type of resonant mirror biosensor evidence that is used in an automatic assertion.
resonant mirror biosensor evidence used in automatic assertion
A type of high-performance liquid chromatography evidence that is used in an automatic assertion.
high-performance liquid chromatography evidence used in automatic assertion
A type of ectopic expression evidence that is used in an automatic assertion.
ectopic expression evidence used in automatic assertion
A type of electrophoretic mobility shift assay evidence that is used in an automatic assertion.
electrophoretic mobility shift assay evidence used in automatic assertion
A type of reverse transcription polymerase chain reaction evidence that is used in an automatic assertion.
reverse transcription polymerase chain reaction evidence used in automatic assertion
A type of in vivo polyADP-ribosylation assay evidence that is used in an automatic assertion.
in vivo polyADP-ribosylation assay evidence used in automatic assertion
A type of DNA dot blot assay evidence that is used in an automatic assertion.
DNA dot blot assay evidence used in automatic assertion
A type of random mutagenesis evidence that is used in an automatic assertion.
random mutagenesis evidence used in automatic assertion
A type of biological system reconstruction evidence by experimental evidence from single species that is used in an automatic assertion.
biological system reconstruction evidence by experimental evidence from single species used in automatic assertion
A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in an automatic assertion.
biological system reconstruction evidence by experimental evidence from mixed species used in automatic assertion
A type of biological system reconstruction evidence based on orthology evidence that is used in an automatic assertion.
biological system reconstruction evidence based on orthology evidence used in automatic assertion
A type of biological system reconstruction evidence based on homology evidence that is used in an automatic assertion.
biological system reconstruction evidence based on homology evidence used in automatic assertion
A type of biological system reconstruction evidence based on paralogy evidence that is used in an automatic assertion.
biological system reconstruction evidence based on paralogy evidence used in automatic assertion
A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in an automatic assertion.
biological system reconstruction evidence based on inference from background scientific knowledge used in automatic assertion
A type of immunogold labelling evidence that is used in an automatic assertion.
immunogold labelling evidence used in automatic assertion
A type of immunolocalization evidence that is used in an automatic assertion.
immunolocalization evidence used in automatic assertion
A type of flow cytometry evidence that is used in an automatic assertion.
flow cytometry evidence used in automatic assertion
A type of enzyme-linked immunoabsorbent assay evidence that is used in an automatic assertion.
enzyme-linked immunoabsorbent assay evidence used in automatic assertion
A type of high throughput mass spectrometry evidence that is used in an automatic assertion.
high throughput mass spectrometry evidence used in automatic assertion
A type of confocal microscopy evidence that is used in an automatic assertion.
confocal microscopy evidence used in automatic assertion
A type of wide-field microscopy evidence that is used in an automatic assertion.
wide-field microscopy evidence used in automatic assertion
A type of immunogold labelling electron microscopy assay evidence that is used in an automatic assertion.
immunogold labelling electron microscopy assay evidence used in automatic assertion
A type of electron microscopy evidence that is used in an automatic assertion.
electron microscopy evidence used in automatic assertion
A type of immunoperoxidase immunolocalization evidence that is used in an automatic assertion.
immunoperoxidase immunolocalization evidence used in automatic assertion
A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in an automatic assertion.
immunoperoxidase immunolocalization electron microscopy evidence used in automatic assertion
A type of immunofluorescence confocal microscopy evidence that is used in an automatic assertion.
immunofluorescence confocal microscopy evidence used in automatic assertion
A type of immunofluorescence evidence that is used in an automatic assertion.
immunofluorescence evidence used in automatic assertion
A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in an automatic assertion.
two-dimensional polyacrylamide gel electrophoresis evidence used in automatic assertion
A type of alkaline phosphatase reporter gene assay evidence that is used in an automatic assertion.
alkaline phosphatase reporter gene assay evidence used in automatic assertion
A type of beta-galactosidase reporter gene assay evidence that is used in an automatic assertion.
LacZ transcript localization evidence used in automatic assertion
beta-galactosidase reporter gene assay evidence used in automatic assertion
A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in an automatic assertion.
chloramphenicol acetyltransferase reporter gene assay evidence used in automatic assertion
A type of chromatin immunoprecipitation-PCR evidence that is used in an automatic assertion.
chromatin immunoprecipitation-PCR evidence used in automatic assertion
A type of immunoprecipitation evidence that is used in an automatic assertion.
immunoprecipitation evidence used in automatic assertion
A type of copper-phenanthroline footprinting evidence that is used in an automatic assertion.
copper-phenanthroline footprinting evidence used in automatic assertion
A type of nucleic acid binding evidence that is used in an automatic assertion.
nucleic acid binding evidence used in automatic assertion
A type of DNA affinity chromatography evidence that is used in an automatic assertion.
DNA affinity chromatography evidence used in automatic assertion
A type of DNAse footprinting evidence that is used in an automatic assertion.
DNAse footprinting evidence used in automatic assertion
A type of fluorescence anisotropy evidence that is used in an automatic assertion.
fluorescence anisotropy evidence used in automatic assertion
A type of ferric uptake regulator titration assay evidence that is used in an automatic assertion.
ferric uptake regulator titration assay evidence used in automatic assertion
A type of systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion.
systematic evolution of ligands by exponential amplification evidence used in automatic assertion
A type of glutathione S-transferase pull-down assay evidence that is used in an automatic assertion.
glutathione S-transferase pull-down assay evidence used in automatic assertion
A type of beta-glucuronidase reporter gene assay evidence that is used in an automatic assertion.
beta-glucuronidase reporter gene assay evidence used in automatic assertion
A type of heteronuclear single quantum coherence spectroscopy evidence that is used in an automatic assertion.
heteronuclear single quantum coherence spectroscopy evidence used in automatic assertion
A type of hydroxyl-radical footprinting evidence that is used in an automatic assertion.
hydroxyl-radical footprinting evidence used in automatic assertion
A type of isothermal titration calorimetry evidence that is used in an automatic assertion.
isothermal titration calorimetry evidence used in automatic assertion
A type of luciferase reporter gene assay evidence that is used in an automatic assertion.
luciferase reporter gene assay evidence used in automatic assertion
A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in an automatic assertion.
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in automatic assertion
A type of northern blot evidence that is used in an automatic assertion.
northern blot evidence used in automatic assertion
A type of methylation interference footprinting evidence that is used in an automatic assertion.
premethylation interference footprinting evidence used in automatic assertion
methylation interference footprinting evidence used in automatic assertion
A type of primer extension assay evidence that is used in an automatic assertion.
primer extension assay evidence used in automatic assertion
A type of quantitative polymerase chain reaction evidence that is used in an automatic assertion.
quantitative polymerase chain reaction evidence used in automatic assertion
A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in an automatic assertion.
rapid amplification of cDNA ends polymerase chain reaction evidence used in automatic assertion
A type of S1 nuclease protection assay evidence that is used in an automatic assertion.
S1 nuclease protection assay evidence used in automatic assertion
A type of site-directed mutagenesis evidence that is used in an automatic assertion.
site-directed mutagenesis evidence used in automatic assertion
A type of survival rate analysis evidence that is used in an automatic assertion.
survival rate analysis evidence used in automatic assertion
A type of ultraviolet light footprinting evidence that is used in an automatic assertion.
ultraviolet light footprinting evidence used in automatic assertion
A type of xylE reporter gene assay evidence that is used in an automatic assertion.
xylE reporter gene assay evidence used in automatic assertion
A type of ad-hoc qualitative phenotype observation evidence that is used in an automatic assertion.
ad-hoc qualitative phenotype observation evidence used in automatic assertion
A type of ad-hoc quantitative phenotype observation evidence that is used in an automatic assertion.
ad-hoc quantitative phenotype observation evidence used in automatic assertion
A type of cell transfection experiment evidence that is used in an automatic assertion.
cell transfection experiment evidence used in automatic assertion
A type of yeast 2-hybrid evidence that is used in an automatic assertion.
yeast 2-hybrid evidence used in automatic assertion
A type of Cya fusion reporter assay evidence that is used in an automatic assertion.
Cya fusion reporter assay evidence used in automatic assertion
A type of super-resolution microscopy evidence that is used in an automatic assertion.
super-resolution microscopy evidence used in automatic assertion
A type of fractionation evidence that is used in an automatic assertion.
fractionation evidence used in automatic assertion
A type of electrophysiology assay evidence that is used in an automatic assertion.
electrophysiology assay evidence used in automatic assertion
A type of mRNA interactome capture evidence that is used in an automatic assertion.
mRNA interactome capture evidence used in automatic assertion
A type of patch-clamp recording evidence that is used in an automatic assertion.
patch-clamp recording evidence used in automatic assertion
A type of whole-cell patch-clamp recording evidence that is used in an automatic assertion.
whole-cell patch-clamp recording evidence used in automatic assertion
A type of author statement from published clinical study that is used in an automatic assertion.
traceable author statement from published clinical study used in automatic assertion
author statement from published clinical study used in automatic assertion
A type of inference based on individual clinical experience that is used in an automatic assertion.
inference based on individual clinical experience used in automatic assertion
A type of biofilm formation assay evidence that is used in an automatic assertion.
biofilm formation assay evidence used in automatic assertion
A type of microtiter plate biofilm assay evidence that is used in an automatic assertion.
microtiter plate biofilm assay evidence used in automatic assertion
A type of air-liquid interface assay evidence that is used in an automatic assertion.
air-liquid interface assay evidence used in automatic assertion
A type of colony biofilm assay evidence that is used in an automatic assertion.
colony biofilm assay evidence used in automatic assertion
A type of Kadouri drip-fed biofilm assay evidence that is used in an automatic assertion.
Kadouri drip-fed biofilm assay evidence used in automatic assertion
A type of co-immunoprecipitation evidence that is used in an automatic assertion.
co-immunoprecipitation evidence used in automatic assertion
A type of optogenetic evidence that is used in an automatic assertion.
optogenetic evidence used in automatic assertion
A type of fluorescent sensor evidence that is used in an automatic assertion.
fluorescent sensor evidence used in automatic assertion
A type of genetically encoded fluorescent sensor evidence that is used in an automatic assertion.
genetically encoded fluorescent sensor evidence used in automatic assertion
A type of genetically encoded fluorescent electrophysiology assay evidence that is used in an automatic assertion.
genetically encoded fluorescent electrophysiology assay evidence used in automatic assertion
A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in an automatic assertion.
genetically encoded fluorescent ion concentration sensor assay evidence used in automatic assertion
A type of cell fractionation evidence that is used in an automatic assertion.
cell fractionation evidence used in automatic assertion
A type of extracellular recording evidence that is used in an automatic assertion.
extracellular recording evidence used in automatic assertion
A type of single-unit extracellular recording evidence that is used in an automatic assertion.
single-unit extracellular recording evidence used in automatic assertion
A type of field potential recording evidence that is used in an automatic assertion.
field potential recording evidence used in automatic assertion
A type of anti-sense experiment evidence that is used in an automatic assertion.
anti-sense experiment evidence used in automatic assertion
A type of morpholino experiment evidence that is used in an automatic assertion.
morpholino experiment evidence used in automatic assertion
A type of RNAi evidence that is used in an automatic assertion.
RNAi evidence used in automatic assertion
A type of pharmacological assay evidence that is used in an automatic assertion.
pharmacological assay evidence used in automatic assertion
A type of immunofluorescence wide-field microscopy evidence that is used in an automatic assertion.
immunofluorescence wide-field microscopy evidence used in automatic assertion
A type of wide-field fluorescence microscopy evidence that is used in an automatic assertion.
wide-field fluorescence microscopy evidence used in automatic assertion
A type of over expression analysis evidence that is used in an automatic assertion.
over expression analysis evidence used in automatic assertion
A type of cell-free assay evidence that is used in an automatic assertion.
cell-free assay evidence used in automatic assertion
A type of fluorescence recovery after photobleaching evidence that is used in an automatic assertion.
fluorescence recovery after photobleaching evidence used in automatic assertion
A type of immuno-labelling electron microscopy evidence that is used in an automatic assertion.
immuno-labelling electron microscopy evidence used in automatic assertion
A type of immunofluorescence super resolution microscopy evidence that is used in an automatic assertion.
immunofluorescence super resolution microscopy evidence used in automatic assertion
A type of co-purification evidence that is used in an automatic assertion.
co-purification evidence used in automatic assertion
A type of yeast one-hybrid evidence that is used in an automatic assertion.
yeast one-hybrid evidence used in automatic assertion
A type of split-ubiquitin assay evidence that is used in an automatic assertion.
split-ubiquitin assay evidence used in automatic assertion
A type of far-Western blotting evidence that is used in an automatic assertion.
far-Western blotting evidence used in automatic assertion
A type of affinity chromatography evidence that is used in an automatic assertion.
affinity chromatography evidence used in automatic assertion
A type of ribohomopolymer binding assay evidence that is used in an automatic assertion.
ribohomopolymer binding assay evidence used in automatic assertion
A type of protein:ion binding evidence that is used in an automatic assertion.
protein:ion binding evidence used in automatic assertion
A type of Southwestern blot evidence that is used in an automatic assertion.
Southwestern blot evidence used in automatic assertion
A type of Northwestern blot evidence that is used in an automatic assertion.
Northwestern blot evidence used in automatic assertion
A type of bacterial one-hybrid evidence that is used in an automatic assertion.
bacterial one-hybrid evidence used in automatic assertion
A type of protein-binding microarray evidence that is used in an automatic assertion.
protein-binding microarray evidence used in automatic assertion
A type of functional complementation evidence that is used in an automatic assertion.
functional complementation evidence used in automatic assertion
A type of transgenic rescue experiment evidence that is used in an automatic assertion.
transgenic rescue experiment evidence used in automatic assertion
A type of transient rescue experiment evidence that is used in an automatic assertion.
transient rescue experiment evidence used in automatic assertion
A type of suppressor/enhancer interaction evidence that is used in an automatic assertion.
suppressor/enhancer interaction evidence used in automatic assertion
A type of double mutant phenotype evidence that is used in an automatic assertion.
double mutant phenotype evidence used in automatic assertion
A type of epistatic interaction evidence that is used in an automatic assertion.
epistatic interaction evidence used in automatic assertion
A type of functional complementation in heterologous system evidence that is used in an automatic assertion.
functional complementation in heterologous system evidence used in automatic assertion
A type of temperature-sensitive mutant phenotype evidence that is used in an automatic assertion.
temperature-sensitive mutant phenotype evidence used in automatic assertion
A type of recessive mutant phenotype evidence that is used in an automatic assertion.
recessive mutant phenotype evidence used in automatic assertion
A type of high throughput mutant phenotype evidence that is used in an automatic assertion.
high throughput mutant phenotype evidence used in automatic assertion
A type of high throughput genetic interaction evidence that is used in an automatic assertion.
high throughput genetic interaction evidence used in automatic assertion
A type of high throughput direct assay evidence that is used in an automatic assertion.
high throughput direct assay evidence used in automatic assertion
A type of high throughput expression pattern evidence that is used in an automatic assertion.
high throughput expression pattern evidence used in automatic assertion
A type of radioligand binding assay evidence that is used in an automatic assertion.
radioligand binding assay evidence used in automatic assertion
A type of combinatorial evidence from author knowledge and experimental evidence that is used in an automatic assertion.
combinatorial evidence from author knowledge and experimental evidence used in automatic assertion
A type of combinatorial evidence from curator knowledge and experimental evidence that is used in an automatic assertion.
combinatorial evidence from curator knowledge and experimental evidence used in automatic assertion
A type of voltammetry evidence that is used in an automatic assertion.
voltammetry evidence used in automatic assertion
A type of photoconversion evidence that is used in an automatic assertion.
photoconversion evidence used in automatic assertion
A type of agglutination test evidence that is used in an automatic assertion.
agglutination test evidence used in automatic assertion
A type of slide agglutination test evidence that is used in an automatic assertion.
slide agglutination test evidence used in automatic assertion
A type of direct Coombs test evidence that is used in an automatic assertion.
direct Coombs test evidence used in automatic assertion
A type of indirect Coombs test evidence that is used in an automatic assertion.
indirect Coombs test evidence used in automatic assertion
A type of direct hemagglutination assay evidence that is used in an automatic assertion.
direct hemagglutination assay evidence used in automatic assertion
A type of viral hemagglutination inhibition assay evidence that is used in an automatic assertion.
viral hemagglutination inhibition assay evidence used in automatic assertion
A type of compement fixation assay evidence that is used in an automatic assertion.
compement fixation assay evidence used in automatic assertion
A type of neutralization test assay evidence that is used in an automatic assertion.
neutralization test assay evidence used in automatic assertion
A type of copper transport assay evidence that is used in an automatic assertion.
copper transport assay evidence used in automatic assertion
A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in an automatic assertion.
5-cyano-2,3-ditolyl tetrazolium chloride staining evidence used in automatic assertion
A type of plaque assay evidence that is used in an automatic assertion.
plaque assay evidence used in automatic assertion
A type of epifluorescence microscopy evidence that is used in an automatic assertion.
epifluorescence microscopy evidence used in automatic assertion
A type of transmission electron microscopy evidence that is used in an automatic assertion.
transmission electron microscopy evidence used in automatic assertion
A type of scanning electron microscopy evidence that is used in an automatic assertion.
scanning electron microscopy evidence used in automatic assertion
A type of time-lapsed microscopy evidence that is used in an automatic assertion.
time-lapsed microscopy evidence used in automatic assertion
A type of phase contrast microscopy evidence that is used in an automatic assertion.
phase contrast microscopy evidence used in automatic assertion
A type of transmitted light brightfied mircoscopy evidence that is used in an automatic assertion.
transmitted light brightfied mircoscopy evidence used in automatic assertion
A type of koehler illumination microscopy evidence that is used in an automatic assertion.
koehler illumination microscopy evidence used in automatic assertion
A type of differential interference contrast microscopy evidence that is used in an automatic assertion.
differential interference contrast microscopy evidence used in automatic assertion
A type of extended field laser confocal microscopy evidence that is used in an automatic assertion.
extended field laser confocal microscopy evidence used in automatic assertion
A type of confocal laser scanning microscopy evidence that is used in an automatic assertion.
confocal laser scanning microscopy evidence used in automatic assertion
A type of light scattering assay evidence that is used in an automatic assertion.
light scattering assay evidence used in automatic assertion
A type of dynamic light scattering assay evidence that is used in an automatic assertion.
dynamic light scattering assay evidence used in automatic assertion
A type of static light scattering assay evidence that is used in an automatic assertion.
static light scattering assay evidence used in automatic assertion
A type of colony papillation assay evidence that is used in an automatic assertion.
colony papillation assay evidence used in automatic assertion
A type of crystal violet staining evidence that is used in an automatic assertion.
crystal violet staining evidence used in automatic assertion
A type of flow cell biofilm assay evidence that is used in an automatic assertion.
flow cell biofilm assay evidence used in automatic assertion
A type of bacterial 2-hybrid assay evidence that is used in an automatic assertion.
bacterial 2-hybrid assay evidence used in automatic assertion
A type of phenomic profiling assay evidence that is used in an automatic assertion.
phenomic profiling assay evidence used in automatic assertion
A type of colony morphology evidence that is used in an automatic assertion.
colony morphology evidence used in automatic assertion
A type of colony color evidence that is used in an automatic assertion.
colony color evidence used in automatic assertion
A type of colony size evidence that is used in an automatic assertion.
colony size evidence used in automatic assertion
A type of zone of inhibition evidence that is used in an automatic assertion.
zone of inhibition evidence used in automatic assertion
A type of Etest evidence that is used in an automatic assertion.
Etest evidence used in automatic assertion
A type of ribosome profiling evidence that is used in an automatic assertion.
ribosome profiling evidence used in automatic assertion
A type of evidence based on computational logical inference that is used in a manual assertion.
evidence based on computational logical inference used in manual assertion
A type of transcriptional activation assay evidence that is used in a manual assertion.
transcriptional activation assay evidence used in manual assertion
A type of transcriptional activation assay evidence that is used in an automatic assertion.
transcriptional activation assay evidence used in automatic assertion
A type of experimental phenotypic evidence that is used in a manual assertion.
experimental phenotypic evidence used in manual assertion
A type of experimental phenotypic evidence that is used in an automatic assertion.
experimental phenotypic evidence used in automatic assertion
The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides.
Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
Interacting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair.
A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so.
Any process that modulates the frequency, rate, extent or direction of cell growth.
DTOR is positively regulated by DRheb-GTP, Drosophila melanogaster
Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).
translation initiation ternary complex assembly
formation of translation initiation ternary complex
The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules.
Any process that modulates the frequency, rate, or extent of production of a cytokine.
Any process that stops, prevents, or reduces the rate of production of a cytokine.
negative regulation of cytokine production
Any process that activates or increases the frequency, rate or extent of production of a cytokine.
positive regulation of cytokine production
Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
The controlled release of a peptide from a cell or a tissue.
Any process that modulates the frequency, rate, or extent of peptide secretion.
Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion.
negative regulation of peptide secretion
Any process that activates or increases the frequency, rate, or extent of peptide secretion.
positive regulation of peptide secretion
Any process that modulates the frequency, rate, or extent of a response to biotic stimulus.
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.
regulation of response to biotic stimulus
Any process that stops, prevents, or reduces the frequency, rate, or extent of a response to biotic stimulus.
down regulation of response to biotic stimulus
down-regulation of response to biotic stimulus
downregulation of response to biotic stimulus
inhibition of response to biotic stimulus
negative regulation of response to biotic stimulus
Any process that activates or increases the frequency, rate, or extent of a response to biotic stimulus.
up regulation of response to biotic stimulus
up-regulation of response to biotic stimulus
upregulation of response to biotic stimulus
activation of response to biotic stimulus
stimulation of response to biotic stimulus
positive regulation of response to biotic stimulus
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
Interacting selectively and non-covalently with any nucleic acid.
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
Catalysis of the hydrolysis of ester linkages within nucleic acids.
Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', and 'DNA-(apurinic or apyrimidinic site) lyase activity ; GO:0003906' do not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis.
Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
3'- incision of DNA by XPG in GG-NER, Arabidopsis thaliana
3'- incision of DNA by XPG in GG-NER, Danio rerio
3'- incision of DNA by XPG in GG-NER, Gallus gallus
3'- incision of DNA by XPG in GG-NER, Rattus norvegicus
3'- incision of DNA by XPG in GG-NER, Taeniopygia guttata
3'- incision of DNA by XPG in GG-NER, Xenopus tropicalis
Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Danio rerio
3'- incision of DNA by XPG in GG-NER, Homo sapiens
Cleavage of mRNA at the 3'-end, Arabidopsis thaliana
Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Rattus norvegicus
Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Xenopus tropicalis
Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Taeniopygia guttata
Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Gallus gallus
Cleavage of mRNA at the 3'-end, Drosophila melanogaster
Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Canis familiaris
Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Mus musculus
Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Bos taurus
Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Sus scrofa
Displacement of DNA glycosylase and endonucleolytic cleavage by DNA-lyase, Gallus gallus
Cleavage of mRNA at the 3'-end, Homo sapiens
Cleavage of mRNA at the 3'-end, Bos taurus
Removal of 3'-phosphate moiety from DSB ends, Homo sapiens
Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Homo sapiens
Cleavage of mRNA at the 3'-end, Taeniopygia guttata
3'- incision of DNA by XPG in GG-NER, Canis familiaris
Cleavage of mRNA at the 3'-end, Canis familiaris
3'- incision of DNA by XPG in GG-NER, Caenorhabditis elegans
3'- incision of DNA by XPG in GG-NER, Saccharomyces cerevisiae
3'- incision of DNA by XPG in GG-NER, Bos taurus
Cleavage of mRNA at the 3'-end, Mus musculus
3'- incision of DNA by XPG in GG-NER, Oryza sativa
Cleavage of mRNA at the 3'-end, Xenopus tropicalis
3'- incision of DNA by XPG in GG-NER, Schizosaccharomyces pombe
3'- incision of DNA by XPG in GG-NER, Mus musculus
3'- incision of DNA by XPG in GG-NER, Sus scrofa
3'- incision of DNA by XPG in GG-NER, Drosophila melanogaster
Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
5'-incision of DNA by ERCC1-XPF in GG-NER, Danio rerio
5' incision leading to excision of DNA fragment with lesion in TC-NER, Caenorhabditis elegans
APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Dictyostelium discoideum
APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Rattus norvegicus
3' incision of the lesioned strand of DNA in TC-NER, Xenopus tropicalis
APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Danio rerio
5' incision leading to excision of DNA fragment with lesion in TC-NER, Schizosaccharomyces pombe
APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Taeniopygia guttata
APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Sus scrofa
3' incision of the lesioned strand of DNA in TC-NER, Drosophila melanogaster
3' incision of the lesioned strand of DNA in TC-NER, Canis familiaris
APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Xenopus tropicalis
3' incision of the lesioned strand of DNA in TC-NER, Sus scrofa
3' incision of the lesioned strand of DNA in TC-NER, Danio rerio
5'-incision of DNA by ERCC1-XPF in GG-NER, Xenopus tropicalis
3' incision of the lesioned strand of DNA in TC-NER, Taeniopygia guttata
5' incision leading to excision of DNA fragment with lesion in TC-NER, Gallus gallus
5' incision leading to excision of DNA fragment with lesion in TC-NER, Taeniopygia guttata
3' incision of the lesioned strand of DNA in TC-NER, Gallus gallus
3' incision of the lesioned strand of DNA in TC-NER, Homo sapiens
5'-incision of DNA by ERCC1-XPF in GG-NER, Homo sapiens
APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Homo sapiens
Removal of SPO11 and Resection of 5' Ends of DNA (yeast), Saccharomyces cerevisiae
Removal of SPO11 and Resection of 5' Ends of DNA, Homo sapiens
5' incision leading to excision of DNA fragment with lesion in TC-NER, Bos taurus
3' incision of the lesioned strand of DNA in TC-NER, Rattus norvegicus
3' incision of the lesioned strand of DNA in TC-NER, Dictyostelium discoideum
5' incision leading to excision of DNA fragment with lesion in TC-NER, Arabidopsis thaliana
APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Caenorhabditis elegans
3' incision of the lesioned strand of DNA in TC-NER, Schizosaccharomyces pombe
5' incision leading to excision of DNA fragment with lesion in TC-NER, Oryza sativa
3' incision of the lesioned strand of DNA in TC-NER, Saccharomyces cerevisiae
3' incision of the lesioned strand of DNA in TC-NER, Bos taurus
5' incision leading to excision of DNA fragment with lesion in TC-NER, Sus scrofa
5' incision leading to excision of DNA fragment with lesion in TC-NER, Dictyostelium discoideum
APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Mus musculus
3' incision of the lesioned strand of DNA in TC-NER, Caenorhabditis elegans
3' incision of the lesioned strand of DNA in TC-NER, Oryza sativa
5' incision leading to excision of DNA fragment with lesion in TC-NER, Homo sapiens
5' incision leading to excision of DNA fragment with lesion in TC-NER, Mus musculus
5' incision leading to excision of DNA fragment with lesion in TC-NER, Canis familiaris
5'-incision of DNA by ERCC1-XPF in GG-NER, Rattus norvegicus
APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Drosophila melanogaster
5' incision leading to excision of DNA fragment with lesion in TC-NER, Rattus norvegicus
5' incision leading to excision of DNA fragment with lesion in TC-NER, Danio rerio
3' incision of the lesioned strand of DNA in TC-NER, Arabidopsis thaliana
5' incision leading to excision of DNA fragment with lesion in TC-NER, Drosophila melanogaster
APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Canis familiaris
5'-incision of DNA by ERCC1-XPF in GG-NER, Mus musculus
5' incision leading to excision of DNA fragment with lesion in TC-NER, Xenopus tropicalis
5' incision leading to excision of DNA fragment with lesion in TC-NER, Saccharomyces cerevisiae
APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Bos taurus
3' incision of the lesioned strand of DNA in TC-NER, Mus musculus
Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
caspase-activated deoxyribonuclease activity
Cleavage of DNA by DFF40, Xenopus tropicalis
Cleavage of DNA by DFF40, Taeniopygia guttata
Cleavage of DNA by DFF40, Rattus norvegicus
Cleavage of DNA by DFF40, Canis familiaris
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.
Virion-associated M2 protein mediated ion infusion, Homo sapiens
Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
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. 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 "no data" (ND), is used to indicate this.
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside and nucleotide metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
nucleobase-containing compound metabolic process
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'.
Activation of ATR in response to replication stress, Mus musculus
Activation of claspin, Xenopus tropicalis
Activation of ATR in response to replication stress, Gallus gallus
Stalling of DNA replication fork and RPA binding, Taeniopygia guttata
Recruitment and activation of Chk1, Gallus gallus
Activation of ATR in response to replication stress, Xenopus tropicalis
Loading of claspin onto DNA during replication origin firing, Danio rerio
Stalling of DNA replication fork and RPA binding, Gallus gallus
Recruitment of Rad17-RFC complex to DNA, Gallus gallus
Binding of ATR-ATRIP to the RPA-ssDNA complex, Bos taurus
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Drosophila melanogaster
Recruitment and activation of Chk1, Canis familiaris
Activation of ATR in response to replication stress, Danio rerio
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Caenorhabditis elegans
Recruitment and activation of Chk1, Bos taurus
Loading of claspin onto DNA during replication origin firing, Mus musculus
Binding of ATR-ATRIP to the RPA-ssDNA complex, Xenopus tropicalis
Activation of ATR in response to replication stress, Bos taurus
Activation of ATR in response to replication stress, Drosophila melanogaster
Stalling of DNA replication fork and RPA binding, Rattus norvegicus
Activation of ATR in response to replication stress, Saccharomyces cerevisiae
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Gallus gallus
Activation of ATR in response to replication stress, Schizosaccharomyces pombe
Binding of ATR-ATRIP to the RPA-ssDNA complex, Taeniopygia guttata
Activation of ATR in response to replication stress, Rattus norvegicus
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Taeniopygia guttata
Activation of claspin, Rattus norvegicus
Recruitment of Rad17-RFC complex to DNA, Xenopus tropicalis
Loading of claspin onto DNA during replication origin firing, Rattus norvegicus
Recruitment of Rad17-RFC complex to DNA, Mus musculus
Recruitment and activation of Chk1, Taeniopygia guttata
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Dictyostelium discoideum
Recruitment and activation of Chk1, Xenopus tropicalis
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Rattus norvegicus
Loading of claspin onto DNA during replication origin firing, Canis familiaris
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Homo sapiens
Loading of claspin onto DNA during replication origin firing, Homo sapiens
Activation of ATR in response to replication stress, Homo sapiens
Recruitment of Rad17-RFC complex to DNA, Homo sapiens
Recruitment and activation of Chk1, Homo sapiens
Stalling of DNA replication fork and RPA binding, Homo sapiens
Binding of ATR-ATRIP to the RPA-ssDNA complex, Homo sapiens
Stalling of DNA replication fork and RPA binding, Canis familiaris
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Canis familiaris
Activation of ATR in response to replication stress, Dictyostelium discoideum
Loading of claspin onto DNA during replication origin firing, Taeniopygia guttata
Recruitment and activation of Chk1, Sus scrofa
Loading of claspin onto DNA during replication origin firing, Bos taurus
Recruitment of Rad17-RFC complex to DNA, Canis familiaris
Recruitment of Rad17-RFC complex to DNA, Danio rerio
Binding of ATR-ATRIP to the RPA-ssDNA complex, Danio rerio
Binding of ATR-ATRIP to the RPA-ssDNA complex, Rattus norvegicus
Stalling of DNA replication fork and RPA binding, Mus musculus
Recruitment and activation of Chk1, Rattus norvegicus
Binding of ATR-ATRIP to the RPA-ssDNA complex, Canis familiaris
Recruitment of Rad17-RFC complex to DNA, Rattus norvegicus
Recruitment of Rad17-RFC complex to DNA, Bos taurus
Binding of ATR-ATRIP to the RPA-ssDNA complex, Gallus gallus
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Schizosaccharomyces pombe
Activation of ATR in response to replication stress, Sus scrofa
Loading of claspin onto DNA during replication origin firing, Drosophila melanogaster
Stalling of DNA replication fork and RPA binding, Bos taurus
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Danio rerio
Recruitment of Rad17-RFC complex to DNA, Taeniopygia guttata
Recruitment and activation of Chk1, Danio rerio
Activation of ATR in response to replication stress, Canis familiaris
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Mus musculus
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Xenopus tropicalis
Stalling of DNA replication fork and RPA binding, Danio rerio
Stalling of DNA replication fork and RPA binding, Xenopus tropicalis
Activation of ATR in response to replication stress, Taeniopygia guttata
Activation of claspin, Taeniopygia guttata
Binding of ATR-ATRIP to the RPA-ssDNA complex, Mus musculus
Recruitment and activation of Chk1, Mus musculus
Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Bos taurus
Loading of claspin onto DNA during replication origin firing, Gallus gallus
Activation of ATR in response to replication stress, Caenorhabditis elegans
Loading of claspin onto DNA during replication origin firing, Xenopus tropicalis
Any process that modulates the frequency, rate or extent of DNA replication.
The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.
The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties.
The addition of alkyl groups to many positions on all four bases of DNA. Alkylating agents can also modify the bases of incoming nucleotides in the course of DNA synthesis.
The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
DNA fragmentation involved in apoptotic nuclear change
endonucleolytic DNA catabolic process involved in apoptosis
DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases. In human, these include DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in PMID:15723341). Caution is needed when apoptotic DNA laddering assays show presence of fragmented DNA. A positive assay may simply reflect the end point of a whole apoptotic process. Unless clear experimental evidence is available to show that a gene product is directly involved in fragmenting DNA, please do not annotate to GO:0006309 'apoptotic DNA fragmentation' and consider annotating instead to a more upstream process such as, e.g., GO:0042981 'regulation of apoptotic process', GO:0006915 'apoptotic process', GO:0097190 'apoptotic signaling pathway'. Also, note that gene products involved in compartmentalization of apoptotic nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341).
Apoptosis induced DNA fragmentation, Bos taurus
Apoptosis induced DNA fragmentation, Sus scrofa
Apoptosis induced DNA fragmentation, Xenopus tropicalis
Apoptosis induced DNA fragmentation, Plasmodium falciparum
Apoptosis induced DNA fragmentation, Homo sapiens
Apoptosis induced DNA fragmentation, Rattus norvegicus
Apoptosis induced DNA fragmentation, Mus musculus
Apoptosis induced DNA fragmentation, Drosophila melanogaster
Apoptosis induced DNA fragmentation, Taeniopygia guttata
Apoptosis induced DNA fragmentation, Canis familiaris
Apoptosis induced DNA fragmentation, Gallus gallus
Apoptosis induced DNA fragmentation, Danio rerio
Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
The cellular synthesis of RNA on a template of DNA.
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
regulation of cellular transcription, DNA-dependent
regulation of transcription, DNA-dependent
regulation of gene-specific transcription
regulation of transcription, DNA-templated
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
Eukaryotic Translation Initiation, Gallus gallus
Eukaryotic Translation Initiation, Xenopus tropicalis
Eukaryotic Translation Initiation, Homo sapiens
Eukaryotic Translation Initiation, Dictyostelium discoideum
Eukaryotic Translation Initiation, Oryza sativa
Eukaryotic Translation Initiation, Caenorhabditis elegans
Eukaryotic Translation Initiation, Taeniopygia guttata
Eukaryotic Translation Initiation, Drosophila melanogaster
Eukaryotic Translation Initiation, Rattus norvegicus
Eukaryotic Translation Initiation, Bos taurus
Eukaryotic Translation Initiation, Schizosaccharomyces pombe
Eukaryotic Translation Initiation, Arabidopsis thaliana
Eukaryotic Translation Initiation, Plasmodium falciparum
Eukaryotic Translation Initiation, Mus musculus
Eukaryotic Translation Initiation, Canis familiaris
Eukaryotic Translation Initiation, Sus scrofa
Eukaryotic Translation Initiation, Saccharomyces cerevisiae
Eukaryotic Translation Initiation, Danio rerio
The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
Eukaryotic Translation Elongation, Dictyostelium discoideum
Eukaryotic Translation Elongation, Canis familiaris
Eukaryotic Translation Elongation, Gallus gallus
Eukaryotic Translation Elongation, Escherichia coli
Eukaryotic Translation Elongation, Mus musculus
Eukaryotic Translation Elongation, Danio rerio
Eukaryotic Translation Elongation, Xenopus tropicalis
Eukaryotic Translation Elongation, Taeniopygia guttata
Eukaryotic Translation Elongation, Caenorhabditis elegans
Eukaryotic Translation Elongation, Homo sapiens
Eukaryotic Translation Elongation, Arabidopsis thaliana
Eukaryotic Translation Elongation, Sus scrofa
Eukaryotic Translation Elongation, Bos taurus
Eukaryotic Translation Elongation, Rattus norvegicus
Eukaryotic Translation Elongation, Drosophila melanogaster
Eukaryotic Translation Elongation, Saccharomyces cerevisiae
Eukaryotic Translation Elongation, Schizosaccharomyces pombe
Eukaryotic Translation Elongation, Oryza sativa
Eukaryotic Translation Elongation, Plasmodium falciparum
The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Taeniopygia guttata
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Dictyostelium discoideum
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Danio rerio
Eukaryotic Translation Termination, Saccharomyces cerevisiae
Eukaryotic Translation Termination, Oryza sativa
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Caenorhabditis elegans
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Taeniopygia guttata
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Plasmodium falciparum
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Schizosaccharomyces pombe
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Danio rerio
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Oryza sativa
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Schizosaccharomyces pombe
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Caenorhabditis elegans
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Plasmodium falciparum
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Mus musculus
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Gallus gallus
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Rattus norvegicus
Eukaryotic Translation Termination, Rattus norvegicus
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Gallus gallus
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Gallus gallus
Eukaryotic Translation Termination, Gallus gallus
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Saccharomyces cerevisiae
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Rattus norvegicus
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Homo sapiens
Eukaryotic Translation Termination, Homo sapiens
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Homo sapiens
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Canis familiaris
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Xenopus tropicalis
Eukaryotic Translation Termination, Danio rerio
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Drosophila melanogaster
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Canis familiaris
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Oryza sativa
Eukaryotic Translation Termination, Drosophila melanogaster
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Dictyostelium discoideum
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Mus musculus
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Homo sapiens
GTP bound eRF3:eRF1 complex binds the peptidyl-tRNA:mRNA:Ribosome complex, Saccharomyces cerevisiae
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Saccharomyces cerevisiae
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Arabidopsis thaliana
Eukaryotic Translation Termination, Schizosaccharomyces pombe
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Dictyostelium discoideum
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Xenopus tropicalis
Eukaryotic Translation Termination, Canis familiaris
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Arabidopsis thaliana
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Caenorhabditis elegans
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Xenopus tropicalis
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Drosophila melanogaster
Eukaryotic Translation Termination, Plasmodium falciparum
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Plasmodium falciparum
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Arabidopsis thaliana
Eukaryotic Translation Termination, Xenopus tropicalis
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Taeniopygia guttata
Eukaryotic Translation Termination, Dictyostelium discoideum
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Canis familiaris
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Danio rerio
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Oryza sativa
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Schizosaccharomyces pombe
Eukaryotic Translation Termination, Taeniopygia guttata
Eukaryotic Translation Termination, Caenorhabditis elegans
Eukaryotic Translation Termination, Mus musculus
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Drosophila melanogaster
Eukaryotic Translation Termination, Arabidopsis thaliana
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Mus musculus
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
Any process that modulates the frequency, rate or extent of translational initiation.
Any process that modulates the frequency, rate, extent or accuracy of translational elongation.
Any process that modulates the frequency, rate or extent of translational termination.
The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
cellular aromatic compound metabolic process
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Transport of inorganic cations/anions and amino acids/oligopeptides, Xenopus tropicalis
Transport of inorganic cations/anions and amino acids/oligopeptides, Staphylococcus aureus N315
Transport of inorganic cations/anions and amino acids/oligopeptides, Sus scrofa
Transport of inorganic cations/anions and amino acids/oligopeptides, Saccharomyces cerevisiae
Transport of inorganic cations/anions and amino acids/oligopeptides, Arabidopsis thaliana
Transport of inorganic cations/anions and amino acids/oligopeptides, Homo sapiens
Transport of inorganic cations/anions and amino acids/oligopeptides, Oryza sativa
Transport of inorganic cations/anions and amino acids/oligopeptides, Mus musculus
Transport of inorganic cations/anions and amino acids/oligopeptides, Danio rerio
Transport of inorganic cations/anions and amino acids/oligopeptides, Gallus gallus
Transport of inorganic cations/anions and amino acids/oligopeptides, Caenorhabditis elegans
Transport of inorganic cations/anions and amino acids/oligopeptides, Escherichia coli
Transport of inorganic cations/anions and amino acids/oligopeptides, Bos taurus
Transport of inorganic cations/anions and amino acids/oligopeptides, Dictyostelium discoideum
Transport of inorganic cations/anions and amino acids/oligopeptides, Drosophila melanogaster
Transport of inorganic cations/anions and amino acids/oligopeptides, Mycobacterium tuberculosis
Transport of inorganic cations/anions and amino acids/oligopeptides, Canis familiaris
Transport of inorganic cations/anions and amino acids/oligopeptides, Rattus norvegicus
Transport of inorganic cations/anions and amino acids/oligopeptides, Plasmodium falciparum
Transport of inorganic cations/anions and amino acids/oligopeptides, Taeniopygia guttata
Transport of inorganic cations/anions and amino acids/oligopeptides, Schizosaccharomyces pombe
The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
NRIF signals cell death from the nucleus, Danio rerio
NRAGE signals death through JNK, Taeniopygia guttata
NADE modulates death signalling, Rattus norvegicus
NRAGE signals death through JNK, Xenopus tropicalis
NADE modulates death signalling, Sus scrofa
NRIF signals cell death from the nucleus, Xenopus tropicalis
NRAGE signals death through JNK, Mus musculus
NRAGE signals death through JNK, Arabidopsis thaliana
NRAGE signals death through JNK, Schizosaccharomyces pombe
NRAGE signals death through JNK, Dictyostelium discoideum
NADE modulates death signalling, Homo sapiens
NRAGE signals death through JNK, Homo sapiens
NRIF signals cell death from the nucleus, Homo sapiens
NRAGE signals death through JNK, Saccharomyces cerevisiae
NRAGE signals death through JNK, Caenorhabditis elegans
NRAGE signals death through JNK, Oryza sativa
NRAGE signals death through JNK, Canis familiaris
NRAGE signals death through JNK, Gallus gallus
NRAGE signals death through JNK, Drosophila melanogaster
NADE modulates death signalling, Bos taurus
NRIF signals cell death from the nucleus, Canis familiaris
NADE modulates death signalling, Canis familiaris
NRAGE signals death through JNK, Rattus norvegicus
NRIF signals cell death from the nucleus, Gallus gallus
NRIF signals cell death from the nucleus, Rattus norvegicus
NRIF signals cell death from the nucleus, Sus scrofa
NRIF signals cell death from the nucleus, Mus musculus
NRIF signals cell death from the nucleus, Taeniopygia guttata
NADE modulates death signalling, Mus musculus
NRAGE signals death through JNK, Danio rerio
NRIF signals cell death from the nucleus, Bos taurus
NRAGE signals death through JNK, Bos taurus
NRAGE signals death through JNK, Sus scrofa
The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
cellular component disassembly involved in apoptotic process
cellular component disassembly involved in apoptosis
cellular component disassembly involved in execution phase of apoptosis
Apoptotic execution phase, Taeniopygia guttata
Apoptotic execution phase, Saccharomyces cerevisiae
Apoptotic execution phase, Schizosaccharomyces pombe
Apoptotic execution phase, Rattus norvegicus
Apoptotic execution phase, Dictyostelium discoideum
Apoptotic execution phase, Drosophila melanogaster
Apoptotic execution phase, Canis familiaris
Apoptotic execution phase, Xenopus tropicalis
Apoptotic execution phase, Arabidopsis thaliana
Apoptotic execution phase, Plasmodium falciparum
Apoptotic execution phase, Caenorhabditis elegans
Apoptotic execution phase, Gallus gallus
The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
Note that in GO cellular components include whole cells (cell is_a cellular component).
movement of cell or subcellular component
The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular response to DNA damage stimulus
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus.
Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
EGFR interacts with phospholipase C-gamma, Gallus gallus
EGFR interacts with phospholipase C-gamma, Canis familiaris
EGFR interacts with phospholipase C-gamma, Oryza sativa
EGFR interacts with phospholipase C-gamma, Arabidopsis thaliana
EGFR interacts with phospholipase C-gamma, Mycobacterium tuberculosis
EGFR interacts with phospholipase C-gamma, Drosophila melanogaster
EGFR interacts with phospholipase C-gamma, Bos taurus
EGFR interacts with phospholipase C-gamma, Dictyostelium discoideum
EGFR interacts with phospholipase C-gamma, Saccharomyces cerevisiae
EGFR interacts with phospholipase C-gamma, Sus scrofa
EGFR interacts with phospholipase C-gamma, Caenorhabditis elegans
EGFR interacts with phospholipase C-gamma, Plasmodium falciparum
EGFR interacts with phospholipase C-gamma, Schizosaccharomyces pombe
EGFR interacts with phospholipase C-gamma, Homo sapiens
EGFR interacts with phospholipase C-gamma, Rattus norvegicus
EGFR interacts with phospholipase C-gamma, Xenopus tropicalis
EGFR interacts with phospholipase C-gamma, Taeniopygia guttata
EGFR interacts with phospholipase C-gamma, Danio rerio
EGFR interacts with phospholipase C-gamma, Mus musculus
A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
The cell aging process that results in the nucleolus breaking down into fragments.
Any process in which a protein is transported to, or maintained in, a specific location.
establishment and maintenance of asymmetric protein localization
establishment and maintenance of protein localization
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
metabolic process resulting in cell growth
multicellular organism metabolic process
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term.
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.
Any process that activates or increases the rate or extent of cell proliferation.
positive regulation of cell proliferation
Any process that stops, prevents or reduces the rate or extent of cell proliferation.
negative regulation of cell proliferation
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.
multicellular organismal 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.
multicellular organismal macromolecule catabolic 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.
multicellular organismal 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.
The synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA.
The controlled release of proteins from a cell.
protein secretion during cell fate commitment
protein secretion resulting in cell fate commitment
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 external 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.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances.
negative regulation of biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
positive regulation of biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
negative regulation of organismal metabolism
inhibition of organismal metabolic process
negative regulation of multicellular organismal metabolic process
negative regulation of metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
positive regulation of multicellular organismal metabolic process
positive regulation of organismal metabolism
stimulation of organismal metabolic process
up-regulation of organismal metabolic process
positive regulation of metabolic process
Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.
negative regulation of catabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances.
positive regulation of catabolic process
Any process that modulates the frequency, rate or extent of signal transduction.
Any process that activates or increases the frequency, rate or extent of signal transduction.
positive regulation of signaling pathway
positive regulation of signalling pathway
positive regulation of signal transduction
Activated DTOR also phosphorylates D4EBP, Drosophila melanogaster
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
negative regulation of signaling pathway
negative regulation of signalling pathway
negative regulation of signal transduction
DTSC1 AND DTSC2 form a complex, Drosophila melanogaster
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
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 mycotoxin stimulus. A mycotoxin is a toxic chemical substance produced by fungi.
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 organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
Gene Expression, Drosophila melanogaster
Gene Expression, Staphylococcus aureus N315
Gene Expression, Mycobacterium tuberculosis
Gene Expression, Dictyostelium discoideum
Gene Expression, Schizosaccharomyces pombe
Gene Expression, Saccharomyces cerevisiae
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA 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.
This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation.
Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
regulation of macromolecule biosynthetic process
Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
positive regulation of macromolecule biosynthetic process
Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
negative regulation of macromolecule biosynthetic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
positive regulation of macromolecule metabolic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
negative regulation of macromolecule metabolic process
Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript.
posttranscriptional regulation of gene expression
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA 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.
Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA 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.
This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation.
Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
positive regulation of organelle organisation
positive regulation of organelle organization and biogenesis
positive regulation of organelle organization
Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
negative regulation of organelle organisation
negative regulation of organelle organization and biogenesis
negative regulation of organelle organization
Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
positive regulation of cell communication
Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
negative regulation of cell communication
Any process in which a lipid is transported to, or maintained in, a specific location.
The cellular component assembly that is part of the initial shaping of the component during its developmental progression.
cellular component assembly involved in morphogenesis
Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in 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.
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'.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Enables the transfer of an ion from one side of a membrane to the other.
Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules.
Enables the transfer of an inorganic molecular entity from the outside of a cell to the inside of the cell across a membrane. An inorganic molecular entity is a molecular entity that contains no carbon.
inorganic solute uptake transmembrane transporter activity
Renamed term see https://github.com/geneontology/go-ontology/issues/14372
inorganic molecular entity transmembrane transporter activity
The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage.
The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Fatty acids are aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
The directed movement of long-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
non-developmental growth of a unicellular organism
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
Metabolism of RNA, Schizosaccharomyces pombe
Metabolism of RNA, Dictyostelium discoideum
Metabolism of RNA, Plasmodium falciparum
Metabolism of RNA, Caenorhabditis elegans
Metabolism of RNA, Saccharomyces cerevisiae
Metabolism of RNA, Drosophila melanogaster
The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes.
posttranscriptional gene silencing by siRNA
Note that this term refers specifically to posttranscriptional mechanisms by which small interfering RNAs down-regulate gene expression. Also consider annotating to other descendants of 'gene silencing by RNA ; GO:0031047'.
The inactivation of gene expression by a posttranscriptional mechanism.
Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression.
long-term maintenance of gene inactivation
This is a rather broad grouping term. While it was originally defined for long-term, heritable, epigenetic effects, short term effects on expression mediated by RNA are also frequently referred to as gene silencing, and are grouped under this class.
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.
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
Hydrolysis of phosphatidylcholine, Bos taurus
Partial proteolysis of antigen in phagolysosomes, Homo sapiens
Hydrolysis of phosphatidylcholine, Homo sapiens
Hydrolysis of phosphatidylcholine, Danio rerio
Hydrolysis of phosphatidylcholine, Xenopus tropicalis
Hydrolysis of phosphatidylcholine, Gallus gallus
Hydrolysis of phosphatidylcholine, Canis familiaris
Hydrolysis of phosphatidylcholine, Mus musculus
Hydrolysis of phosphatidylcholine, Taeniopygia guttata
Hydrolysis of phosphatidylcholine, Rattus norvegicus
Catalysis of the hydrolysis of any ester bond.
hydrolase activity, acting on ester bonds
Deacylation of Acyl Ghrelin, Mus musculus
uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Xenopus tropicalis
Deacylation of Acyl Ghrelin, Homo sapiens
uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Homo sapiens
uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Mus musculus
uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Danio rerio
Deacylation of Acyl Ghrelin, Rattus norvegicus
Deacylation of Acyl Ghrelin, Gallus gallus
Deacylation of Acyl Ghrelin, Canis familiaris
uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Sus scrofa
uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Rattus norvegicus
uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Canis familiaris
uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Bos taurus
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
down regulation of protein biosynthetic process
down-regulation of protein biosynthetic process
downregulation of protein biosynthetic process
negative regulation of protein anabolism
negative regulation of protein biosynthesis
negative regulation of protein biosynthetic process
negative regulation of protein formation
negative regulation of protein synthesis
inhibition of protein biosynthetic process
protein biosynthetic process inhibitor activity
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).
Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
regulation of nucleobase-containing compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
regulation of multicellular organismal metabolic process
regulation of organismal metabolic process
The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
aromatic hydrocarbon biosynthetic process
The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
The chemical reactions and pathways involving a protein. Includes protein modification.
protein metabolic process and modification
multicellular organismal protein metabolic process
A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
A cellular process that results in the breakdown of a cellular component.
cellular component disassembly at cellular level
Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis.
regulation of anatomical structure morphogenesis
The aggregation, arrangement and bonding together of a cellular component.
cellular component assembly at cellular level
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.
ribonucleoprotein complex biogenesis and assembly
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.
Enables the transfer of a single solute from one side of a membrane to the other by a mechanism involving conformational change, either by facilitated diffusion or in a membrane potential dependent process if the solute is charged.
passive transmembrane transporter activity
Passive I- efflux mediated by SMCT1, Staphylococcus aureus N315
Passive I- efflux mediated by SMCT1, Xenopus tropicalis
Passive I- efflux mediated by SMCT1, Mus musculus
Passive I- efflux mediated by SMCT1, Bos taurus
Passive I- efflux mediated by SMCT1, Taeniopygia guttata
Passive I- efflux mediated by SMCT1, Rattus norvegicus
Passive I- efflux mediated by SMCT1, Canis familiaris
Passive I- efflux mediated by SMCT1, Sus scrofa
Passive I- efflux mediated by SMCT1, Gallus gallus
Passive I- efflux mediated by SMCT1, Danio rerio
Passive I- efflux mediated by SMCT1, Homo sapiens
Enables the energy-independent facilitated diffusion, mediated by passage of a specific solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules.
Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
substrate-specific transmembrane transporter activity
uptake transmembrane transporter activity
GLUT9 transports glucose, fructose and urate, Gallus gallus
GLUT9 transports glucose, fructose and urate, Xenopus tropicalis
Egress of internalized antigen to the cytosol via sec61, Homo sapiens
GLUT9 transports glucose, fructose and urate, Plasmodium falciparum
GLUT9 transports glucose, fructose and urate, Dictyostelium discoideum
GLUT9 transports glucose, fructose and urate, Mycobacterium tuberculosis
GLUT9 transports glucose, fructose and urate, Arabidopsis thaliana
GLUT9 transports glucose, fructose and urate, Oryza sativa
GLUT9 transports glucose, fructose and urate, Homo sapiens
GLUT9 transports glucose, fructose and urate, Canis familiaris
GLUT9 transports glucose, fructose and urate, Bos taurus
GLUT9 transports glucose, fructose and urate, Taeniopygia guttata
GLUT9 transports glucose, fructose and urate, Mus musculus
GLUT9 transports glucose, fructose and urate, Rattus norvegicus
Any process that modulates the frequency, rate or extent of transmembrane transporter activity.
regulation of transmembrane transporter activity
Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another.
regulation of gene expression as a consequence of signal transmission
signal transduction involved in regulation of gene expression
Any process that modulates the frequency, rate or extent of a signaling process.
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.
positive regulation of signalling process
positive regulation of signaling process
Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
negative regulation of signaling process
negative regulation of signalling process
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
cell projection organization and biogenesis
cell surface structure organization and biogenesis
Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.
Assembly of actin filaments by the addition of actin monomers to a filament.
The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis.
Any process that activates or increases the frequency, rate, extent or direction of cell growth.
Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
DRheb is inhibited by the TSC1/2 complex, Drosophila melanogaster
Any process that modulates the frequency, rate or extent of cell migration.
Any process that activates or increases the frequency, rate or extent of cell migration.
Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
Any process in which RNA molecules inactivate expression of target genes.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
regulation of cellular metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
down regulation of cellular metabolic process
down-regulation of cellular metabolic process
downregulation of cellular metabolic process
negative regulation of cellular metabolism
inhibition of cellular metabolic process
negative regulation of cellular metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
positive regulation of cellular metabolism
up regulation of cellular metabolic process
up-regulation of cellular metabolic process
upregulation of cellular metabolic process
activation of cellular metabolic process
stimulation of cellular metabolic process
positive regulation of cellular metabolic process
ChREBP activates metabolic gene expression, Mus musculus
ChREBP activates metabolic gene expression, Escherichia coli
ChREBP activates metabolic gene expression, Caenorhabditis elegans
ChREBP activates metabolic gene expression, Plasmodium falciparum
ChREBP activates metabolic gene expression, Drosophila melanogaster
ChREBP activates metabolic gene expression, Xenopus tropicalis
ChREBP activates metabolic gene expression, Homo sapiens
ChREBP activates metabolic gene expression, Arabidopsis thaliana
ChREBP activates metabolic gene expression, Mycobacterium tuberculosis
ChREBP activates metabolic gene expression, Canis familiaris
ChREBP activates metabolic gene expression, Saccharomyces cerevisiae
ChREBP activates metabolic gene expression, Taeniopygia guttata
ChREBP activates metabolic gene expression, Oryza sativa
ChREBP activates metabolic gene expression, Dictyostelium discoideum
ChREBP activates metabolic gene expression, Danio rerio
ChREBP activates metabolic gene expression, Rattus norvegicus
ChREBP activates metabolic gene expression, Staphylococcus aureus N315
ChREBP activates metabolic gene expression, Gallus gallus
ChREBP activates metabolic gene expression, Schizosaccharomyces pombe
ChREBP activates metabolic gene expression, Bos taurus
ChREBP activates metabolic gene expression, Sus scrofa
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
regulation of cellular biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
down regulation of cellular biosynthetic process
down-regulation of cellular biosynthetic process
downregulation of cellular biosynthetic process
negative regulation of cellular anabolism
negative regulation of cellular biosynthesis
negative regulation of cellular formation
negative regulation of cellular synthesis
inhibition of cellular biosynthetic process
negative regulation of cellular biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
positive regulation of cellular anabolism
positive regulation of cellular biosynthesis
positive regulation of cellular formation
positive regulation of cellular synthesis
up regulation of cellular biosynthetic process
up-regulation of cellular biosynthetic process
upregulation of cellular biosynthetic process
activation of cellular biosynthetic process
stimulation of cellular biosynthetic process
positive regulation of cellular biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
regulation of cellular catabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
down regulation of cellular catabolic process
down-regulation of cellular catabolic process
downregulation of cellular catabolic process
negative regulation of cellular breakdown
negative regulation of cellular catabolism
negative regulation of cellular degradation
inhibition of cellular catabolic process
negative regulation of cellular catabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
positive regulation of cellular breakdown
positive regulation of cellular catabolism
positive regulation of cellular degradation
up regulation of cellular catabolic process
up-regulation of cellular catabolic process
upregulation of cellular catabolic process
activation of cellular catabolic process
stimulation of cellular catabolic process
positive regulation of cellular catabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly.
down regulation of protein complex assembly
down-regulation of protein complex assembly
downregulation of protein complex assembly
negative regulation of protein complex assembly
Any process that activates or increases the frequency, rate or extent of protein complex assembly.
up regulation of protein complex assembly
up-regulation of protein complex assembly
upregulation of protein complex assembly
positive regulation of protein complex assembly
Any process that modulates the frequency, rate or extent of cell killing, the process in which a cell brings about the death of another cell, either in the same or a different organism.
Any process that stops, prevents, or reduces the frequency, rate or extent of cell killing.
Any process that activates or increases the frequency, rate or extent of cell killing.
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.
regulation of cell projection organisation
regulation of cell projection organization and biogenesis
regulation of cell projection organization
Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.
down regulation of cell projection organization
down-regulation of cell projection organization
downregulation of cell projection organization
negative regulation of cell projection organisation
inhibition of cell projection organization
negative regulation of cell projection organization and biogenesis
negative regulation of cell projection organization
Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.
positive regulation of cell projection organisation
up regulation of cell projection organization
up-regulation of cell projection organization
upregulation of cell projection organization
activation of cell projection organization
stimulation of cell projection organization
positive regulation of cell projection organization and biogenesis
positive regulation of cell projection organization
The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.
Any process that modulates the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids.
Any process that modulates the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid.
regulation of deoxyribonuclease activity
Any process that modulates the frequency, rate or extent of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
regulation of endodeoxyribonuclease activity
Any process that stops or reduces the rate of nuclease activity, the hydrolysis of ester linkages within nucleic acids.
negative regulation of nuclease activity
Any process that activates or increases the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids.
positive regulation of nuclease activity
Any process that stops or reduces the rate of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid.
down regulation of deoxyribonuclease activity
down-regulation of deoxyribonuclease activity
downregulation of deoxyribonuclease activity
inhibition of deoxyribonuclease activity
negative regulation of deoxyribonuclease activity
Any process that activates or increases the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid.
up regulation of deoxyribonuclease activity
up-regulation of deoxyribonuclease activity
upregulation of deoxyribonuclease activity
activation of deoxyribonuclease activity
stimulation of deoxyribonuclease activity
positive regulation of deoxyribonuclease activity
Any process that stops or reduces the rate of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
down regulation of endodeoxyribonuclease activity
down-regulation of endodeoxyribonuclease activity
downregulation of endodeoxyribonuclease activity
inhibition of endodeoxyribonuclease activity
negative regulation of endodeoxyribonuclease activity
Any process that activates or increases the frequency, rate or extent of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
up regulation of endodeoxyribonuclease activity
up-regulation of endodeoxyribonuclease activity
upregulation of endodeoxyribonuclease activity
activation of endodeoxyribonuclease activity
stimulation of endodeoxyribonuclease activity
positive regulation of endodeoxyribonuclease activity
Any process that modulates the frequency, rate or extent of a response to an external stimulus.
regulation of response to external stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus.
down regulation of response to external stimulus
down-regulation of response to external stimulus
downregulation of response to external stimulus
inhibition of response to external stimulus
negative regulation of response to external stimulus
Any process that activates, maintains or increases the rate of a response to an external stimulus.
up regulation of response to external stimulus
up-regulation of response to external stimulus
upregulation of response to external stimulus
activation of response to external stimulus
stimulation of response to external stimulus
positive regulation of response to external stimulus
The process in which a methyl group is covalently attached to a molecule.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
regulation of cellular protein metabolism
regulation of cellular protein metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
down regulation of cellular protein metabolic process
down-regulation of cellular protein metabolic process
downregulation of cellular protein metabolic process
negative regulation of cellular protein metabolism
inhibition of cellular protein metabolic process
negative regulation of cellular protein metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
positive regulation of cellular protein metabolism
up regulation of cellular protein metabolic process
up-regulation of cellular protein metabolic process
upregulation of cellular protein metabolic process
activation of cellular protein metabolic process
stimulation of cellular protein metabolic process
positive regulation of cellular protein metabolic process
Any process that modulates the frequency, rate or extent of the controlled release of an icosanoid from a cell.
Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of an icosanoid from a cell.
negative regulation of eicosanoid secretion
negative regulation of icosanoid secretion
Any process that activates or increases the frequency, rate or extent of the controlled release of an icosanoid from a cell.
positive regulation of eicosanoid secretion
positive regulation of icosanoid secretion
The controlled release of icosanoids, any of a group of C20 polyunsaturated fatty acids from a cell or a tissue.
Any process that modulates the frequency, rate or extent of 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.
Any process that stops, prevents, or reduces the frequency, rate or extent of 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.
Any process that activates or increases the frequency, rate or extent of 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.
Any process that modulates the activity of a transporter.
Any process that stops or reduces the activity of a transporter.
negative regulation of transporter activity
Any process that activates or increases the activity of a transporter.
positive regulation of transporter activity
Any process that modulates the activity of an ion transporter.
regulation of ion transmembrane transporter activity
Any process that stops or reduces the activity of an ion transporter.
down regulation of ion transporter activity
down-regulation of ion transporter activity
downregulation of ion transporter activity
negative regulation of ion transporter activity
negative regulation of ion transmembrane transporter activity
Any process that activates or increases the activity of an ion transporter.
positive regulation of ion transporter activity
up regulation of ion transporter activity
up-regulation of ion transporter activity
upregulation of ion transporter activity
positive regulation of ion transmembrane transporter activity
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF').
Any process that modulates the frequency, rate, or extent of tumor necrosis factor production.
regulation of tumor necrosis factor-alpha production
regulation of tumor necrosis factor production
Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production.
down regulation of tumor necrosis factor production
down-regulation of tumor necrosis factor production
downregulation of tumor necrosis factor production
negative regulation TNF-alpha production
negative regulation tumor necrosis factor-alpha production
inhibition of tumor necrosis factor production
negative regulation of tumor necrosis factor production
Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
positive regulation of TNF-alpha production
positive regulation of tumor necrosis factor-alpha production
up regulation of tumor necrosis factor production
up-regulation of tumor necrosis factor production
upregulation of tumor necrosis factor production
activation of tumor necrosis factor production
stimulation of tumor necrosis factor production
positive regulation of tumor necrosis factor production
The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication.
Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study.
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
Any process that modulates the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
down regulation of organic acid transport
down-regulation of organic acid transport
downregulation of organic acid transport
negative regulation of organic acid transport
Any process that activates or increases the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
positive regulation of organic acid transport
The controlled release of a substance by a cell.
The disaggregation of a protein-containing macromolecular complex into its constituent components.
cellular macromolecule complex disassembly
The process in which cellular structures, including whole cells or cell parts, are generated and organized.
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
Any process in which a macromolecule is transported to, or maintained in, a specific location.
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
regulation of organelle organization and biogenesis
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome.
regulation of chromosome organization and biogenesis
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
A process in which an ion is transported across a membrane.
Note that this term is not intended for use in annotating lateral movement within membranes.
Ion channel transport, Rattus norvegicus
Ion transport by P-type ATPases, Canis familiaris
Ion transport by P-type ATPases, Taeniopygia guttata
Ion channel transport, Caenorhabditis elegans
Ion transport by P-type ATPases, Drosophila melanogaster
Ion transport by P-type ATPases, Homo sapiens
Ligand-gated ion channel transport, Homo sapiens
Ion transport by P-type ATPases, Arabidopsis thaliana
Ion channel transport, Plasmodium falciparum
Ion channel transport, Mycobacterium tuberculosis
Ion channel transport, Arabidopsis thaliana
Ion channel transport, Taeniopygia guttata
Ion transport by P-type ATPases, Bos taurus
Ion transport by P-type ATPases, Xenopus tropicalis
Ion channel transport, Xenopus tropicalis
Ion transport by P-type ATPases, Caenorhabditis elegans
Ion transport by P-type ATPases, Sus scrofa
Ion transport by P-type ATPases, Oryza sativa
Ion transport by P-type ATPases, Mus musculus
Ion transport by P-type ATPases, Rattus norvegicus
Ion transport by P-type ATPases, Mycobacterium tuberculosis
Ion transport by P-type ATPases, Plasmodium falciparum
Ion transport by P-type ATPases, Danio rerio
Ion channel transport, Drosophila melanogaster
Ion transport by P-type ATPases, Gallus gallus
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides.
regulation of cellular amide metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides.
negative regulation of cellular amide metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides.
positive regulation of cellular amide metabolic process
Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell.
cellular protein-containing complex assembly
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular nitrogen compound metabolic process
Metabolism of amino acids and derivatives, Mycobacterium tuberculosis
Metabolism of amino acids and derivatives, Escherichia coli
Metabolism of amino acids and derivatives, Arabidopsis thaliana
Metabolism of amino acids and derivatives, Xenopus tropicalis
Metabolism of amino acids and derivatives, Sus scrofa
Metabolism of amino acids and derivatives, Homo sapiens
Metabolism of amino acids and derivatives, Saccharomyces cerevisiae
Metabolism of amino acids and derivatives, Caenorhabditis elegans
Metabolism of amino acids and derivatives, Rattus norvegicus
Metabolism of amino acids and derivatives, Mus musculus
Metabolism of amino acids and derivatives, Staphylococcus aureus N315
Metabolism of amino acids and derivatives, Gallus gallus
Metabolism of amino acids and derivatives, Taeniopygia guttata
Metabolism of amino acids and derivatives, Bos taurus
Metabolism of amino acids and derivatives, Drosophila melanogaster
Metabolism of amino acids and derivatives, Oryza sativa
Metabolism of amino acids and derivatives, Plasmodium falciparum
Metabolism of amino acids and derivatives, Danio rerio
Metabolism of amino acids and derivatives, Canis familiaris
Metabolism of amino acids and derivatives, Dictyostelium discoideum
Metabolism of amino acids and derivatives, Schizosaccharomyces pombe
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells.
cellular biopolymer biosynthetic process
cellular macromolecule biosynthetic process
The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid anabolism
nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis
nucleobase, nucleoside, nucleotide and nucleic acid formation
nucleobase, nucleoside, nucleotide and nucleic acid synthesis
nucleobase-containing compound biosynthetic process
The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid breakdown
nucleobase, nucleoside, nucleotide and nucleic acid catabolism
nucleobase, nucleoside, nucleotide and nucleic acid degradation
nucleobase, nucleoside, nucleotide and nucleic acid catabolic process
nucleobase-containing compound catabolic process
The chemical reactions and pathways involving non-coding RNA transcripts (ncRNAs).
Metabolism of non-coding RNA, Sus scrofa
Metabolism of non-coding RNA, Canis familiaris
Metabolism of non-coding RNA, Homo sapiens
Metabolism of non-coding RNA, Rattus norvegicus
Metabolism of non-coding RNA, Taeniopygia guttata
Metabolism of non-coding RNA, Gallus gallus
Metabolism of non-coding RNA, Drosophila melanogaster
Metabolism of non-coding RNA, Danio rerio
Metabolism of non-coding RNA, Xenopus tropicalis
Metabolism of non-coding RNA, Bos taurus
Metabolism of non-coding RNA, Mus musculus
A protein complex that possesses methyltransferase activity.
Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other.
down regulation of transmembrane transport
down-regulation of transmembrane transport
downregulation of transmembrane transport
negative regulation of membrane transport
negative regulation of transmembrane transport
Any process that activates or increases the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other.
positive regulation of membrane transport
up regulation of transmembrane transport
up-regulation of transmembrane transport
positive regulation of transmembrane transport
Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
regulation of transmembrane ion transport
regulation of ion transmembrane transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
down regulation of transmembrane ion transport
down-regulation of transmembrane ion transport
downregulation of transmembrane ion transport
negative regulation of ion membrane transport
negative regulation of transmembrane ion transport
inhibition of transmembrane ion transport
negative regulation of ion transmembrane transport
Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
positive regulation of ion membrane transport
positive regulation of transmembrane ion transport
up regulation of transmembrane ion transport
up-regulation of transmembrane ion transport
upregulation of transmembrane ion transport
activation of transmembrane ion transport
stimulation of transmembrane ion transport
positive regulation of ion transmembrane transport
Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation.
RNA-mediated posttranscriptional gene silencing
posttranscriptional gene silencing by RNA
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mycotoxin stimulus. A mycotoxin is a toxic chemical substance produced by fungi.
The increase in size or mass of an entire organism, a part of an organism or a cell.
See also the biological process term 'cell growth ; GO:0016049'.
Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
Self-propelled movement of a cell or organism from one location to another.
Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.
Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism.
Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism.
Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.
regulation of gene expression, epigenetic
regulation of molecular function, epigenetic
Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya.
Any process, mediated by small non-coding RNAs, that stops, prevents or reduces the rate that mRNAs are effectively translated into protein.
down regulation of mRNA translation, ncRNA-mediated
down-regulation of mRNA translation, ncRNA-mediated
downregulation of mRNA translation, ncRNA-mediated
inhibition of mRNA translation, ncRNA-mediated
negative regulation of translation, ncRNA-mediated
The series of events that restore integrity to a damaged tissue, following an injury.
A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
Any process that modulates the frequency, rate or extent of cell proliferation.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
The directed movement of a motile cell or organism in response to an external stimulus.
directed movement in response to stimulus
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
A process in which planktonically growing microorganisms grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
The chemical reactions and pathways involving antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis.
The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the occurrence or rate of cell death by apoptotic process.
This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.
Regulation of Apoptosis, Rattus norvegicus
Regulation of Apoptosis, Drosophila melanogaster
Regulation of Apoptosis, Taeniopygia guttata
Regulation of Apoptosis, Xenopus tropicalis
Regulation of Apoptosis, Caenorhabditis elegans
Regulation of Apoptosis, Canis familiaris
The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide.
Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is positively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.
positive regulation of apoptotic process
Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is negatively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used.
negative regulation of apoptotic process
p75NTR signals via NF-kB, Canis familiaris
p75NTR signals via NF-kB, Taeniopygia guttata
p75NTR signals via NF-kB, Drosophila melanogaster
p75NTR signals via NF-kB, Rattus norvegicus
p75NTR signals via NF-kB, Xenopus tropicalis
Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
regulation of non-apoptotic programmed cell death
Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
positive regulation of non-apoptotic programmed cell death
positive regulation of programmed cell death
Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
down regulation of programmed cell death
down-regulation of programmed cell death
negative regulation of non-apoptotic programmed cell death
negative regulation of programmed cell death
Any process that activates or increases the activity of an enzyme.
positive regulation of metalloenzyme activity
positive regulation of catalytic activity
Any process that stops or reduces the activity of an enzyme.
down-regulation of metalloenzyme activity
down regulation of metalloenzyme activity
downregulation of metalloenzyme activity
negative regulation of metalloenzyme activity
negative regulation of catalytic activity
Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location.
establishment and maintenance of translational machinery localization
establishment and maintenance of translational protein localization
regulation of translation by machinery localisation
regulation of translation by machinery localization
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.
multicellular organismal macromolecule metabolic process
A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.
down regulation of protein complex disassembly
down-regulation of protein complex disassembly
downregulation of protein complex disassembly
inhibition of protein complex disassembly
negative regulation of protein complex disassembly
Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.
up regulation of protein complex disassembly
up-regulation of protein complex disassembly
upregulation of protein complex disassembly
activation of protein complex disassembly
stimulation of protein complex disassembly
positive regulation of protein complex disassembly
Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components.
regulation of protein complex disassembly
Any process that modulates the frequency, rate or extent of protein complex assembly.
Any process that modulates the frequency, rate or extent of 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.
Any process that activates or increases the frequency, rate or extent of 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.
Any process that stops, prevents, or reduces the frequency, rate or extent of 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.
Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties.
The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule.
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.
The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
The disaggregation of a protein complex into its constituent components, occurring at the level of an individual cell. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups.
Any process that modulates the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
negative regulation of multi-organism process
Any process that activates or increases the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
positive regulation of multi-organism process
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.
cellular macromolecular complex organization
cellular macromolecular complex subunit organisation
cellular macromolecular complex subunit organization
macromolecular complex subunit organisation
macromolecular complex subunit organization
protein-containing complex subunit organization
Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
Any process that modulates the frequency, rate or extent of 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.
A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.
cellular component biogenesis at cellular level
Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component.
regulation of cellular component biogenesis
Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component.
positive regulation of cellular component biogenesis
Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
negative regulation of molecular function
Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
positive regulation of molecular function
Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA-binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding".
transcription regulatory region DNA binding
The chemical reactions and pathways by which individual cells transform chemical substances.
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
cellular macromolecule metabolic process
The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells.
cellular macromolecule catabolic process
The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
Metabolism of proteins, Arabidopsis thaliana
Metabolism of proteins, Dictyostelium discoideum
Metabolism of proteins, Xenopus tropicalis
Metabolism of proteins, Schizosaccharomyces pombe
Metabolism of proteins, Canis familiaris
Metabolism of proteins, Taeniopygia guttata
Metabolism of proteins, Escherichia coli
Metabolism of proteins, Saccharomyces cerevisiae
Metabolism of proteins, Drosophila melanogaster
Metabolism of proteins, Rattus norvegicus
Metabolism of proteins, Caenorhabditis elegans
Metabolism of proteins, Plasmodium falciparum
The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds.
cellular nitrogen compound catabolic process
The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.
cellular nitrogen compound biosynthetic process
Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
Any constituent part of a cell, the basic structural and functional unit of all organisms.
The process of adding or removing a methyl group from one or more nucleotides within an DNA molecule.
Any process that is carried out at the cellular level which involves another organism of the same or different species.
Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
The directed movement of a protein to a specific location.
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
positive regulation of protein anabolism
positive regulation of protein biosynthesis
positive regulation of protein biosynthetic process
positive regulation of protein formation
positive regulation of protein synthesis
up regulation of protein biosynthetic process
up-regulation of protein biosynthetic process
upregulation of protein biosynthetic process
activation of protein biosynthetic process
stimulation of protein biosynthetic process
Activated DTOR phosphorylates DS6K, Drosophila melanogaster
Any process that activates or increases the frequency, rate or extent of DNA replication.
Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
down regulation of transcription, DNA-dependent
down-regulation of transcription, DNA-dependent
downregulation of transcription, DNA-dependent
negative regulation of cellular transcription, DNA-dependent
negative regulation of transcription, DNA-dependent
inhibition of transcription, DNA-dependent
down regulation of gene-specific transcription
down-regulation of gene-specific transcription
downregulation of gene-specific transcription
inhibition of gene-specific transcription
negative regulation of gene-specific transcription
negative regulation of transcription, DNA-templated
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
positive regulation of cellular transcription, DNA-dependent
positive regulation of transcription, DNA-dependent
up regulation of transcription, DNA-dependent
up-regulation of transcription, DNA-dependent
upregulation of transcription, DNA-dependent
activation of transcription, DNA-dependent
stimulation of gene-specific transcription
stimulation of transcription, DNA-dependent
activation of gene-specific transcription
positive regulation of gene-specific transcription
up regulation of gene-specific transcription
up-regulation of gene-specific transcription
upregulation of gene-specific transcription
positive regulation of transcription, DNA-templated
Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation.
down regulation of translational elongation
down-regulation of translational elongation
downregulation of translational elongation
negative regulation of translational elongation
Any process that activates or increases the frequency, rate or extent of translational elongation.
up regulation of translational elongation
up-regulation of translational elongation
upregulation of translational elongation
positive regulation of translational elongation
Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination.
down regulation of translational termination
down-regulation of translational termination
downregulation of translational termination
negative regulation of translational termination
Any process that activates or increases the frequency, rate or extent of translational termination.
up regulation of translational termination
up-regulation of translational termination
upregulation of translational termination
stimulation of translational termination
positive regulation of translational termination
Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism.
Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
inhibition of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
negative regulation of nucleobase-containing compound metabolic process
Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
positive regulation of nucleobase-containing compound metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.
down regulation of translational initiation
down-regulation of translational initiation
downregulation of translational initiation
negative regulation of translational initiation
Any process that activates or increases the frequency, rate or extent of translational initiation.
up regulation of translational initiation
up-regulation of translational initiation
upregulation of translational initiation
positive regulation of translational initiation
Any process, mediated by small non-coding RNAs, that modulates the frequency, rate or extent that mRNAs are effectively translated into protein.
regulation of translation, ncRNA-mediated
The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
The controlled release of acid by a cell or a tissue.
The controlled release of a substance by a cell or a tissue.
The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-).
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
positive regulation of physiological process
positive regulation of biological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
negative regulation of physiological process
negative regulation of biological process
Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
positive regulation of cellular physiological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
negative regulation of cellular physiological process
The process that gives rise to the configuration of the constituent parts of an anatomical structure. This process pertains to the physical shaping of a rudimentary structure. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
anatomical structure structural organization
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
positive regulation of response to stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
negative regulation of response to stimulus
The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
formation of an anatomical structure involved in morphogenesis
Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense.
anatomical structure formation involved in morphogenesis
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
The controlled release of arachidonic acid from a cell or a tissue.
This term should be used to annotate release of arachidonic acid from the cell. For the hydrolytic release of arachidonic acid from a phospholipid, consider instead annotating to 'phospholipase A2 activity ; GO:0004623'.
The regulated release of cytokines from a cell. Cytokines are any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
Any process that modulates the frequency, rate or extent of the regulated release of cytokines from a cell.
Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell.
Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell.
negative regulation of protein secretion
Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of cytokines from a cell.
negative regulation of cytokine secretion
Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
positive regulation of protein secretion
Any process that activates or increases the frequency, rate or extent of the regulated release of cytokines from a cell.
positive regulation of cytokine secretion
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
Any process that modulates the activity of an enzyme.
Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
regulation of cellular physiological process
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue.
Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue.
Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue.
Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA.
down regulation of DNA metabolic process
down-regulation of DNA metabolic process
negative regulation of DNA metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA.
positive regulation of DNA metabolic process
Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
down regulation of developmental process
down-regulation of developmental process
negative regulation of developmental process
Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
positive regulation of developmental process
Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
regulation of cellular component organisation
regulation of cellular component organization and biogenesis
regulation of cellular component organization
Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
negative regulation of cell organisation
negative regulation of cellular component organization and biogenesis
negative regulation of cellular component organization
Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
positive regulation of cell organisation
positive regulation of cellular component organization and biogenesis
positive regulation of cellular component organization
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
regulation of nitrogen metabolic process
regulation of nitrogen compound metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
down regulation of nitrogen metabolic process
down-regulation of nitrogen metabolic process
downregulation of nitrogen metabolic process
negative regulation of nitrogen metabolic process
negative regulation of nitrogen metabolism
inhibition of nitrogen metabolic process
negative regulation of nitrogen compound metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
positive regulation of nitrogen metabolic process
positive regulation of nitrogen metabolism
up regulation of nitrogen metabolic process
up-regulation of nitrogen metabolic process
upregulation of nitrogen metabolic process
activation of nitrogen metabolic process
stimulation of nitrogen metabolic process
positive regulation of nitrogen compound metabolic process
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
establishment and maintenance of localization
establishment and maintenance of position
establishment and maintenance of cellular component location
establishment and maintenance of substance location
establishment and maintenance of substrate location
Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
positive regulation of protein transport
Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
negative regulation of protein transport
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.
regulation of multicellular organismal process
Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
up regulation of multicellular organismal process
up-regulation of multicellular organismal process
upregulation of multicellular organismal process
activation of multicellular organismal process
stimulation of multicellular organismal process
positive regulation of multicellular organismal process
Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
down regulation of multicellular organismal process
down-regulation of multicellular organismal process
downregulation of multicellular organismal process
inhibition of multicellular organismal process
negative regulation of multicellular organismal process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein.
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein.
positive regulation of protein metabolism
up regulation of protein metabolic process
up-regulation of protein metabolic process
upregulation of protein metabolic process
stimulation of protein metabolic process
positive regulation of protein metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein.
down regulation of protein metabolic process
down-regulation of protein metabolic process
downregulation of protein metabolic process
negative regulation of protein metabolism
negative regulation of protein metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA.
down regulation of RNA metabolic process
down-regulation of RNA metabolic process
negative regulation of RNA metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA.
positive regulation of RNA metabolic process
Any process that modulates the frequency, rate or extent of the movement of a cellular component.
regulation of cellular component movement
Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component.
negative regulation of cellular component motion
negative regulation of cellular component movement
Any process that activates or increases the frequency, rate or extent of the movement of a cellular component.
positive regulation of cellular component motion
positive regulation of cellular component movement
A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds.
positive regulation of hydrolase activity
Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds.
negative regulation of hydrolase activity
A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane.
establishment and maintenance of cellular localization
establishment and maintenance of localization in cell or cell membrane
Any process in which a cell is transported to, and/or maintained in, a specific location.
establishment and maintenance of cell localization
establishment and maintenance of localization of cell
A biological process which involves another organism of the same or different species.
physiological interaction between organisms
physiological interaction with other organism
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
Transmembrane transport requires transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes.
SLC-mediated transmembrane transport, Taeniopygia guttata
SLC-mediated transmembrane transport, Caenorhabditis elegans
SLC-mediated transmembrane transport, Escherichia coli
SLC-mediated transmembrane transport, Sus scrofa
Transmembrane transport of small molecules, Staphylococcus aureus N315
Transmembrane transport of small molecules, Caenorhabditis elegans
SLC-mediated transmembrane transport, Canis familiaris
SLC-mediated transmembrane transport, Xenopus tropicalis
SLC-mediated transmembrane transport, Staphylococcus aureus N315
Transmembrane transport of small molecules, Plasmodium falciparum
ABC-family proteins mediated transport, Mus musculus
ABC-family proteins mediated transport, Staphylococcus aureus N315
ABC-family proteins mediated transport, Escherichia coli
ABC-family proteins mediated transport, Plasmodium falciparum
ABC-family proteins mediated transport, Mycobacterium tuberculosis
ABC-family proteins mediated transport, Homo sapiens
Transmembrane transport of small molecules, Homo sapiens
SLC-mediated transmembrane transport, Homo sapiens
ABC-family proteins mediated transport, Taeniopygia guttata
SLC-mediated transmembrane transport, Gallus gallus
Transmembrane transport of small molecules, Canis familiaris
ABC-family proteins mediated transport, Canis familiaris
Transmembrane transport of small molecules, Saccharomyces cerevisiae
Transmembrane transport of small molecules, Rattus norvegicus
SLC-mediated transmembrane transport, Bos taurus
ABC-family proteins mediated transport, Sus scrofa
SLC-mediated transmembrane transport, Danio rerio
Transmembrane transport of small molecules, Bos taurus
SLC-mediated transmembrane transport, Plasmodium falciparum
SLC-mediated transmembrane transport, Saccharomyces cerevisiae
ABC-family proteins mediated transport, Bos taurus
ABC-family proteins mediated transport, Rattus norvegicus
ABC-family proteins mediated transport, Schizosaccharomyces pombe
ABC-family proteins mediated transport, Caenorhabditis elegans
Transmembrane transport of small molecules, Oryza sativa
SLC-mediated transmembrane transport, Mus musculus
SLC-mediated transmembrane transport, Rattus norvegicus
Transmembrane transport of small molecules, Escherichia coli
ABC-family proteins mediated transport, Oryza sativa
Transmembrane transport of small molecules, Drosophila melanogaster
Transmembrane transport of small molecules, Schizosaccharomyces pombe
SLC-mediated transmembrane transport, Oryza sativa
ABC-family proteins mediated transport, Xenopus tropicalis
Transmembrane transport of small molecules, Taeniopygia guttata
Transmembrane transport of small molecules, Gallus gallus
SLC-mediated transmembrane transport, Schizosaccharomyces pombe
ABC-family proteins mediated transport, Arabidopsis thaliana
SLC-mediated transmembrane transport, Mycobacterium tuberculosis
Transmembrane transport of small molecules, Mycobacterium tuberculosis
ABC-family proteins mediated transport, Gallus gallus
Transmembrane transport of small molecules, Dictyostelium discoideum
Transmembrane transport of small molecules, Mus musculus
ABC-family proteins mediated transport, Drosophila melanogaster
ABC-family proteins mediated transport, Danio rerio
SLC-mediated transmembrane transport, Dictyostelium discoideum
Transmembrane transport of small molecules, Sus scrofa
SLC-mediated transmembrane transport, Arabidopsis thaliana
Transmembrane transport of small molecules, Arabidopsis thaliana
ABC-family proteins mediated transport, Saccharomyces cerevisiae
Transmembrane transport of small molecules, Xenopus tropicalis
SLC-mediated transmembrane transport, Drosophila melanogaster
Transmembrane transport of small molecules, Danio rerio
ABC-family proteins mediated transport, Dictyostelium discoideum
Any process that modulates the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism.
regulation of posttranscriptional gene silencing
Any process that increases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism.
positive regulation of posttranscriptional gene silencing
Any process that decreases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism.
negative regulation of posttranscriptional gene silencing
Any process that modulates the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA.
regulation of antisense RNA transcription
Any process that decreases the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA.
negative regulation of antisense RNA transcription
Any process that increases the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA.
positive regulation of antisense RNA transcription
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
regulation of macromolecule metabolic process
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).
Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell.
Any process that modulates the rate, frequency, or extent of cell projection assembly.
Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
Any apoptotic process that contributes to the shaping of an anatomical structure.
apoptotic process involved in morphogenesis
Any process that regulates the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes.
Any process that decreases the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes.
negative regulation of gene silencing by RNA
Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
Any process that decreases the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a platelet aggregation inhibitor stimulus.
response to platelet aggregation inhibitor
The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
Any process that modulates a measurable attribute of any biological process, quality or function.
Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location.
regulation of establishment of protein localisation
regulation of establishment of protein localization
A process of negative regulation of translation that is mediated by the association of small interfering RNAs (siRNAs) with a cognate target mRNA.
RNA interference, negative regulation of translation
down regulation of translation involved in RNA interference
down-regulation of translation involved in RNA interference
downregulation of translation involved in RNA interference
inhibition of translation involved in RNA interference
negative regulation of translation involved in RNA interference
Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
cellular response to organic cyclic substance
cellular response to organic cyclic compound
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
cellular response to organonitrogen compound
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism.
cellular response to endogenous stimulus
The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon.
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
organic molecular entity metabolic process
The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
tumor necrosis factor superfamily cytokine production
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.
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.
RNA-protein complex subunit organization
protein-RNA complex subunit organization
ribonucleoprotein complex subunit organisation
ribonucleoprotein complex subunit organization
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation or biogenesis
cellular component organisation or biogenesis at cellular level
cellular component organization or biogenesis at cellular level
cellular component organization or biogenesis
The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytochalasin B stimulus.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
Any process that modulates the frequency, rate or extent of a cellular response to stress. Cellular response to stress is a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
regulation of cellular response to stress
Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the rate, frequency, or extent of arachidonic acid secretion, the controlled release of arachidonic acid from a cell or a tissue.
regulation of arachidonic acid secretion
Any process that increases the rate, frequency, or extent of arachidonic acid secretion, the controlled release of arachidonic acid from a cell or a tissue.
positive regulation of arachidonic acid secretion
Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
Any cellular metabolic process involving nucleic acids.
The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
nucleic acid phosphodiester bond hydrolysis
Any process that modulates the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan.
Any process that increases the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan.
Any process that decreases the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan.
Synthesis of DNA that is a part of the process of duplicating one or more molecules of DNA.
DNA synthesis involved in DNA replication
Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure.
A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
induction of apoptosis by extracellular signals
This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways.
Death Receptor Signalling, Xenopus tropicalis
FasL/ CD95L signaling, Rattus norvegicus
FASL binds FAS Receptor, Taeniopygia guttata
Cell death signalling via NRAGE, NRIF and NADE, Drosophila melanogaster
Cell death signalling via NRAGE, NRIF and NADE, Canis familiaris
Extrinsic Pathway for Apoptosis, Homo sapiens
Ceramide signalling, Caenorhabditis elegans
Cell death signalling via NRAGE, NRIF and NADE, Oryza sativa
FASL binds FAS Receptor, Rattus norvegicus
Cell death signalling via NRAGE, NRIF and NADE, Rattus norvegicus
FASL binds FAS Receptor, Canis familiaris
Cell death signalling via NRAGE, NRIF and NADE, Sus scrofa
Extrinsic Pathway for Apoptosis, Canis familiaris
Extrinsic Pathway for Apoptosis, Caenorhabditis elegans
FasL/ CD95L signaling, Xenopus tropicalis
Cell death signalling via NRAGE, NRIF and NADE, Dictyostelium discoideum
FASL binds FAS Receptor, Xenopus tropicalis
Cell death signalling via NRAGE, NRIF and NADE, Homo sapiens
Death Receptor Signalling, Taeniopygia guttata
Death Receptor Signalling, Gallus gallus
Ceramide signalling, Taeniopygia guttata
Ceramide signalling, Drosophila melanogaster
Extrinsic Pathway for Apoptosis, Xenopus tropicalis
Cell death signalling via NRAGE, NRIF and NADE, Taeniopygia guttata
Extrinsic Pathway for Apoptosis, Gallus gallus
Extrinsic Pathway for Apoptosis, Bos taurus
Cell death signalling via NRAGE, NRIF and NADE, Danio rerio
Cell death signalling via NRAGE, NRIF and NADE, Gallus gallus
Death Receptor Signalling, Canis familiaris
Cell death signalling via NRAGE, NRIF and NADE, Schizosaccharomyces pombe
Cell death signalling via NRAGE, NRIF and NADE, Xenopus tropicalis
Ceramide signalling, Schizosaccharomyces pombe
Cell death signalling via NRAGE, NRIF and NADE, Arabidopsis thaliana
Cell death signalling via NRAGE, NRIF and NADE, Bos taurus
Extrinsic Pathway for Apoptosis, Sus scrofa
Extrinsic Pathway for Apoptosis, Danio rerio
Cell death signalling via NRAGE, NRIF and NADE, Caenorhabditis elegans
Ceramide signalling, Saccharomyces cerevisiae
Extrinsic Pathway for Apoptosis, Taeniopygia guttata
FasL/ CD95L signaling, Taeniopygia guttata
Death Receptor Signalling, Rattus norvegicus
Extrinsic Pathway for Apoptosis, Rattus norvegicus
Cell death signalling via NRAGE, NRIF and NADE, Saccharomyces cerevisiae
Extrinsic Pathway for Apoptosis, Mus musculus
Cell death signalling via NRAGE, NRIF and NADE, Mus musculus
A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are 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.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
Any constituent part of a neuron, the basic cellular unit of nervous tissue. A typical neuron consists of a cell body (often called the soma), an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
The cellular synthesis of RNA on a template of nucleic acid (DNA or RNA).
Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.
The ion channels through which current flows during an action potential should be annotated to the process 'action potential'. Gene products involved in modulating the characteristics of an action potential via changing the expression levels or the activity of these channels (e.g. modulating their kinetics or voltage sensitivity) should be annotated to this regulation term.
Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon.
plasma membrane bounded cell projection assembly
Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly.
regulation of plasma membrane bounded cell projection assembly
Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly.
negative regulation of plasma membrane bounded cell projection assembly
Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly.
positive regulation of plasma membrane bounded cell projection assembly
Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections.
regulation of plasma membrane bounded cell projection organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon.
plasma membrane bounded cell projection organization
Catalytic activity that acts to modify DNA.
Any process that modulates the frequency, rate or extent of execution phase of apoptosis.
regulation of execution phase of apoptosis
Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis.
down regulation of execution phase of apoptosis
down-regulation of execution phase of apoptosis
downregulation of execution phase of apoptosis
inhibition of execution phase of apoptosis
negative regulation of execution phase of apoptosis
Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis.
up regulation of execution phase of apoptosis
up-regulation of execution phase of apoptosis
upregulation of execution phase of apoptosis
activation of execution phase of apoptosis
positive regulation of execution phase of apoptosis
Any process that stops, prevents or reduces the frequency, rate or extent of arachidonic acid secretion.
down regulation of arachidonic acid secretion
down-regulation of arachidonic acid secretion
downregulation of arachidonic acid secretion
inhibition of arachidonic acid secretion
negative regulation of arachidonic acid secretion
Any process that modulates the frequency, rate or extent of RNA interference.
regulation of posttranscriptional gene silencing by siRNA
Any process that stops, prevents or reduces the frequency, rate or extent of RNA interference.
down regulation of posttranscriptional gene silencing by siRNA
down-regulation of posttranscriptional gene silencing by siRNA
downregulation of posttranscriptional gene silencing by siRNA
inhibition of posttranscriptional gene silencing by siRNA
negative regulation of posttranscriptional gene silencing by siRNA
Any process that activates or increases the frequency, rate or extent of RNA interference.
activation of posttranscriptional gene silencing by siRNA
positive regulation of posttranscriptional gene silencing by siRNA
up regulation of posttranscriptional gene silencing by siRNA
up-regulation of posttranscriptional gene silencing by siRNA
upregulation of posttranscriptional gene silencing by siRNA
Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex.
regulation of translation initiation ternary complex assembly
regulation of formation of translation initiation ternary complex
Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation initiation ternary complex.
down regulation of formation of translation initiation ternary complex
down regulation of translation initiation ternary complex assembly
down-regulation of formation of translation initiation ternary complex
down-regulation of translation initiation ternary complex assembly
downregulation of formation of translation initiation ternary complex
downregulation of translation initiation ternary complex assembly
inhibition of translation initiation ternary complex assembly
negative regulation of translation initiation ternary complex assembly
inhibition of formation of translation initiation ternary complex
negative regulation of formation of translation initiation ternary complex
Any process that activates or increases the frequency, rate or extent of formation of translation initiation ternary complex.
activation of translation initiation ternary complex assembly
positive regulation of translation initiation ternary complex assembly
up regulation of formation of translation initiation ternary complex
up regulation of translation initiation ternary complex assembly
up-regulation of formation of translation initiation ternary complex
up-regulation of translation initiation ternary complex assembly
upregulation of formation of translation initiation ternary complex
upregulation of translation initiation ternary complex assembly
activation of formation of translation initiation ternary complex
positive regulation of formation of translation initiation ternary complex
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 cytochalasin B stimulus.
The chemical reactions and pathways involving organic cyclic compound.
organic cyclic compound metabolic process
The chemical reactions and pathways resulting in the breakdown of organic cyclic compound.
organic cyclic compound catabolic process
The chemical reactions and pathways resulting in the formation of organic cyclic compound.
organic cyclic compound biosynthetic process
Interacting selectively and non-covalently with heterocyclic compound.
The chemical reactions and pathways involving organonitrogen compound.
organonitrogen compound metabolic process
The chemical reactions and pathways resulting in the formation of organonitrogen compound.
organonitrogen compound biosynthetic process
The directed movement of a fatty acid derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon.
organic molecular entity catabolic process
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
organic molecular entity biosynthetic process
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus.
cellular response to nitrogen molecular entity
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 oxygen-containing compound stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus.
cellular response to oxygen molecular entity
cellular response to oxygen-containing compound
Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis.
regulation of apoptosis involved in morphogenesis
regulation of apoptosis involved in development
regulation of apoptotic process involved in morphogenesis
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis.
down regulation of apoptotic process involved in morphogenesis
down-regulation of apoptotic process involved in morphogenesis
downregulation of apoptotic process involved in morphogenesis
down regulation of apoptosis involved in morphogenesis
down-regulation of apoptosis involved in morphogenesis
downregulation of apoptosis involved in morphogenesis
inhibition of apoptosis involved in morphogenesis
inhibition of apoptotic process involved in morphogenesis
negative regulation of apoptosis involved in morphogenesis
down regulation of apoptosis involved in development
down regulation of morphogenetic apoptosis
down-regulation of apoptosis involved in development
down-regulation of morphogenetic apoptosis
downregulation of apoptosis involved in development
downregulation of morphogenetic apoptosis
inhibition of apoptosis involved in development
negative regulation of apoptosis involved in development
negative regulation of morphogenetic apoptosis
negative regulation of apoptotic process involved in morphogenesis
Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis.
up regulation of apoptotic process involved in morphogenesis
up-regulation of apoptotic process involved in morphogenesis
upregulation of apoptotic process involved in morphogenesis
activation of apoptosis involved in morphogenesis
activation of apoptotic process involved in morphogenesis
positive regulation of apoptosis involved in morphogenesis
up regulation of apoptosis involved in morphogenesis
up-regulation of apoptosis involved in morphogenesis
upregulation of apoptosis involved in morphogenesis
activation of apoptosis involved in development
positive regulation of apoptosis involved in development
positive regulation of morphogenetic apoptosis
up regulation of apoptosis involved in development
up regulation of morphogenetic apoptosis
up-regulation of apoptosis involved in development
up-regulation of morphogenetic apoptosis
upregulation of apoptosis involved in development
positive regulation of apoptotic process involved in morphogenesis
A protein complex which is capable of catalytic activity.
Any process that modulates the frequency, rate or extent of apoptotic DNA fragmentation.
regulation of DNA catabolic process during apoptosis
regulation of DNA catabolism during apoptosis
regulation of DNA fragmentation involved in apoptotic nuclear change
regulation of endonucleolytic DNA catabolic process involved in apoptosis
DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases (see GO:0006309 'apoptotic DNA fragmentation'). Gene products involved in compartmentalization of such 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).
regulation of apoptotic DNA fragmentation
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic DNA fragmentation.
down regulation of DNA catabolic process during apoptosis
down regulation of DNA catabolism during apoptosis
down regulation of DNA fragmentation involved in apoptotic nuclear change
down regulation of apoptotic DNA fragmentation
down regulation of endonucleolytic DNA catabolic process involved in apoptosis
down-regulation of DNA catabolic process during apoptosis
down-regulation of DNA catabolism during apoptosis
down-regulation of DNA fragmentation involved in apoptotic nuclear change
down-regulation of apoptotic DNA fragmentation
down-regulation of endonucleolytic DNA catabolic process involved in apoptosis
downregulation of DNA catabolic process during apoptosis
downregulation of DNA catabolism during apoptosis
downregulation of DNA fragmentation involved in apoptotic nuclear change
downregulation of apoptotic DNA fragmentation
downregulation of endonucleolytic DNA catabolic process involved in apoptosis
negative regulation of DNA catabolic process during apoptosis
negative regulation of DNA catabolism during apoptosis
negative regulation of DNA fragmentation involved in apoptotic nuclear change
negative regulation of endonucleolytic DNA catabolic process involved in apoptosis
inhibition of DNA catabolic process during apoptosis
inhibition of DNA catabolism during apoptosis
inhibition of DNA fragmentation involved in apoptotic nuclear change
inhibition of apoptotic DNA fragmentation
inhibition of endonucleolytic DNA catabolic process involved in apoptosis
negative regulation of apoptotic DNA fragmentation
Any process that activates or increases the frequency, rate or extent of apoptotic DNA fragmentation.
positive regulation of DNA catabolic process during apoptosis
positive regulation of DNA catabolism during apoptosis
positive regulation of DNA fragmentation involved in apoptotic nuclear change
positive regulation of endonucleolytic DNA catabolic process involved in apoptosis
up regulation of DNA catabolic process during apoptosis
up regulation of DNA catabolism during apoptosis
up regulation of DNA fragmentation involved in apoptotic nuclear change
up regulation of apoptotic DNA fragmentation
up regulation of endonucleolytic DNA catabolic process involved in apoptosis
up-regulation of DNA catabolic process during apoptosis
up-regulation of DNA catabolism during apoptosis
up-regulation of DNA fragmentation involved in apoptotic nuclear change
up-regulation of apoptotic DNA fragmentation
up-regulation of endonucleolytic DNA catabolic process involved in apoptosis
upregulation of DNA catabolic process during apoptosis
upregulation of DNA catabolism during apoptosis
upregulation of DNA fragmentation involved in apoptotic nuclear change
upregulation of apoptotic DNA fragmentation
upregulation of endonucleolytic DNA catabolic process involved in apoptosis
activation of DNA catabolic process during apoptosis
activation of DNA catabolism during apoptosis
activation of DNA fragmentation involved in apoptotic nuclear change
activation of apoptotic DNA fragmentation
activation of endonucleolytic DNA catabolic process involved in apoptosis
positive regulation of apoptotic DNA fragmentation
Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process.
down regulation of RNA biosynthetic process
down-regulation of RNA biosynthetic process
downregulation of RNA biosynthetic process
negative regulation of RNA biosynthetic process
Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process.
up regulation of RNA biosynthetic process
up-regulation of RNA biosynthetic process
upregulation of RNA biosynthetic process
positive regulation of RNA biosynthetic process
Any apoptotic process that is involved in anatomical structure development.
apoptotic cell death involved in anatomical structure development
apoptotic cell death involved in development of an anatomical structure
apoptotic process involved in anatomical structure development
apoptotic process involved in development of an anatomical structure
apoptotic programmed cell death involved in anatomical structure development
apoptotic programmed cell death involved in development of an anatomical structure
programmed cell death by apoptosis involved in anatomical structure development
programmed cell death by apoptosis involved in development of an anatomical structure
activation of apoptosis involved in anatomical structure development
activation of apoptosis involved in development of an anatomical structure
apoptosis involved in anatomical structure development
apoptosis involved in development of an anatomical structure
apoptosis signaling involved in anatomical structure development
apoptosis signaling involved in development of an anatomical structure
apoptotic program involved in anatomical structure development
apoptotic program involved in development of an anatomical structure
type I programmed cell death involved in anatomical structure development
type I programmed cell death involved in development of an anatomical structure
apoptosis activator activity involved in anatomical structure development
apoptosis activator activity involved in development of an anatomical structure
commitment to apoptosis involved in anatomical structure development
commitment to apoptosis involved in development of an anatomical structure
induction of apoptosis by p53 involved in anatomical structure development
induction of apoptosis by p53 involved in development of an anatomical structure
induction of apoptosis involved in anatomical structure development
induction of apoptosis involved in development of an anatomical structure
signaling (initiator) caspase activity involved in anatomical structure development
signaling (initiator) caspase activity involved in development of an anatomical structure
apoptotic process involved in development
Any process that modulates the frequency, rate or extent of response to wounding.
regulation of physiological response to wounding
Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding.
down regulation of physiological response to wounding
down-regulation of physiological response to wounding
downregulation of physiological response to wounding
negative regulation of physiological response to wounding
inhibition of physiological response to wounding
negative regulation of response to wounding
Any process that activates or increases the frequency, rate or extent of response to wounding.
positive regulation of physiological response to wounding
up regulation of physiological response to wounding
up-regulation of physiological response to wounding
upregulation of physiological response to wounding
activation of physiological response to wounding
positive regulation of response to wounding
Any process that modulates the frequency, rate or extent of nucleus organization.
regulation of nuclear organization and biogenesis
regulation of nucleus organization and biogenesis
Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription.
regulation of nucleic acid-templated transcription
Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
down regulation of nucleic acid-templated transcription
down-regulation of nucleic acid-templated transcription
downregulation of nucleic acid-templated transcription
inhibition of nucleic acid-templated transcription
negative regulation of nucleic acid-templated transcription
Any process that activates or increases the frequency, rate or extent of nucleic acid-templated transcription.
up regulation of nucleic acid-templated transcription
up-regulation of nucleic acid-templated transcription
upregulation of nucleic acid-templated transcription
activation of nucleic acid-templated transcription
positive regulation of nucleic acid-templated transcription
Any process that modulates the frequency, rate or extent of secretion by cell.
Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell.
negative regulation of cellular secretion
negative regulation of secretion by cell
Any process that activates or increases the frequency, rate or extent of secretion by cell.
positive regulation of cellular secretion
positive regulation of secretion by cell
Any process that modulates the frequency, rate or extent of tumor necrosis factor superfamily cytokine production.
regulation of TNF superfamily production
regulation of tumor necrosis factor superfamily cytokine production
Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor superfamily cytokine production.
down regulation of TNFSF cytokine production
down regulation of tumor necrosis factor superfamily cytokine production
down-regulation of TNFSF cytokine production
down-regulation of tumor necrosis factor superfamily cytokine production
downregulation of TNFSF cytokine production
downregulation of tumor necrosis factor superfamily cytokine production
negative regulation of TNFSF cytokine production
inhibition of tumor necrosis factor superfamily cytokine production
down regulation of TNF superfamily production
down-regulation of TNF superfamily production
downregulation of TNF superfamily production
inhibition of TNF superfamily production
negative regulation of TNF superfamily production
negative regulation of tumor necrosis factor superfamily cytokine production
Any process that activates or increases the frequency, rate or extent of tumor necrosis factor superfamily cytokine production.
positive regulation of TNFSF cytokine production
up regulation of TNFSF cytokine production
up regulation of tumor necrosis factor superfamily cytokine production
up-regulation of TNFSF cytokine production
up-regulation of tumor necrosis factor superfamily cytokine production
upregulation of TNFSF cytokine production
upregulation of tumor necrosis factor superfamily cytokine production
activation of tumor necrosis factor superfamily cytokine production
activation of TNF superfamily production
positive regulation of TNF superfamily production
up regulation of TNF superfamily production
up-regulation of TNF superfamily production
upregulation of TNF superfamily production
positive regulation of tumor necrosis factor superfamily cytokine production
Any process that modulates the frequency, rate or extent of DNA catabolic process.
Any process that stops, prevents or reduces the frequency, rate or extent of DNA catabolic process.
down regulation of DNA catabolic process
down-regulation of DNA catabolic process
negative regulation of DNA catabolic process
Any process that activates or increases the frequency, rate or extent of DNA catabolic process.
positive regulation of DNA catabolic process
Any process that stops, prevents or reduces the frequency, rate or extent of anion transport.
Any process that activates or increases the frequency, rate or extent of anion transport.
Any process that modulates the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
regulation of cellular protein localisation
regulation of channel localizer activity
regulation of cellular protein localization
Any process that stops, prevents or reduces the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
down regulation of cellular protein localisation
down regulation of cellular protein localization
down-regulation of cellular protein localisation
down-regulation of cellular protein localization
downregulation of cellular protein localisation
downregulation of cellular protein localization
negative regulation of cellular protein localisation
down regulation of channel localizer activity
down-regulation of channel localizer activity
downregulation of channel localizer activity
inhibition of cellular protein localisation
inhibition of cellular protein localization
inhibition of channel localizer activity
negative regulation of channel localizer activity
negative regulation of cellular protein localization
Any process that activates or increases the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
positive regulation of cellular protein localisation
up regulation of cellular protein localisation
up regulation of cellular protein localization
up-regulation of cellular protein localisation
up-regulation of cellular protein localization
upregulation of cellular protein localisation
upregulation of cellular protein localization
activation of cellular protein localisation
activation of cellular protein localization
activation of channel localizer activity
positive regulation of channel localizer activity
up regulation of channel localizer activity
up-regulation of channel localizer activity
upregulation of channel localizer activity
positive regulation of cellular protein localization
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.
Any process that modulates the frequency, rate or extent of bleb assembly.
Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly.
Any process that activates or increases the frequency, rate or extent of bleb assembly.
Any process that modulates the frequency, rate or extent of tumor necrosis factor secretion.
regulation of TNF superfamily, member 2 secretion
regulation of tumor necrosis factor alpha secretion
regulation of tumor necrosis factor ligand superfamily member 2 secretion
regulation of tumor necrosis factor secretion
Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor secretion.
down regulation of TNF superfamily, member 2 secretion
down regulation of tumor necrosis factor alpha secretion
down regulation of tumor necrosis factor ligand superfamily member 2 secretion
down regulation of tumor necrosis factor secretion
down-regulation of TNF superfamily, member 2 secretion
down-regulation of tumor necrosis factor alpha secretion
down-regulation of tumor necrosis factor ligand superfamily member 2 secretion
down-regulation of tumor necrosis factor secretion
downregulation of TNF superfamily, member 2 secretion
downregulation of tumor necrosis factor alpha secretion
downregulation of tumor necrosis factor ligand superfamily member 2 secretion
downregulation of tumor necrosis factor secretion
negative regulation of TNF superfamily, member 2 secretion
negative regulation of TNF-alpha secretion
negative regulation of cachectin secretion
negative regulation of tumor necrosis factor alpha secretion
negative regulation of tumor necrosis factor ligand superfamily member 2 secretion
inhibition of TNF superfamily, member 2 secretion
inhibition of tumor necrosis factor alpha secretion
inhibition of tumor necrosis factor ligand superfamily member 2 secretion
inhibition of tumor necrosis factor secretion
negative regulation of tumor necrosis factor secretion
Any process that activates or increases the frequency, rate or extent of tumor necrosis factor secretion.
positive regulation of TNF superfamily, member 2 secretion
positive regulation of TNF-alpha secretion
positive regulation of cachectin secretion
positive regulation of tumor necrosis factor alpha secretion
positive regulation of tumor necrosis factor ligand superfamily member 2 secretion
up regulation of TNF superfamily, member 2 secretion
up regulation of tumor necrosis factor alpha secretion
up regulation of tumor necrosis factor ligand superfamily member 2 secretion
up regulation of tumor necrosis factor secretion
up-regulation of TNF superfamily, member 2 secretion
up-regulation of tumor necrosis factor alpha secretion
up-regulation of tumor necrosis factor ligand superfamily member 2 secretion
up-regulation of tumor necrosis factor secretion
upregulation of TNF superfamily, member 2 secretion
upregulation of tumor necrosis factor alpha secretion
upregulation of tumor necrosis factor ligand superfamily member 2 secretion
upregulation of tumor necrosis factor secretion
activation of TNF superfamily, member 2 secretion
activation of tumor necrosis factor alpha secretion
activation of tumor necrosis factor ligand superfamily member 2 secretion
activation of tumor necrosis factor secretion
positive regulation of tumor necrosis factor secretion
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development.
down regulation of apoptotic cell death involved in anatomical structure development
down regulation of apoptotic cell death involved in development of an anatomical structure
down regulation of apoptotic process involved in anatomical structure development
down regulation of apoptotic process involved in development
down regulation of apoptotic process involved in development of an anatomical structure
down regulation of apoptotic programmed cell death involved in anatomical structure development
down regulation of apoptotic programmed cell death involved in development of an anatomical structure
down regulation of programmed cell death by apoptosis involved in anatomical structure development
down regulation of programmed cell death by apoptosis involved in development of an anatomical structure
down-regulation of apoptotic cell death involved in anatomical structure development
down-regulation of apoptotic cell death involved in development of an anatomical structure
down-regulation of apoptotic process involved in anatomical structure development
down-regulation of apoptotic process involved in development
down-regulation of apoptotic process involved in development of an anatomical structure
down-regulation of apoptotic programmed cell death involved in anatomical structure development
down-regulation of apoptotic programmed cell death involved in development of an anatomical structure
down-regulation of programmed cell death by apoptosis involved in anatomical structure development
down-regulation of programmed cell death by apoptosis involved in development of an anatomical structure
downregulation of apoptotic cell death involved in anatomical structure development
downregulation of apoptotic cell death involved in development of an anatomical structure
downregulation of apoptotic process involved in anatomical structure development
downregulation of apoptotic process involved in development
downregulation of apoptotic process involved in development of an anatomical structure
downregulation of apoptotic programmed cell death involved in anatomical structure development
downregulation of apoptotic programmed cell death involved in development of an anatomical structure
downregulation of programmed cell death by apoptosis involved in anatomical structure development
downregulation of programmed cell death by apoptosis involved in development of an anatomical structure
negative regulation of apoptotic cell death involved in anatomical structure development
negative regulation of apoptotic cell death involved in development of an anatomical structure
negative regulation of apoptotic process involved in anatomical structure development
negative regulation of apoptotic process involved in development of an anatomical structure
negative regulation of apoptotic programmed cell death involved in anatomical structure development
negative regulation of apoptotic programmed cell death involved in development of an anatomical structure
negative regulation of programmed cell death by apoptosis involved in anatomical structure development
negative regulation of programmed cell death by apoptosis involved in development of an anatomical structure
down regulation of activation of apoptosis involved in anatomical structure development
down regulation of activation of apoptosis involved in development of an anatomical structure
down regulation of apoptosis involved in anatomical structure development
down regulation of apoptosis involved in development of an anatomical structure
down regulation of apoptosis signaling involved in anatomical structure development
down regulation of apoptosis signaling involved in development of an anatomical structure
down regulation of apoptotic program involved in anatomical structure development
down regulation of apoptotic program involved in development of an anatomical structure
down regulation of type I programmed cell death involved in anatomical structure development
down regulation of type I programmed cell death involved in development of an anatomical structure
down-regulation of activation of apoptosis involved in anatomical structure development
down-regulation of activation of apoptosis involved in development of an anatomical structure
down-regulation of apoptosis involved in anatomical structure development
down-regulation of apoptosis involved in development of an anatomical structure
down-regulation of apoptosis signaling involved in anatomical structure development
down-regulation of apoptosis signaling involved in development of an anatomical structure
down-regulation of apoptotic program involved in anatomical structure development
down-regulation of apoptotic program involved in development of an anatomical structure
down-regulation of type I programmed cell death involved in anatomical structure development
down-regulation of type I programmed cell death involved in development of an anatomical structure
downregulation of activation of apoptosis involved in anatomical structure development
downregulation of activation of apoptosis involved in development of an anatomical structure
downregulation of apoptosis involved in anatomical structure development
downregulation of apoptosis involved in development of an anatomical structure
downregulation of apoptosis signaling involved in anatomical structure development
downregulation of apoptosis signaling involved in development of an anatomical structure
downregulation of apoptotic program involved in anatomical structure development
downregulation of apoptotic program involved in development of an anatomical structure
downregulation of type I programmed cell death involved in anatomical structure development
downregulation of type I programmed cell death involved in development of an anatomical structure
inhibition of activation of apoptosis involved in anatomical structure development
inhibition of activation of apoptosis involved in development of an anatomical structure
inhibition of apoptosis involved in anatomical structure development
inhibition of apoptosis involved in development of an anatomical structure
inhibition of apoptosis signaling involved in anatomical structure development
inhibition of apoptosis signaling involved in development of an anatomical structure
inhibition of apoptotic cell death involved in anatomical structure development
inhibition of apoptotic cell death involved in development of an anatomical structure
inhibition of apoptotic process involved in anatomical structure development
inhibition of apoptotic process involved in development
inhibition of apoptotic process involved in development of an anatomical structure
inhibition of apoptotic program involved in anatomical structure development
inhibition of apoptotic program involved in development of an anatomical structure
inhibition of apoptotic programmed cell death involved in anatomical structure development
inhibition of apoptotic programmed cell death involved in development of an anatomical structure
inhibition of programmed cell death by apoptosis involved in anatomical structure development
inhibition of programmed cell death by apoptosis involved in development of an anatomical structure
inhibition of type I programmed cell death involved in anatomical structure development
inhibition of type I programmed cell death involved in development of an anatomical structure
negative regulation of activation of apoptosis involved in anatomical structure development
negative regulation of activation of apoptosis involved in development of an anatomical structure
negative regulation of apoptosis involved in anatomical structure development
negative regulation of apoptosis involved in development of an anatomical structure
negative regulation of apoptosis signaling involved in anatomical structure development
negative regulation of apoptosis signaling involved in development of an anatomical structure
negative regulation of apoptotic program involved in anatomical structure development
negative regulation of apoptotic program involved in development of an anatomical structure
negative regulation of type I programmed cell death involved in anatomical structure development
negative regulation of type I programmed cell death involved in development of an anatomical structure
down regulation of apoptosis activator activity involved in anatomical structure development
down regulation of apoptosis activator activity involved in development of an anatomical structure
down regulation of commitment to apoptosis involved in anatomical structure development
down regulation of commitment to apoptosis involved in development of an anatomical structure
down regulation of induction of apoptosis by p53 involved in anatomical structure development
down regulation of induction of apoptosis by p53 involved in development of an anatomical structure
down regulation of induction of apoptosis involved in anatomical structure development
down regulation of induction of apoptosis involved in development of an anatomical structure
down regulation of signaling (initiator) caspase activity involved in anatomical structure development
down regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
down-regulation of apoptosis activator activity involved in anatomical structure development
down-regulation of apoptosis activator activity involved in development of an anatomical structure
down-regulation of commitment to apoptosis involved in anatomical structure development
down-regulation of commitment to apoptosis involved in development of an anatomical structure
down-regulation of induction of apoptosis by p53 involved in anatomical structure development
down-regulation of induction of apoptosis by p53 involved in development of an anatomical structure
down-regulation of induction of apoptosis involved in anatomical structure development
down-regulation of induction of apoptosis involved in development of an anatomical structure
down-regulation of signaling (initiator) caspase activity involved in anatomical structure development
down-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
downregulation of apoptosis activator activity involved in anatomical structure development
downregulation of apoptosis activator activity involved in development of an anatomical structure
downregulation of commitment to apoptosis involved in anatomical structure development
downregulation of commitment to apoptosis involved in development of an anatomical structure
downregulation of induction of apoptosis by p53 involved in anatomical structure development
downregulation of induction of apoptosis by p53 involved in development of an anatomical structure
downregulation of induction of apoptosis involved in anatomical structure development
downregulation of induction of apoptosis involved in development of an anatomical structure
downregulation of signaling (initiator) caspase activity involved in anatomical structure development
downregulation of signaling (initiator) caspase activity involved in development of an anatomical structure
inhibition of apoptosis activator activity involved in anatomical structure development
inhibition of apoptosis activator activity involved in development of an anatomical structure
inhibition of commitment to apoptosis involved in anatomical structure development
inhibition of commitment to apoptosis involved in development of an anatomical structure
inhibition of induction of apoptosis by p53 involved in anatomical structure development
inhibition of induction of apoptosis by p53 involved in development of an anatomical structure
inhibition of induction of apoptosis involved in anatomical structure development
inhibition of induction of apoptosis involved in development of an anatomical structure
inhibition of signaling (initiator) caspase activity involved in anatomical structure development
inhibition of signaling (initiator) caspase activity involved in development of an anatomical structure
negative regulation of apoptosis activator activity involved in anatomical structure development
negative regulation of apoptosis activator activity involved in development of an anatomical structure
negative regulation of commitment to apoptosis involved in anatomical structure development
negative regulation of commitment to apoptosis involved in development of an anatomical structure
negative regulation of induction of apoptosis by p53 involved in anatomical structure development
negative regulation of induction of apoptosis by p53 involved in development of an anatomical structure
negative regulation of induction of apoptosis involved in anatomical structure development
negative regulation of induction of apoptosis involved in development of an anatomical structure
negative regulation of signaling (initiator) caspase activity involved in anatomical structure development
negative regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
U4PR86 in PMID:22801495 inferred from mutant phenotype
negative regulation of apoptotic process involved in development
Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development.
positive regulation of apoptotic cell death involved in anatomical structure development
positive regulation of apoptotic cell death involved in development of an anatomical structure
positive regulation of apoptotic process involved in anatomical structure development
positive regulation of apoptotic process involved in development of an anatomical structure
positive regulation of apoptotic programmed cell death involved in anatomical structure development
positive regulation of apoptotic programmed cell death involved in development of an anatomical structure
positive regulation of programmed cell death by apoptosis involved in anatomical structure development
positive regulation of programmed cell death by apoptosis involved in development of an anatomical structure
up regulation of apoptotic cell death involved in anatomical structure development
up regulation of apoptotic cell death involved in development of an anatomical structure
up regulation of apoptotic process involved in anatomical structure development
up regulation of apoptotic process involved in development
up regulation of apoptotic process involved in development of an anatomical structure
up regulation of apoptotic programmed cell death involved in anatomical structure development
up regulation of apoptotic programmed cell death involved in development of an anatomical structure
up regulation of programmed cell death by apoptosis involved in anatomical structure development
up regulation of programmed cell death by apoptosis involved in development of an anatomical structure
up-regulation of apoptotic cell death involved in anatomical structure development
up-regulation of apoptotic cell death involved in development of an anatomical structure
up-regulation of apoptotic process involved in anatomical structure development
up-regulation of apoptotic process involved in development
up-regulation of apoptotic process involved in development of an anatomical structure
up-regulation of apoptotic programmed cell death involved in anatomical structure development
up-regulation of apoptotic programmed cell death involved in development of an anatomical structure
up-regulation of programmed cell death by apoptosis involved in anatomical structure development
up-regulation of programmed cell death by apoptosis involved in development of an anatomical structure
upregulation of apoptotic cell death involved in anatomical structure development
upregulation of apoptotic cell death involved in development of an anatomical structure
upregulation of apoptotic process involved in anatomical structure development
upregulation of apoptotic process involved in development
upregulation of apoptotic process involved in development of an anatomical structure
upregulation of apoptotic programmed cell death involved in anatomical structure development
upregulation of apoptotic programmed cell death involved in development of an anatomical structure
upregulation of programmed cell death by apoptosis involved in anatomical structure development
upregulation of programmed cell death by apoptosis involved in development of an anatomical structure
activation of activation of apoptosis involved in anatomical structure development
activation of activation of apoptosis involved in development of an anatomical structure
activation of apoptosis signaling involved in anatomical structure development
activation of apoptosis signaling involved in development of an anatomical structure
activation of apoptotic cell death involved in anatomical structure development
activation of apoptotic cell death involved in development of an anatomical structure
activation of apoptotic process involved in anatomical structure development
activation of apoptotic process involved in development
activation of apoptotic process involved in development of an anatomical structure
activation of apoptotic program involved in anatomical structure development
activation of apoptotic program involved in development of an anatomical structure
activation of apoptotic programmed cell death involved in anatomical structure development
activation of apoptotic programmed cell death involved in development of an anatomical structure
activation of programmed cell death by apoptosis involved in anatomical structure development
activation of programmed cell death by apoptosis involved in development of an anatomical structure
activation of type I programmed cell death involved in anatomical structure development
activation of type I programmed cell death involved in development of an anatomical structure
positive regulation of activation of apoptosis involved in anatomical structure development
positive regulation of activation of apoptosis involved in development of an anatomical structure
positive regulation of apoptosis involved in anatomical structure development
positive regulation of apoptosis involved in development of an anatomical structure
positive regulation of apoptosis signaling involved in anatomical structure development
positive regulation of apoptosis signaling involved in development of an anatomical structure
positive regulation of apoptotic program involved in anatomical structure development
positive regulation of apoptotic program involved in development of an anatomical structure
positive regulation of type I programmed cell death involved in anatomical structure development
positive regulation of type I programmed cell death involved in development of an anatomical structure
up regulation of activation of apoptosis involved in anatomical structure development
up regulation of activation of apoptosis involved in development of an anatomical structure
up regulation of apoptosis involved in anatomical structure development
up regulation of apoptosis involved in development of an anatomical structure
up regulation of apoptosis signaling involved in anatomical structure development
up regulation of apoptosis signaling involved in development of an anatomical structure
up regulation of apoptotic program involved in anatomical structure development
up regulation of apoptotic program involved in development of an anatomical structure
up regulation of type I programmed cell death involved in anatomical structure development
up regulation of type I programmed cell death involved in development of an anatomical structure
up-regulation of activation of apoptosis involved in anatomical structure development
up-regulation of activation of apoptosis involved in development of an anatomical structure
up-regulation of apoptosis involved in anatomical structure development
up-regulation of apoptosis involved in development of an anatomical structure
up-regulation of apoptosis signaling involved in anatomical structure development
up-regulation of apoptosis signaling involved in development of an anatomical structure
up-regulation of apoptotic program involved in anatomical structure development
up-regulation of apoptotic program involved in development of an anatomical structure
up-regulation of type I programmed cell death involved in anatomical structure development
up-regulation of type I programmed cell death involved in development of an anatomical structure
upregulation of activation of apoptosis involved in anatomical structure development
upregulation of activation of apoptosis involved in development of an anatomical structure
upregulation of apoptosis involved in anatomical structure development
upregulation of apoptosis involved in development of an anatomical structure
upregulation of apoptosis signaling involved in anatomical structure development
upregulation of apoptosis signaling involved in development of an anatomical structure
upregulation of apoptotic program involved in anatomical structure development
upregulation of apoptotic program involved in development of an anatomical structure
upregulation of type I programmed cell death involved in anatomical structure development
upregulation of type I programmed cell death involved in development of an anatomical structure
activation of apoptosis activator activity involved in anatomical structure development
activation of apoptosis activator activity involved in development of an anatomical structure
activation of commitment to apoptosis involved in anatomical structure development
activation of commitment to apoptosis involved in development of an anatomical structure
activation of induction of apoptosis by p53 involved in anatomical structure development
activation of induction of apoptosis by p53 involved in development of an anatomical structure
activation of induction of apoptosis involved in anatomical structure development
activation of induction of apoptosis involved in development of an anatomical structure
activation of signaling (initiator) caspase activity involved in anatomical structure development
activation of signaling (initiator) caspase activity involved in development of an anatomical structure
positive regulation of apoptosis activator activity involved in anatomical structure development
positive regulation of apoptosis activator activity involved in development of an anatomical structure
positive regulation of commitment to apoptosis involved in anatomical structure development
positive regulation of commitment to apoptosis involved in development of an anatomical structure
positive regulation of induction of apoptosis by p53 involved in anatomical structure development
positive regulation of induction of apoptosis by p53 involved in development of an anatomical structure
positive regulation of induction of apoptosis involved in anatomical structure development
positive regulation of induction of apoptosis involved in development of an anatomical structure
positive regulation of signaling (initiator) caspase activity involved in anatomical structure development
positive regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
up regulation of apoptosis activator activity involved in anatomical structure development
up regulation of apoptosis activator activity involved in development of an anatomical structure
up regulation of commitment to apoptosis involved in anatomical structure development
up regulation of commitment to apoptosis involved in development of an anatomical structure
up regulation of induction of apoptosis by p53 involved in anatomical structure development
up regulation of induction of apoptosis by p53 involved in development of an anatomical structure
up regulation of induction of apoptosis involved in anatomical structure development
up regulation of induction of apoptosis involved in development of an anatomical structure
up regulation of signaling (initiator) caspase activity involved in anatomical structure development
up regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
up-regulation of apoptosis activator activity involved in anatomical structure development
up-regulation of apoptosis activator activity involved in development of an anatomical structure
up-regulation of commitment to apoptosis involved in anatomical structure development
up-regulation of commitment to apoptosis involved in development of an anatomical structure
up-regulation of induction of apoptosis by p53 involved in anatomical structure development
up-regulation of induction of apoptosis by p53 involved in development of an anatomical structure
up-regulation of induction of apoptosis involved in anatomical structure development
up-regulation of induction of apoptosis involved in development of an anatomical structure
up-regulation of signaling (initiator) caspase activity involved in anatomical structure development
up-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
upregulation of apoptosis activator activity involved in anatomical structure development
upregulation of apoptosis activator activity involved in development of an anatomical structure
upregulation of commitment to apoptosis involved in anatomical structure development
upregulation of commitment to apoptosis involved in development of an anatomical structure
upregulation of induction of apoptosis by p53 involved in anatomical structure development
upregulation of induction of apoptosis by p53 involved in development of an anatomical structure
upregulation of induction of apoptosis involved in anatomical structure development
upregulation of induction of apoptosis involved in development of an anatomical structure
upregulation of signaling (initiator) caspase activity involved in anatomical structure development
upregulation of signaling (initiator) caspase activity involved in development of an anatomical structure
positive regulation of apoptotic process involved in development
Any process that modulates the frequency, rate or extent of apoptotic process involved in development.
regulation of apoptotic cell death involved in anatomical structure development
regulation of apoptotic cell death involved in development of an anatomical structure
regulation of apoptotic process involved in anatomical structure development
regulation of apoptotic process involved in development of an anatomical structure
regulation of apoptotic programmed cell death involved in anatomical structure development
regulation of apoptotic programmed cell death involved in development of an anatomical structure
regulation of programmed cell death by apoptosis involved in anatomical structure development
regulation of programmed cell death by apoptosis involved in development of an anatomical structure
regulation of activation of apoptosis involved in anatomical structure development
regulation of activation of apoptosis involved in development of an anatomical structure
regulation of apoptosis involved in anatomical structure development
regulation of apoptosis involved in development of an anatomical structure
regulation of apoptosis signaling involved in anatomical structure development
regulation of apoptosis signaling involved in development of an anatomical structure
regulation of apoptotic program involved in anatomical structure development
regulation of apoptotic program involved in development of an anatomical structure
regulation of type I programmed cell death involved in anatomical structure development
regulation of type I programmed cell death involved in development of an anatomical structure
regulation of apoptosis activator activity involved in anatomical structure development
regulation of apoptosis activator activity involved in development of an anatomical structure
regulation of commitment to apoptosis involved in anatomical structure development
regulation of commitment to apoptosis involved in development of an anatomical structure
regulation of induction of apoptosis by p53 involved in anatomical structure development
regulation of induction of apoptosis by p53 involved in development of an anatomical structure
regulation of induction of apoptosis involved in anatomical structure development
regulation of induction of apoptosis involved in development of an anatomical structure
regulation of signaling (initiator) caspase activity involved in anatomical structure development
regulation of signaling (initiator) caspase activity involved in development of an anatomical structure
Q10943 in PMID:22801495, inferred from mutant phenotype
regulation of apoptotic process involved in development
Any process that modulates the frequency, rate or extent of core promoter binding.
Any process that stops, prevents or reduces the frequency, rate or extent of core promoter binding.
down regulation of core promoter binding
down-regulation of core promoter binding
negative regulation of core promoter binding
Any process that activates or increases the frequency, rate or extent of core promoter binding.
positive regulation of core promoter binding
Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization.
down regulation of establishment of protein localisation
down regulation of establishment of protein localization
down-regulation of establishment of protein localisation
down-regulation of establishment of protein localization
downregulation of establishment of protein localisation
downregulation of establishment of protein localization
negative regulation of establishment of protein localisation
negative regulation of protein positioning
negative regulation of protein recruitment
inhibition of establishment of protein localisation
inhibition of establishment of protein localization
negative regulation of establishment of protein localization
Any process that activates or increases the frequency, rate or extent of establishment of protein localization.
positive regulation of establishment of protein localisation
positive regulation of protein positioning
positive regulation of protein recruitment
up regulation of establishment of protein localisation
up regulation of establishment of protein localization
up-regulation of establishment of protein localisation
up-regulation of establishment of protein localization
upregulation of establishment of protein localisation
upregulation of establishment of protein localization
activation of establishment of protein localisation
activation of establishment of protein localization
positive regulation of establishment of protein localization
Any process that stops, prevents or reduces the frequency, rate or extent of DNA methylation.
Any process that activates or increases the frequency, rate or extent of DNA methylation.
Any process that modulates the frequency, rate or extent of lipid localization.
Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization.
negative regulation of lipid localisation
negative regulation of lipid localization
Any process that activates or increases the frequency, rate or extent of lipid localization.
positive regulation of lipid localisation
positive regulation of lipid localization
A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor).
The regulated release of tumor necrosis factor from a cell. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
tumor necrosis factor ligand superfamily member 2 secretion
Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process.
regulation of cellular biopolymer biosynthetic process
regulation of cellular macromolecule anabolism
regulation of cellular macromolecule biosynthesis
regulation of cellular macromolecule formation
regulation of cellular macromolecule synthesis
regulation of cellular macromolecule biosynthetic process
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process.
negative regulation of cellular biopolymer biosynthetic process
negative regulation of cellular macromolecule anabolism
negative regulation of cellular macromolecule biosynthesis
negative regulation of cellular macromolecule formation
negative regulation of cellular macromolecule synthesis
negative regulation of cellular macromolecule biosynthetic process
Any process that modulates the frequency, rate or extent of cell motility.
Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility.
negative regulation of movement of a cell
Any process that activates or increases the frequency, rate or extent of cell motility.
positive regulation of movement of a cell
Any process that modulates the frequency, rate or extent of fatty acid transport.
Any process that stops, prevents, or reduces the frequency, rate or extent of fatty acid transport.
negative regulation of fatty acid transport
Any process that activates or increases the frequency, rate or extent of fatty acid transport.
positive regulation of fatty acid transport
Any process that modulates the frequency, rate or extent of DNA biosynthetic process.
Any process that stops, prevents or reduces the frequency, rate or extent of DNA biosynthetic process.
negative regulation of DNA biosynthetic process
Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process.
positive regulation of DNA biosynthetic process
Any process that modulates the frequency, rate or extent of transcription regulatory region DNA binding.
regulation of transcription regulatory region DNA binding
Any process that stops, prevents or reduces the frequency, rate or extent of transcription regulatory region DNA binding.
negative regulation of transcription regulatory region DNA binding
Any process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding.
positive regulation of transcription regulatory region DNA binding
Any process that modulates the frequency, rate or extent of response to DNA damage stimulus.
regulation of cellular DNA damage response
regulation of cellular response to DNA damage stimulus
regulation of response to genotoxic stress
regulation of response to DNA damage stimulus
Any process that stops, prevents or reduces the frequency, rate or extent of response to DNA damage stimulus.
negative regulation of DNA damage response
negative regulation of cellular DNA damage response
negative regulation of cellular response to DNA damage stimulus
negative regulation of response to genotoxic stress
negative regulation of response to DNA damage stimulus
Any process that activates or increases the frequency, rate or extent of response to DNA damage stimulus.
positive regulation of DNA damage response
positive regulation of cellular DNA damage response
positive regulation of cellular response to DNA damage stimulus
positive regulation of response to genotoxic stress
positive regulation of response to DNA damage stimulus
Any process that modulates the frequency, rate or extent of response to drug.
regulation of drug susceptibility/resistance
Any process that stops, prevents or reduces the frequency, rate or extent of response to drug.
negative regulation of drug susceptibility/resistance
Any process that activates or increases the frequency, rate or extent of response to drug.
positive regulation of drug susceptibility/resistance
Any process that modulates the frequency, rate or extent of cellular response to drug.
Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to drug.
negative regulation of cellular response to drug
Any process that activates or increases the frequency, rate or extent of cellular response to drug.
positive regulation of cellular response to drug
Any process that modulates the frequency, rate or extent of RNA biosynthetic process.
Any process that modulates the frequency, rate or extent of apoptotic signaling pathway.
regulation of apoptotic signalling pathway
regulation of apoptotic signaling pathway
Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway.
negative regulation of apoptotic signalling pathway
negative regulation of apoptotic signaling pathway
Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.
positive regulation of apoptotic signalling pathway
positive regulation of apoptotic signaling pathway
Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization.
negative regulation of chromosome organisation
negative regulation of chromosome organization and biogenesis
negative regulation of maintenance of genome integrity
negative regulation of nuclear genome maintenance
negative regulation of chromosome organization
Any process that activates or increases the frequency, rate or extent of chromosome organization.
positive regulation of chromosome organisation
positive regulation of chromosome organization and biogenesis
positive regulation of maintenance of genome integrity
positive regulation of nuclear genome maintenance
positive regulation of chromosome organization
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
software
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
PERSON: Chris Stoeckert
GROUP: OBI
information carrier
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
A quality of an information bearer that imparts the information content
12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Jonathan Rees
data
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.
10 feet. 3 ml.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
dot plot
Dot plot of SSC-H and FSC-H.
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
person:Allyson Lister
person:Chris Stoeckert
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
data format specification
A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
OBI branch derived
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
data about an ontology part is a data item about a part of an ontology, for example a term
data about an ontology part
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
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
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
material information bearer
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:Chris Stoeckert
PERSON:James Malone
PERSON:Melanie Courtot
heatmap
A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
dendrogram
Dendrograms are often used in computational biology to illustrate the clustering of genes.
A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
A scalar measurement datum that is the result of measuring a temporal interval
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
time measurement datum
line graph
A line graph is a type of graph created by connecting a series of data points together with a line.
line chart
WEB: http://en.wikipedia.org/wiki/Line_chart
infection
A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population.
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
Person:Jennifer Fostel
OBI
regulator role
biological feature identification objective
Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
Jennifer Fostel
regulatory role
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
GROUP: Role branch
OBI, CDISC
govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
Jackson Labs is an organization which provide mice as experimental material
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
Supplier role is a special kind of service, e.g. biobank
PERSON:Jennifer Fostel
material supplier role
A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
classified data set
Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html
a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
reference substance role
chromatography column
Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms.
Frank Gibson
open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178
xenotransplantation
is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans
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.
chromatography device
a device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.
chromatography instrument
mass spectrometer
LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific
A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum
allotransplantation
is the transplantation of organs between members of the same species.
gamma counter
A processed material which measures gamma radiation
evaluant role
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
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.
measuring
scientific observation
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
Person: Jennifer Fostel, Jie Zheng
culture medium
Buffer, dye, a catalyst, a solvating agent.
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
PERSON:Matthew Brush
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
(copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
reagent role
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
study subject role
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
GROUP: Role Branch
Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
participant under investigation role
transplantation
a protocol application to replace an organ or tissue of an organism
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample 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.
blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
specimen role
sequence feature identification objective
Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
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
molecular feature identification objective
Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
cell co-culturing
Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay
A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
cDNA library
PMID:6110205. collection of cDNA derived from mouse splenocytes.
Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
PERSON: Luisa Montecchi
PERSON: Philippe Rocca-Serra
GROUP: PSI
PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction
imaging assay
An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
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
Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material.
An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material.
cellular feature identification objective
Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.
enzymatic cleavage
Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828
enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
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.
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
organism feature identification objective
Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
adding a material entity into a target
Glucose in blood (measured in an assay to determine the concentration of glucose).
A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
analyte role
An assay with the objective to determine interactions between proteins, such as protein-protein binding.
20091101, Bjoern Peters: This class may be overly broad. Lot's of assays would seem to classify under it, and I have the feeling that the intend would be to limit this to determining protein-protein interactions as they occur within an organism, rather than e.g. peptide:MHC binding assays.
protein-protein interaction detection
transcription factor binding site identification
Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19. PMID: 17638031
An assay with objective to find DNA region specifically recognized by proteins that function as transcription factors
JZ: add equivalent axiom for classification add alternative term 'TF binding' which was used in BCBC database
JZ: fixed inconsistency issue and relabel the term see tracker: https://sourceforge.net/p/obi/obi-terms/767/
transcription factor binding site assay
eluate
Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263
a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase
need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role
eluted material
drug added to a buffer contained in a tube; substance injected into an animal;
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
9 March 09 from discussion with PA branch
material to be added role
histological sample preparation
histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
PERSON:Bjoern Peters
mass analyzer
The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation
A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply.
ion source
The ion source of a Voyager-DE??? STR Biospectrometry Workstation
An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))).
ion detector
The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation
An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q.
Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019
metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism
metabolite profiling
light emission function
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
magnify function
A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
contain function
A contain function is a function to constrain a material entities location in space
heat function
A heat function is a function that increases the internal kinetic energy of a material
material separation function
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
excitation function
A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
synthesizing function
A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
perturb function
A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function.
filter function
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
mechanical function
A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
electricity supply function
the function of supplying current during a neuroscience experiment.
An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment.
power supply
ionization function
An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
cool function
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
energy supply function
An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy
image acquisition function
An image acquisition function is a function to acquire an image of a material
image acquisition device
An image creation device is a device which captures a digitized image of an object
image creation device
Taped, glued, pinned, dried or molecularly bonded to a solid support
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
solid support function
environment control function
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
sort function
A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.
PCR product
PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
is double stranded DNA that is the specified output of a polymerase chain reaction
We are using PCR and not the written out words, as this is the most common used.
a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
nucleic acid template role
pBluescript plays the role of a cloning vector
A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
JZ: related tracker: https://sourceforge.net/p/obi/obi-terms/102/
cloning vector role
Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
PCR
polymerase chain reaction
cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process"
cloning insert role
reverse transcriptase
enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
extract
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
an extract is a material entity which results from an extraction process
extracted material
Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot
gene expression profiling
transcription profiling assay
enzyme
(protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
polyacrylamide gel
Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143
a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution
creating a mouse infected with LCM virus
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
adding material objective
High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
an assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.
genotype profiling, SNP genotyping
genotyping assay
The objective to measure the concentration of glucose in a blood sample
an assay objective to determine the presence or concentration of an analyte in the evaluant
analyte measurement objective
agarose gel
Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269
a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
the objective to determine the weight of a mouse.
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
assay objective
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration'))
PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch
analyte assay
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
target of material addition role
intra cellular electrophysiology recording
An intracellular electrophysiology recording is a process where the recording location of the electrode is intracellular
regulatory agency
A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
extracellular electrophysiology recording
The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron
An extracellular electrophysiology recording is process where the recording location of the electrode is extracellular and data
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
material transformation objective
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
manufacturing
is the objective to manufacture a material of a certain function (device)
manufacturing objective
Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides.
An assay that identifies 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.
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that carries out a study design
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
affinity column
An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention.
PERSON:Daniel Schober
gel filtration column
A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers.
reverse transcribed polymerase chain reaction
Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
reverse transcription polymerase chain reaction
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
the sodium and chloride ions in a glass of salt water
a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
Collective
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
scattered molecular aggregate
chromatography consumable
A chromatography consumable is a consumable that is used in a chromatography experiment.
size exclusion column
A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size.
Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202
NMR spectroscopy is a process which exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures.
Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858
DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology. Godsland IF, Johnston DG. Metabolism. 2008 Sep;57(9):1190-7. PMID: 18702943
hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments
Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J. Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979
an assay which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion.
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
A clustered data set is the output of a K means clustering data transformation
A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
data set with assigned discovered class labels
clustered data set
differential expression analysis data transformation
A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of
James Malone
Monnie McGee
a portion of urine collected from an organism
4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
are we happy calling collection of urine a material separation?
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.
Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification
a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
class prediction data transformation
A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
supervised classification data transformation
PERSON: James Malone
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 BrdU.
A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies.
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.
a material obtained from an organism in order to be a representative of the whole
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
The objective to obtain multiple aliquots of an enzyme preparation.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
creating a mixture of molecules in solution
is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations.
is an objective to obtain an output material that contains several input materials.
PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time
Need to point out more specifically that survival / death is measured.
A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space.
A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
decision tree building data transformation
A decision tree building data transformation is a data transformation that has objective decision tree induction.
PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120.
is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors.
a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
WEB: http://www.broadinstitute.org/cancer/software/genepattern/
PMID: 19275939 ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. Methods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9.
an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
chromatin immunoprecipitation sequencing assay
made some modification based on the discussion on 2011/4/4 obi dev call, using DNA sequencing instead of union of some specific DNA sequencing processes
PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.
is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
adapted from information provided by Solid web site
Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold
k-nearest neighbors
A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
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.
is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material entity that has the material sample role
CART
A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.
In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
study design independent variable
A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate
Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia
A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides.
The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality
cross linking can be used as a probe to link proteins together, to check protein protein interactions
A process in which bonds are created that link one polymer to another
An objective specification maintains some or all of the qualities of a material over time.
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
DNA that has been produced in an enzymatic amplification process
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus
An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system.
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
Extraction of chromosomal DNA from mammalian cells by first isolating nucei
The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
A person or organization that has a manufacturer role
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
A primer in a PCR reaction. A probe on an Affymetrix chip.
A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence
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
Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified.
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.
material obtained through a liver biopsy from a human patient
a specimen that was taken from a live organism
MO_705 premortem
detection of specific nucleic acid polymers with complementary probes
Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays.
An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes.
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
A cytometry assay that monitors a cell population to track how many are killed by other cells.
Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells.
A cell killing assay that measures if and how many target cells are killed within an organism.
secondary structure of sequence macromolecule
A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford.
2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO
Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation.
A cytometry assay which measures the degreee to which input cells are replicating.
PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. Li C, Weber G, Ekman P, Lagercrantz J, Norlen BJ, Akerström G, Nordenskjöld M, Bergerheim US. Hum Mutat. 1998;Suppl 1:S31-3.
Southern blot analysis is a an assay used in molecular biology to assert the presence/absence status of a specific DNA sequence in DNA samples. DNA samples to be assayed are first digested by restriction enzymes, fragments are then resolved by gel electrophoresis following by a blotting ensuring transfer to nitrocellulose or nylon membrane. Immobilization of DNA fragments to the membrane is achieved by UV crosslinking and/or baking. Probes raised against the specific sequences are then hybridized to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager.
2010-01-31: Philippe Rocca-Serra: need extra work on 'labeled probe'
2010-01-31: Philippe Rocca-Serra: departure from naming convention as the assay is named after Edwin Southern.
real time polymerase chain reaction assay
A laboratory technique based on the PCR, which is used to amplify and simultaneously quantify a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.
quantitative real time polymerase chain reaction
WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
a specimen that was taken from a dead organism
MO_416 postmortem
A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture.
real time reverse-transcription polymerase chain reaction assay
Is_a PCR real time preceded by a reverse transcription step (reverse transcription step = an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase)
Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes.
A 3D structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest.
promoter activity detection by reporter gene assay
A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color.
An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene.
Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody.
A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution.
a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call
A specimen that has been modified in order to be able to detect it in future experiments
is a material entity bearing the disposition to infect an organism
IEDB
infectious agent
A measurement device that is used to calculate the heat flow of a chemical reaction or physical change.
the part of the execution of an intervention design study which is varied between two or more subjects in the study
A device with a separation function realized in a planed process
The Edinburgh handedness assay is a specific method of determing handedness
A handedness assay measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure.
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
An assay in which a measurement is made by observing entities located in a live cell.
Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells.
An assay in which a measurement is made by observing entities located in an organism.
A device that can be used to restrict the location of material entities over time
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
sequence data
cell-cell binding detection by flow cytometry assay
Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates.
A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels.
an assay in which a measurement is made by observing entities located in a container.
A study design in which the independent variable is the environmental condition in which the specimen is growing
A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent.
A microscope that produces an image of an object by targeting it with an electron beam
The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth.
Right now this may be incomplete. Should also cover e.g. sound, light as well.
PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters
A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
Need to clarify if this is a document or a directive information entity (or what their connection is))
PERSON: Jessica Turner
Merriam-Webster
Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
A planned process that captures an image of an object.
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
a single-nucleotide-resolution nucleic acid structure mapping assay which relies on proteins acting as enzymatic probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study.
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.
binding constant determination assay
Determination of KD value for an antibody binding a protein using a BIACORE assay.
A binding assay where the specified output is a binding constant
PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
a device which has a function to emit light.
A perturbation device is a device which is designed to perform a perturb function
A growth chamber is an environmental control device.
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
A device that moves charged particles through a medium by using an electric field induced by electrodes.
high performance liquid chromatography instrument
A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column.
A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane.
A device used in electrophysiology that allows the study of single or multiple ion channels in cells.
A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level.
A device that is used to generate X-rays.
A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated
a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
binding constant
The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes".
A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process
10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class.
3D structure determination of bound complex assay
Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody.
A 3D structure determination assay in which a complex of 2 or more material enties is characterized which provides information on their binding configuration.
Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen.nnThe following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture.
An assay with the objective to characterize the disposition of two or more material entities to form a complex.
PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum
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.
gene knock out
a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.
MO_771 gene_knock_out
gene knock in
a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion.
MO_437 gene_knock_in
WEB: http://en.wikipedia.org/wiki/Gene_Knock-in
genetically modified material
a material entity, organism or cell, that is the output of a genetic transformation process.
PERSON: Jie Zheng
term is proposed by BP on Oct 25, 2010 dev call
a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
transfection
genetic transformation objective
a material transformation objective aims to create genetically modified organism or cell
Person: Jie Zheng
suggested to be added by BP and AR during Oct 25, 2010 dev call
induced mutation
a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation.
MO_564 induced_mutation
The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR.
A measurement datum that describes the structural orientation of a material entity in 3D space.
PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters
The time it takes for 50% of a class of stochastic processes to occur.
A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve.
RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact
BP 12/21:Created based on a request from Melanie
half maximal effective concentration (EC50)
Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed.
half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time.
A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is.
half maximal inhibitory concentration (IC50)
Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited.
Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect.
in vivo design
A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
MO_454 in_vivo_design
genotyping by high throughput sequencing design
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques.
ex vivo design
A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.
MO_808 ex_vivo_design
genetic population background information
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
proposed and discussed on San Diego OBI workshop, March 2011
Group: OBI group
epigenetic modification identification objective
A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
Chris Stoeckert, Jie Zheng
Person: Chris Stoeckert
transcription profiling by high thoughput sequencing design
A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance
Group: ArrayExpress production team
transcription profiling by high throughput sequencing design
genotyping by high throughput sequencing assay
An assay in which high througput sequencer is used to detect polymorphisms in DNA samples
EFO_0002771: genotyping by high throughput sequencing
ChIP-chip assay
an assay that aims to investigate the interactions between protein and DNA relying on chromatin immunoprecipitation ('ChIP') combined with microarray technology ('chip'). Specially, it allows the identification of protein binding sites on a genome-wide basis.
WEB: http://en.wikipedia.org/wiki/ChIP-on-chip
ChIP-seq design
A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications.
Person: Chris Stoeckert, Jie Zheng
DNA methylation profiling by high throughput sequencing assay
An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology
Group: ArrayExpress production team, James Malone, Helen Parkinson
EFO_0002761 methylation profiling by high throughput sequencing
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
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
DNA methylation profiling by array design
A study design in which the methylation state of DNA is determined and is compared between samples using array technology.
GROUP: ArrayExpress production team
in vitro design
A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
MO_347 in_vitro_design
transcription profiling by array design
A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
genotype information
Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
discussed on San Diego OBI workshop, March 2011
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).
proteomic profiling by array assay
An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology
EFO_0002765 proteomic profiling by array
transcription profiling identification objective
A molecular feature identification objective that aims to characterize the abundance of transcripts
Group: Penn Group
DNA methylation profiling by array assay
An assay in which the methylation state of DNA is determined and is compared between samples using array technology
EFO_0002759 methylation profiling by array
post-transcriptional modification design
A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
MO_392 cellular_modification_design
post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases
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
genetic alteration information
a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
cellular process design
A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
MO_810 cellular_process_design
stimulus or stress design
A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
MO_568 stimulus_or_stress_design
protein and DNA interaction identification objective
A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
MO_933 binding_site_identification_design
ChIP-chip design
A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays.
genetic characteristics information
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
MO_66 IndividualGeneticCharacteristics
MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
protein binding site identification design
A study design that investigates protein binding sites on nucleic acids.
transcription profiling design
A study design that identifies forms and abundance of transcripts in the genome.
proteomic profiling by array design
A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology.
Person: Chris Stoeckert, Jie Zheng, Dan Berrios
genotyping design
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
MO_560 genotyping_design
genetic modification design
A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out.
MO_447 genetic_modification_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/
EFO_0002768: transcription profiling by array
specimen from organism
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
tissue specimen
binding assay that uses radioactivity detection as an indicator of binding
binding assay that uses fluorescence detection as an indicator of binding
Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for.
An assay in which a material's fluorescence is determined.
purification
A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
specimen with pre- or post-mortem status
A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
organizational term, used in description of specimen that is created from known pre- or post-mortem status
KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb
A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate)
KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens.
A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate)
The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
A scalar measurement datum that represents the number of events occuring over a time interval
equilibrium dissociation constant (KD) approximated by IC50
A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor.
The part of a FASTA file that contains the letters ACTGGGAA
A sequence data item that is about the primary structure of DNA
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
equilibrium dissociation constant (KD) approximated by EC50
A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand.
Assay Development: Fundamentals and Practices, By Ge Wu, page 74
The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate.
A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association.
A peptide binding to an MHC molecule to form a complex.
The process of material entities forming complexes.
9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.
binding off rate measurement datum (koff)
A rate measurement datum of how quickly bound complexes disassociate
A rate measurement datum of how quickly bound complexes form
Detection of the presence of blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column.
An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material.
Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies within the tissue structure.
An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material.
Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye.
A detection of molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity.
A mixture of peptide molecules that has been run through an HPLC column to remove 65
A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component
A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (delta H) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell .
A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy.
antibody binding detection by fluorescence quenching
The binding affinity of Fab 4-4-20 for the fluorescein molecule was determined using the fluorescence quenching assay, by placing the Fab and the fluorescein together in a well and measuring the fluorescence after each addition of increasing concentrations of the Fab (PMID: 8637844).
A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope).
RNA protection assay
Absolute concentrations of mRNA for type I and type VI collagen in the canine meniscus in normal and ACL-deficient knee joints obtained by RNase protection assay. Wildey GM, Billetz AC, Matyas JR, Adams ME, McDevitt CA. J Orthop Res. 2001 Jul;19(4):650-8. PMID: 11518275
RPA is a technique to assess the presence and estimate abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest.
PERSON:Philippe Rocca-Serra; Marcus Chibucos
RPA; RNAse protection assay
adapted from wikipedia + PMID:16491611
electrophoretic mobility shift assay
Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein. Puranik S, Kumar K, Srivastava PS, Prasad M. Plant Signal Behav. 2011 Oct;6(10):1588-90. Epub 2011 Oct 1. PMID: 21918373
is an assay which aims to provide information about Protein-DNA or Protein-RNA interaction and which used gel electrophoresis and relies on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid.
EMSA,gel shift assay, gel mobility shift assay, band shift assay, gel retardation assay
gene knock-down assay
is an assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells.
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
nano-CAGE
PMID: 20543846
cap analysis of gene expression
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Takahashi H, Lassmann T, Murata M, Carninci P. Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005. PMID: 22362160
An assay which aims at monitoring RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome
CAGE
yeast one-hybrid
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods. 2011 Oct 30;8(12):1050-2. doi: 10.1038/nmeth.1764. PMID: 22037702
The one-hybrid variation of this technique is designed to investigate protein–DNA interactions and uses a single fusion protein in which the AD is linked directly to the binding domain.
Y1H
PMID: 22218861
add regulatory region DNA binding;obo:GO:0000975;
bacterial one-hybrid
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA. Nucleic Acids Res. 2008 May;36(8):2547-60. Epub 2008 Mar 10. PMID: 18332042
is a method for identifying the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence
B1H
chromosome organization assay by fluorescence in situ hybridization
Duplication of intrachromosomal insertion segments 4q32→q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization.PMID:22384449
is an in situ hybridization assay that uses fluorescence as means of detection chromosomal integrity
Changed label from fluorescence in situ hybridization as per tracker item #788
FISH
methylation-specific polymerase chain reaction
Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID: 18219662
is an assay which uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA.
2015-03-30 OBI dev call: The assay was defined as equvivalent to (assay and (has_specified_input some 'binding complex 3D structure determination assay') and (has_specified_output some ('data item' and ('is about' some 'regulation of DNA methylation')))) and (achieves_planned_objective some 'epigenetic modification identification objective') 'binding complex 3D structure determination assay' is a process and cannot be the input of another process which cause inconsistent. In the call, we decided to remove axiom and will discuss it in the assay harmonization discussion. see tracker: https://sourceforge.net/p/obi/obi-terms/747/
MSP
amplification of intermethylated sites (AIMS) assay
Analysis of DNA methylation by amplification of intermethylated sites (AIMS).PMID:18987810
amplification of intermethylated sites (AIMS) is an assay appropriate for genome-wide estimates of DNA methylation and the discovery of specific methylated sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences.
AIMS assay,intermethylated site amplification
PMID: 18987810
in situ hybridization
Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265
is an assay using artificially induced nucleic hybridization to localize a specific DNA or RNA sequence in a portion or section of tissue
ISH
cytochalasin-induced inhibition of actin polymerization assay
is an assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041).
add ;actin filament polymerization obo:GO:0070358;
cellular structure feature identification objective
is an objective specification which aims to discover cellular structure properties
PERSON:Philippe Rocca-Serra
OBI group
Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum.
An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies.
paired-end library preparation
A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process.
methylation-sensitive restriction enzyme sequencing assay
Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842]
An assay that identifies unmethylated CpGs by use of methylation sensitive restriction enzymes to fragment DNA.
Person: Venkat Malladi, Chris Stoeckert, Jie Zheng
assay array
A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface.
PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg
reagent
A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at 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 examples, see editor note on OBI:device.
(copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
cell freezing medium
multiplex ligation-mediated amplification
A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation.
Multiplex ligation-dependent probe amplification
web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/
chromosome conformation identification objective
A molecular feature identification objective that aims to determine spatial organization of chromatin.
Carbon-copy chromosome conformation capture assay
van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094]
An assay that is used to analyze the organization of chromosomes at the genome-wide scale.
Venkat Malladi, Chris Stoeckert, Jie Zheng
"Dostie et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 October; 16(10):1299-309.[PMID:16954542]"
chromatin immunoprecipitation with exonuclease sequencing assay
Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082]
A ChIP-seq assay to identify protein binding sites using an exonuclease to provide greater binding resolution of immunoprecipitation assay by genome wide sequencing.
A value specification that is specifies one category out of a fixed number of nominal categories
A value specification that consists of two parts: a numeral and a unit label
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay
PMID: 6379641 Gilmour & Lis. Proc Natl Acad Sci U S A. 1984 Jul;81(14):4275-9. and can be found linked from here:
An assay in which protein-DNA complexes are extracted from short regions of chromatin and are reversibly cross linked, immunoprecipitated with antibodies or tags, purified, and amplified with the aim of analysis gene- and promoter-specific known targets
adapted from CHS protocols, wikipedia, life tech, ChIP-seq term definition
as per user (pployd) request and proposal by Alan Ruttenberg http://sourceforge.net/p/obi/obi-terms/707/
ChIP assay
assay using chromatin immunoprecipitation
an assay which uses immunoprecipitation and which produces data about protein-DNA interaction or DNA epigenetic modification
An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells.
An assay that measures properties of cells.
A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other.
Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray.
An analyte assay where binding of the analyte to immobilized matrix is measured.
Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques.
An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section.
An assay that identifies epigenetic modification including histone modifications, open chromatin, and DNA methylation.
A mass spectrometry assay in which an unknown protein of interest is cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer. These masses are then compared to values in a database containing known protein sequences.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/
ERO:0001668 (http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting)
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
reporter gene assay
An assay in which expression of a reporter gene is detected that was inserted under the control of a regulatory sequence of interest.
tracker item: 781
Chris Stoeckert, Paul D. Thomas
reporter gene detection assay
Paul D. Thomas, Yang Chai; FaceBase
physical store
a freezer. a humidity controlled box.
A container with an environmental control function.
For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/
Chris Stoeckert
Duke Biobank, OBIB
Biobank
A reverse transcribed polymerase chain reaction that is used to amplify a mRNA sequence between a defined internal site and the 5' or 3' end of the mRNA.
For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/
Jason Hilton, Chris Stoeckert
ENCODE
rapid amplification of cDNA ends
high performance liquid chromotography assay
On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml.
An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution.
Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy.
An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye.
An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied.
A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy.
A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples.
An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies.
An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen.
An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage changes or electric current (or other associated variables such as impedence or capacitance).
Note that electrophysiological manipulations also exist which involve processes that alter the electrophysiological properties of cells and tissues.
An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations.
A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell.
A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell.
A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations.
A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels.
An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface.
An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique.
Can be used on any cell, not just neurons.
An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue.
histologic grade according to AJCC 7th edition
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
histologic grade according to the Fuhrman Nuclear Grading System
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
Histologic Grade (Fuhrman Nuclear Grading System)
A categorical value specification that is a histologic grade assigned to a ovarian tumor.
histologic grade for ovarian tumor according to a two-tier grading system
A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
histologic grade for ovarian tumor according to the World Health Organization
A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
pathologic lymph node stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pathologic lymph node stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
pathologic distant metastases stage for colon according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: colon distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: lung distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: kidney distant Metastases (AJCC 7th Edition)
pathologic distant metastases stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: ovarian distant metastases (AJCC 7th Edition)
clinical tumor stage group according to AJCC 7th edition
A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
Clinical tumor stage group (AJCC 7th Edition)
International Federation of Gynecology and Obstetrics cervical cancer stage value specification
A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
Eastern Cooperative Oncology Group score value specification
A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei.
A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR.
A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes.
measurand role
A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library.
An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes.
Epstein Barr virus transformed B cell
PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8.
A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity
organism
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
organ section
A liver slice used in a perfusion experiment. Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521
A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
PERSON: Helen Parkinson
GROUP: CEBS
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
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.
PERSON: Elisabetta Manduchi
leave one out cross validation method
The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368
is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178
k-means clustering
A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
WEB: http://en.wikipedia.org/wiki/K-means
hierarchical clustering
A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering
dimensionality reduction
A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.
principal components analysis dimensionality reduction
A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
pca data reduction
mass spectrometry analysis
A data transformation which has the objective of spectrum analysis.
Generation of a heatmap from a microarray dataset
An planned process that creates images, diagrams or animations from the input data.
Tina Boussard
visualization
PERSON: Tina Boussard
Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding
data visualization
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
partitioning data transformation
A partitioning data transformation is a data transformation that has objective partitioning.
partitioning objective
A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
class discovery data transformation
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
unsupervised classification data transformation
class discovery objective
A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
discriminant analysis objective
unsupervised classification objective
class prediction objective
A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
supervised classification objective
cross validation objective
A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
rotation estimation objective
WEB: http://en.wikipedia.org/wiki/Cross_validation
A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type.
Calculation of characteristic path length in mass spectrometry
is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process.
pool of specimens
A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
chemical solution
PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution.
A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute.
liquid chemical solution
PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors.
solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation
adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation)
solvent role
PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure.
solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution
adapted from wikipedia (http://en.wikipedia.org/wiki/Solute)
solute role
comet assay
PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay.
a comet assay is an assay which utilizes gel electrophoresis on cell exposed to a challenge with the objective to assess DNA damage (DNA breakage) by determining the size and shape of DNA migration in cell placed in an electric field in specific conditions.
SCGE assay
single cell gel electrophoresis assay
PMID:7686265 .Mutat Res. 1993 Jul;288(1):47-63.The single cell gel electrophoresis assay (comet assay): a European review.
A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436
an organism that is the output of a genetic transformation process
OBI Biomaterial
genetically modified organism
Salt molecules that have been mixed into water
A material entity that has been going through a process of being put into solution
dissolved material entity
nucleic acid extraction using phenol chloroform
A material separation in which a desired component of an input material is separated from the remainder
Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
extraction
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
staining
PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3.
polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight
PRS:22102008: need to import catalyst from CHEBI 35223
polymerization
PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202.
An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity
enzymatic ligation
PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
nucleic acid hybridization
PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13.
the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions)
elution
flow cytometer analyzer
FACS Calibur, Luminex 100
An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis.
John Quinn
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
flow cytometer
FACS Calibur
A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium.
light source
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
Elizabeth M. Goralczyk
Olga Tchuvatkina
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
obscuration bar
obscuration bar in a flow cytometer
An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device.
Daniel Schober
Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249
optical filter
720 LP filter, 580/30 BP filter
An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.
photodetector
A photomultiplier tube, a photo diode
A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye.
DNA sequencer
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Trish Whetzel
array scanner
GenePix 4200A, GenePix4000B
An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip
hybridization chamber
Glass Array Hybridization Cassette
A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
MO_563 hybridization_chamber
hybridization station
Labnet Problot12
A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature.
MO_497 hybridization station
sonicator
Sonicator 3000
A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions.
spectrophotometer
Helios Gamma Spectrophotometer
A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance.
thermal cycler
Piko(tm) 96-well Thermal Cycler
An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
DNA_amplifier
PCR_machine
Polymerase_Chain_Reaction_ machine
thermocycler
cytometer
A cytometer is an instrument for counting and measuring cells.
gel tank
CHEF gel box, slab gel box, capillary electrophoresis
a device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules.
Person:Kevin Clancy
electrophoresis box
electrophoresis unit
A AC/DC transformer that generates the reqired power for an electrophoresis apparatus
A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time.
PSU
electrical power supply
power pack
power supply unit
PERSON: Daniel Schober
was power_pack, maps to SEP electrical_power_supply
microarray
An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
DNA microarray
Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115
A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
DNA Chip
DNA-array
protein microarray
The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions.
A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions.
droplet sorter
A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal.
microtome
PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
microscope
PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6
A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
clinical study design
PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale.
Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]
The definition needs to be extended to other things than simply patients
Clinical Research Glossary Version 4.0 CDICS glossary group
reference design
PMID: 12933549
A reference experiment design type is where all samples are compared to a common reference.
Philippe Rocca-Serra on behalf of MO
MO_699
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
collecting specimen from organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
administering substance in vivo
Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
Different routes and means of administration should go as children underneath this
Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/
needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
detection of molecular label
Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present
an assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached
OBI developer call, 3-12-12
histology
the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated
the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement
PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
PRS:20090901: addition of alternative term = histopathology
need to incorporate parts\n---\nThis is a very vague term, it should be in the same place as transcriptomics, proteomics metaboloimcs. It is the 'study' of tissues, not the process of studying tissues\n
histology assay
maintaining cell culture
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
substance detection
the detection of phycoerytherin by means of flow cytometry
any protocol which results in the detection of a specified substance
PERSON:Kevin Clancy
artificially induced reverse transcription
The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA
a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA)
It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process.
We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope
cell permeabilization
Electroporation of HeLa cells to allow transfection with pUC19.
A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application
need to add output cell has_quality permeable
definition blessed by Jay, Alan, Randi
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
addition of molecular label
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
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
genetic modification
The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein.
An assay that determines the 3-dimensional configuration of an input material.
preparative chromatography
The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides.
the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity
PERSON:Kevin Clancy; Bjoern Peters
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
specific enzymatic cleavage
The use of a protease to digest a protein into peptides
a protocol application to digest the fraction of input material that is susceptible to that enzyme
gradient separation
the use of a sucrose gradient to isolate mitochondria
a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities
electrophoresis
Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change.
a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge
Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers.
selection by survival
The insertion of a gene for antibiotic resistance into a cell population and subsequent growth in the presence of the antibiotic to select for those cells which were successfully transfected
the use of environmental conditions to select for the organism or cells that have a certain trait
DNA cleavage, restriction analysis
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
the use of enzymes to cut DNA molecules, the study of DNA through cleavage, mapping, and analysis of the fragments
restriction enzyme assay
enzymatic amplification
the use of a polymerase chain reaction to amplify a fragment of DNA
the use of enzymes to increase the number of molecules of a biomaterial
recombinant vector cloning
a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material
pa_branch (Alan, Randi, Kevin, Jay, Bjoern)
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
requested by Helen Parkinson for MO
nucleic acid extraction
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
a material separation to recover the nucleic acid fraction of an input material
requested by Helen Parkinson for MO. Could be defined class
phage display library
PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]
a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
display library
WEB: http://www.immuneepitope.org/home.do
transgenic organism
HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162
a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it
PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application
the detrimental process in which an infectious agent colonizes or replicates in a host environment
infection process
is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes.
adaptive immune receptor
is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture
experimental infection of cell culture
is a material entity that has the antigen role
antigen
Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease
disposition to infect an organism
A mixture of peptides that is being added into a cell culture.
a material that is added to another one in a material combination process
10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export
2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes
A cell culture into which a mixture of peptides is being added.
A material entity into which another is being added in a material combinatino process
10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
Any molecule recognized by the adaptive immune receptors? Recognized means bound with a certain affinity? From GO ag binding:Interacting selectively with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. see OBI_1110120 below
assay antigen role
abnormal, harmful processes caused by or associated with a disease
pathologic process
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.
A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together.
An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
quality of a single physical entity
A physical object quality which inheres in a single-bearer.
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity.
A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet.
Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof.
Definition defined by OBI developers: an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule
A protein that is a translation product of the Aspergillus oryzae nucS gene or a 1:1 ortholog thereof.
molecular label role
a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role)
a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
primary structure of sequence macromolecule
A fluid that is composed of blood plasma and erythrocytes.
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
Anatomical group that has its parts adjacent to one another.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
Excretion that is the output of a kidney
A unit which is a standard measure of the distance between two points.
A unit which is a standard measure of the amount of matter/energy of a physical object.
A unit which is a standard measure of the dimension in which events occur in sequence.
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
A unit which is a standardised quantity of an element or compound with uniform composition.
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
A unit which is a standard measure of the number of repetitive actions in a particular time.
A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time .
A unit which represents a standard measurement occurrence of a process per unit time.
A type of quantitative reverse transcription polymerase chain reaction evidence used in automatic assertion.
quantitative reverse transcription polymerase chain reaction evidence used in automatic assertion.
A type of reverse transcription polymerase chain reaction evidence that combines reverse transcription polymerase chain reaction and real time polymerase chain reaction to quantitatively assay for the detection of RNA levels.
real-time quantitative reverse transcription PCR evidence
real-time reverse transcription polymerase chain reaction evidence
quantitative reverse transcription polymerase chain reaction evidence
A type of quantitative reverse transcription polymerase chain reaction evidence used in manual assertion.
quantitative reverse transcription polymerase chain reaction evidence used in manual assertion
example to be eventually removed
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
failed exploratory term
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
ready for release
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
core
placeholder removed
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term imported
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
term split
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
other
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
Terms with this status should eventually replaced with a term from another ontology.
to be replaced with external ontology term
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
requires discussion
Transformation-ML
Transformation-ML file describing parameter transformations used in a GvHD experiment.
Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)
person:Jennifer Fostel
ACS
d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)
XML
RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document
XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)
RDF
A FOAF file, a SKOS file, an OWL file.
RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)
zip
MagicDraw MDZIP archive, Java JAR file.
zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)
tar
Example.tar file.
tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)
FCS
d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)
Compensation-ML
compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment
Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)
Gating-ML
foogate.xml, Gating-ML file describing gates used in a GvHD experiment.
Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)
OWL
OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file.
OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)
An organization which supplies technology, tools and protocols for use in high throughput applications
Affymetrix
GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation.
GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation.
GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations.
GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations.
GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation.
GenePattern module HierarchicalClustering
GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation.
GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation.
GenePattern HeatMapViewer data visualization
The GenePattern process of generating Heat Maps from clustered data.
GenePattern HierarchicalClusteringViewer data visualization
The GenePattern process of generating hierarchical clustering visualization from clustered data.
A GenePattern software module which is used to generate a heatmap view of data.
GenePattern module HierarchicalClusteringViewer
A GenePattern software module which is used to generate a view of data that has been hierarchically clustered.
The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
Advanced Instruments Inc. (AI Companies)
Nimblegen
An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
Pacific Biosciences
An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
NanoString Technologies
An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.
An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
Thermo Fisher Scientific
A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria).
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus).
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s).
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s).
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed.
A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma.
A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential.
A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0).
3: symptomatic in bed more than 50% of the day but not bed ridden
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden.
2: symptomatic but in bed less than 50% of the day
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden.
An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory.
A Karnofsky score vaue specification indicating that a patient is asymptomatic.
A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory.
60-70: symptomatic but in bed less than 50% of the day
A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day.
40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden.
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
A length unit which is equal to one millionth of a meter or 10^[-6] m.
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
A length unit which is equal to 10 [-10] m.
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
A mass unit which is equal to 10^[-12] g.
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
A time unit which is equal to 60 seconds.
A time unit which is equal to 3600 seconds or 60 minutes.
A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
A substance unit equal to a millionth of a mol or 10^[-6] mol.
A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
A unit of molarity which is equal to 10^[-12] M.
A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
A volume unit which is equal to one millionth of a liter or 10^[-6] L.
A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
A volume unit which is equal to 10^[-12] L.
A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
A concentration unit which a measure of viable bacterial numbers in a given volume.
A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
A rate unit which is equal to one over one nanomolar second.
A rate unit which is equal to one over one molar second.
A rate unit which is equal to one over one nanomolar.
A rate unit which is equal to one over one molar.
A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.