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. eco rctauber 08:21:2018 11:52 Evidence & Conclusion Ontology (ECO) A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. example of usage The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition 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 term editor 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 definition source The 'term requester' can credit the person, organization or project who request the ontology term.,The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. IAO ontology term requester Grouping classes used by GO go_groupings GO biological process terms should be used in the GO with/from field valid_with_biological_process GO cellular component terms should be used in the GO with/from field valid_with_cellular_component Chemical entity IDs should be used in the GO with/from field valid_with_chemical_entity Gene IDs should be used in the GO with/from field valid_with_gene GO molecular function terms should be used in the GO with/from field valid_with_molecular_function Protein IDs should be used in the GO with/from field valid_with_protein Protein complex IDs should be used in the GO with/from field valid_with_protein_complex Transcript IDs should be used in the GO with/from field valid_with_transcript description title license subset_property auto-generated-by created_by creation_date date default-namespace has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym id in_subset is_inferred saved-by shorthand 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 BFO:0000050 external part_of part_of part of part of http://www.obofoundry.org/ro/#OBO_REL: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. 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 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 BFO:0000051 external has_part has_part has part 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 realized in 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 realizes 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 http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes precedes A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence. mchibucos 2010-12-09T05:00:20Z ECO:9000000 eco used_in used_in In the future we may use a more generic relation with weaker domain and range constraints taken from IAO, RO or OBI. used_in A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence. GOC:cjm ECO:9000001 eco uses uses uses has 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 person:Alan Ruttenberg 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 has_specified_input see is_input_of example_of_usage A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of 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 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. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output 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. Alan Ruttenberg Liju Fan has_make has_manufacturer is_manufactured_by is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective 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. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has grain 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 PERSON: Alan Ruttenberg 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 has grain supplies 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. GROUP: Relations branch supplies has_supplier 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. PERSON: Alan Rutternberg PERSON: Cristian Cocos PERSON: Frank Gibson PERSON: Melanie Courtot has_supplier objective_achieved_by 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. OBI OBI objective_achieved_by has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification 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 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 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 participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant 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). 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 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 derives from 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 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 located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes RO:0002211 external regulates regulates regulates RO:0002212 external negatively_regulates negatively_regulates negatively regulates RO:0002213 external positively_regulates positively_regulates positively regulates move to BFO? Allen 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. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member has measurement value has specified numeric 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. PERSON: James A. Overton OBI has specified numeric value 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. OBI has specified value entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant 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] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition 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 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] realizable RealizableEntity 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 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] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role 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 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] site Site 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 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] gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function 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 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] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] immaterial ImmaterialEntity 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 ATP 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. ATP peptide 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. peptide deoxyribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. deoxyribonucleic acid molecular entity 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 molecular entity cytochalasin cytochalasin acrylamide A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. acrylamide atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom nucleic acid 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. nucleic acid ribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ribonucleic acid macromolecule 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 macromolecule double-stranded DNA double-stranded DNA 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. 5-bromo-2'-deoxyuridine chromium-51 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. chromium-51 tritiated thymidine Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. tritiated thymidine 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. FM fluorescence imaging fluorescence microscopic imaging CHMO fluorescence microscopy Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. OM light microscopy optical microscopy CHMO light microscopy cell 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. cell cell cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. cultured cell B cell A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. B cell lymphocyte 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. lymphocyte experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. experimentally modified cell in vitro mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form. mononuclear cell A type of information that is used to support an assertion. eco evidence code evidence_code ECO:0000000 evidence A type of information that is used to support an assertion. ECO:MCC A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator. eco ECO:0000001 inference from background scientific knowledge A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator. ECO:SN A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature. ECO:0005006 eco ECO:0000002 direct assay evidence true A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature. ECO:SN A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state. eco ECO:0000003 reconstitution assay evidence A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state. ECO:KAV PMID:26029343 A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient. eco IDA: cell fractionation ECO:0000004 If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology. cell fractionation evidence A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient. ECO:KIM TAIR:TED A type of protein assay evidence where the catalytic activity of an enzyme is determined. ECO:0005001 MI:0415 eco IDA: enzyme assays ECO:0000005 enzyme assay evidence A type of protein assay evidence where the catalytic activity of an enzyme is determined. url:http://www.sciencedirect.com/science/article/pii/S2213020914000068 MI:0415 enzymatic study A type of evidence resulting from manipulation of variables in order to discover cause and effect. ECO:0005023 eco ECO:0000006 experimental evidence true A type of evidence resulting from manipulation of variables in order to discover cause and effect. url:http://holah.co.uk/page/experimental/ A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell. eco IDA: immunofluorescence ECO:0000007 immunofluorescence evidence A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell. ECO:MCC TAIR:TED A type of experimental evidence that is based on characterization of gene expression. eco ECO:0000008 Use this evidence type when the annotation is inferred from the timing or location of expression of a gene. It may be difficult to determine whether the expression pattern truly indicates that a gene plays a role in a given process. expression pattern evidence A type of experimental evidence that is based on characterization of gene expression. ECO:MCC GO:IEP A type of expression pattern evidence where abundance of a transcript is analyzed. ECO:0000048 transcript expression level evidence eco ECO:0000009 transcript expression evidence true A type of expression pattern evidence where abundance of a transcript is analyzed. ECO:RCT A type of expression pattern evidence resulting from protein abundance quantification techniques. eco ECO:0000010 protein expression evidence A type of expression pattern evidence resulting from protein abundance quantification techniques. PMC:4029002 url:https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-protein-expression-systems.html A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products. TAIR:TED eco ECO:0000011 genetic interaction evidence A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products. ECO:RCT PMID:11822023 A type of genetic interaction evidence where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background. eco IGI: functional complementation ECO:0000012 functional complementation evidence A type of genetic interaction evidence where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background. PMID:27403640 A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition. eco ECO:0000013 transgenic rescue experiment evidence A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition. url:http://www.mdpi.com/1420-3049/19/9/13932/pdf url:http://www.nature.com/gt/journal/v11/n15/full/3302282a.html A type of experimental phenotypic evidence derived from the difference in two alleles of a corresponding gene that result from one or more changes in the genome. eco ECO:0000015 mutant phenotype evidence A type of experimental phenotypic evidence derived from the difference in two alleles of a corresponding gene that result from one or more changes in the genome. GO:IMP A type of mutant phenotype evidence where a phenotype is associated with altered gene product which lacks the molecular function of the wild-type gene. eco ECO:0000016 loss-of-function mutant phenotype evidence A type of mutant phenotype evidence where a phenotype is associated with altered gene product which lacks the molecular function of the wild-type gene. SO:0002054 A type of experimental phenotypic evidence where a transgenic strain carrying the construct of a promoter cDNA fusion in which a gene of interest is driven by a defined promoter or enhancer is ectopically expressed in the defined pattern to characterize potential cellular properties and functions of a protein of interest. eco IMP: analysis of overexpression/ectopic expression phenotype ECO:0000017 ectopic expression evidence A type of experimental phenotypic evidence where a transgenic strain carrying the construct of a promoter cDNA fusion in which a gene of interest is driven by a defined promoter or enhancer is ectopically expressed in the defined pattern to characterize potential cellular properties and functions of a protein of interest. PMID:10948520 PMID:19301619 A type of mutant phenotype evidence where a phenotype is observed while expressing an anti-sense version of a gene product in a wild-type (for that gene product) background. eco IMP: anti-sense experiments ECO:0000018 anti-sense experiment evidence A type of mutant phenotype evidence where a phenotype is observed while expressing an anti-sense version of a gene product in a wild-type (for that gene product) background. ECO:SN A type of mutant phenotype evidence where an RNA construct is introduced into a cell and the expression of the gene bearing its complementary sequence is suppressed. eco IMP: RNAi experiment ECO:0000019 RNAi evidence A type of mutant phenotype evidence where an RNA construct is introduced into a cell and the expression of the gene bearing its complementary sequence is suppressed. ECO:MCC A type of protein assay evidence based on the inhibition of the molecular function of a protein. eco ECO:0000020 specific protein inhibition evidence A type of protein assay evidence based on the inhibition of the molecular function of a protein. ECO:MCC A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule. ECO:0005025 MI:0045 eco ECO:0000021 Molecules interacted with might include protein, nucleic acid, ion, or complex. physical interaction evidence A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule. ECO:SN MI:0045 experimental interaction detection A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex. MI:0025 eco IPI: co-purification ECO:0000022 co-purification evidence A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex. TAIR:TED MI:0025 copurification A type of physical interaction evidence that depends on the strength of the interaction between two entities. MI:0400 ligand binding evidence eco ECO:0000023 affinity evidence A type of physical interaction evidence that depends on the strength of the interaction between two entities. ECO:MCC PSI-MI:MI:0400 MI:0400 affinity technology A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex. eco ECO:0000024 protein binding evidence A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex. GO:0005515 url:https://en.wikipedia.org/wiki/Mutation A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein. MI:0090 eco ECO:0000025 Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode. hybrid interaction evidence A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein. ECO:MCC PSI-MI:MI:0090 MI:0090 protein complementation assay A type of experimental genomic evidence resulting from a process in which single stranded nucleic acids are allowed to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences. eco ECO:0000026 This term has been made obsolete with the clean up of experimental genomic evidence branch. nucleic acid hybridization evidence true A type of experimental genomic evidence resulting from a process in which single stranded nucleic acids are allowed to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences. OBI:0302903 A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes. eco ECO:0000027 For GO annotation, in the case of a single gene, an accession for the related gene's sequence is entered in the evidence_with field. structural similarity evidence A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes. ECO:MCC TAIR:TED A type of match to sequence model evidence that is based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence. eco ISS: recognized domains ECO:0000028 motif similarity evidence A type of match to sequence model evidence that is based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence. ECO:SN A type of match to sequence model evidence resulting from a positive match of a protein, or set of proteins to a predictive model (signature) in the InterPro database. eco ECO:0000029 match to InterPro member signature evidence A type of match to sequence model evidence resulting from a positive match of a protein, or set of proteins to a predictive model (signature) in the InterPro database. PMC:2686546 url:http://www.ncbi.nlm.nih.gov/mesh?term=Nucleic+Acid+Hybridization A type of BLAST evidence that is used in a manual assertion. eco curated BLAST analysis ECO:0000030 BLAST evidence used in manual assertion true true A type of BLAST evidence that is used in a manual assertion. ECO:MCC A type of protein BLAST evidence that is used in a manual assertion. GO_REF:0000012 GO_REF:0000027 eco curated protein BLAST analysis ECO:0000031 protein BLAST evidence used in manual assertion true true A type of protein BLAST evidence that is used in a manual assertion. ECO:SN GO_REF:0000012 Pairwise alignment (TIGR) GO_REF:0000027 BLAST search criteria for ISS assignment in PAMGO_GAT A type of nucleotide BLAST evidence that is used in a manual assertion. eco curated nucleic acid BLAST analysis ECO:0000032 nucleotide BLAST evidence used in manual assertion true true A type of nucleotide BLAST evidence that is used in a manual assertion. ECO:SN A type of author statement 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. eco traceable author statement ECO:0000033 author statement supported by traceable reference 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. ECO:RCT GO:TAS A type of author statement that is not associated with results presented or a cited reference. eco non-traceable author statement ECO:0000034 author statement without traceable support A type of author statement that is not associated with results presented or a cited reference. ECO:SN A curator inference that results from research where no information about a biological feature was found in the scientific literature, at biological databases, or within other resources. eco ECO:0000035 An assertion of "no biological data found" carries the assumption that a more-or-less exhaustive search has been conducted. no biological data found A curator inference that results from research where no information about a biological feature was found in the scientific literature, at biological databases, or within other resources. ECO:SN eco ECO:0000037 The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations. not_recorded true eco ECO:0000038 transient rescue experiment evidence A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins. ECO:0005022 eco ECO:0000039 protein assay evidence A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins. PMID:18429326 A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody. ECO:0005018 eco ECO:0000040 immunological assay evidence A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody. ERO:0001362 url:http://www.ncbi.nlm.nih.gov/books/NBK21589/,http://cores.ucsf.edu/protein-assay.html A type of evidence resulting from comparing likeness of distinct biological entities. IS eco inferred from similarity ECO:0000041 similarity evidence A type of evidence resulting from comparing likeness of distinct biological entities. ECO:SN A type of mutant phenotype evidence resulting from a phenotype that is associated with the altered gene product which possesses a new molecular function or a new pattern of gene expression. eco ECO:0000042 gain-of-function mutant phenotype evidence A type of mutant phenotype evidence resulting from a phenotype that is associated with the altered gene product which possesses a new molecular function or a new pattern of gene expression. SO:0002053 url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614608/ A type of similarity based on biomolecular sequence. eco ECO:0000044 A sequence similarity analysis may involve a gene or a gene product, and it could be based on similarity to a single other gene or to a group of other genes. sequence similarity evidence A type of similarity based on biomolecular sequence. ECO:MCC TAIR:TED eco ECO:0000045 spatial pattern of protein expression evidence A type of protein expression evidence resulting from the quantification of protein production in a sample. eco ECO:0000046 protein expression level evidence A type of protein expression evidence resulting from the quantification of protein production in a sample. NBK:22011 url:http://www.informatics.jax.org/glossary/gain-of-function eco ECO:0000047 spatial pattern of transcript expression evidence A type of experimental phenotypic evidence that is based on the expression pattern of a reporter gene. eco IEP: expression of a reporter gene ECO:0000049 reporter gene assay evidence A type of experimental phenotypic evidence that is based on the expression pattern of a reporter gene. TAIR:TED A type of phenotypic evidence based on an author's phenotypic description of a species or higher level group explicitly referencing an observation of a voucher specimen, a specimen with a permanent museum catalog. IVS eco ECO:0000050 voucher specimen analysis evidence A type of phenotypic evidence based on an author's phenotypic description of a species or higher level group explicitly referencing an observation of a voucher specimen, a specimen with a permanent museum catalog. TAIR:TED A type of similarity based on genotype without respect to expression. IGTS eco inferred from genetic similarity ECO:0000051 A genetic similarity analysis might consider genetic markers, polymorphisms, alleles, or other characteristics sometimes considered as part of the field of traditional genetics. Although an attempt has been made to treat as distinct the concepts of "genetic", "genotypic", "genomic", and "sequence", there is considerable overlap in usage throughout the field of biology. genetic similarity evidence A type of similarity based on genotype without respect to expression. ECO:MCC PhenoScape:IGTS A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation. TAIR:TED eco IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals) ECO:0000052 suppressor/enhancer interaction evidence A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation. url:http://biorxiv.org/content/early/2015/10/03/021592 url:http://www.wormbook.org/chapters/www:geneticsuppression/geneticsuppression.html A type of combinatorial analysis where data are combined and evaluated by an algorithm. TAIR:TED eco ECO:0000053 Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments. computational combinatorial evidence A type of combinatorial analysis where data are combined and evaluated by an algorithm. ECO:MCC ECO:go A type of genetic interaction evidence that is based on the phenotypic outcome of two mutations in unrelated genetic loci. eco IGI: double mutant analysis ECO:0000054 double mutant phenotype evidence A type of genetic interaction evidence that is based on the phenotypic outcome of two mutations in unrelated genetic loci. ECO:RCT eco ECO:0000055 This general 'array experiment' term should not be used - replace with the specific type of array (e.g. ECO:0000097, ECO:0000062, ECO:0000104, etc.) array experiment evidence true A type of genetic interaction evidence that is based on the suppression of one allelic effect by an allele at another genetic locus. eco IGI: epistatic interactions ECO:0000056 Epistasis' can be used in different contexts in different areas of genetics. It is sometimes used to mean 'genetic interaction', whereas other times it may be specific to mutations that block the effects of other mutations. epistatic interaction evidence A type of genetic interaction evidence that is based on the suppression of one allelic effect by an allele at another genetic locus. PMID:18852697 A type of similarity based on the expression of a genotype in an environment. IPTS phenotype similarity evidence eco inferred from phenotypic similarity ECO:0000057 Phenotype is defined as the outcome of the expression of a genotype in a given environment. A comparison might involve whole organisms or sub-parts of organisms. phenotypic similarity evidence A type of similarity based on the expression of a genotype in an environment. ECO:MCC PhenoScape:IPTS A type of transcript expression evidence resulting from simultaneous profiling of the expression levels of thousands of genes in a single experiment allowing analysis of genes and their networks. ECO:0000356 differential gene expression evidence from microarray experiment eco ECO:0000058 expression microarray evidence A type of transcript expression evidence resulting from simultaneous profiling of the expression levels of thousands of genes in a single experiment allowing analysis of genes and their networks. url:http://www.illumina.com/techniques/microarrays/gene-expression-arrays.html url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435252/ A type of experimental evidence that is based on the expression of a genotype in an environment. ECO:0000014 ECO:0005017 eco inferred from phenotype ECO:0000059 experimental phenotypic evidence true A type of experimental evidence that is based on the expression of a genotype in an environment. ECO:SN A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements. IPS eco ECO:0000060 positional similarity evidence A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements. TAIR:TED A type of phenotypic evidence that is based on a gene product that is associated with a quantitative trait locus, but has not been cloned. QTL analysis evidence eco IGI: quantitative trait analysis ECO:0000061 quantitative trait analysis evidence A type of phenotypic evidence that is based on a gene product that is associated with a quantitative trait locus, but has not been cloned. TAIR:TED A type of expression microarray evidence where expression level is quantified by sample biotin-labeled cRNA (transcribed from an unknown RNA sample) hybridized to DNA oligonuclotides immoblized on a solid surface. genomic microarray evidence eco ECO:0000062 cRNA to DNA expression microarray evidence A type of expression microarray evidence where expression level is quantified by sample biotin-labeled cRNA (transcribed from an unknown RNA sample) hybridized to DNA oligonuclotides immoblized on a solid surface. url:https://link.springer.com/chapter/10.1007/978-94-017-9716-0_30 A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures. ICS eco ECO:0000063 compositional similarity evidence A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures. TAIR:TED A type of functional complementation evidence that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene. eco IGI: functional complementation in heterologous system ECO:0000064 functional complementation in heterologous system evidence A type of functional complementation evidence that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene. TAIR:TED A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors. MI:0432 eco IPI: yeast one-hybrid assay ECO:0000066 The assay involves screening a library of candidate proteins for the ability bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to a yeast reporter gene (TAIR:TED). yeast one-hybrid evidence A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors. ECO:MCC PSI-MI:MI:0432 TAIR:TED MI:0432 one hybrid A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures. IDS eco ECO:0000067 developmental similarity evidence A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures. TAIR:TED A type of hybrid interaction evidence that is based on detection of protein-protein interaction by activation of a yeast reporter gene after a bait protein fused to a DNA-binding domain (which has been transfected into a yeast cell) is used to screen a cDNA library of clones fused to an activation domain. eco IPI: yeast two-hybrid assay ECO:0000068 yeast 2-hybrid evidence A type of hybrid interaction evidence that is based on detection of protein-protein interaction by activation of a yeast reporter gene after a bait protein fused to a DNA-binding domain (which has been transfected into a yeast cell) is used to screen a cDNA library of clones fused to an activation domain. PMID:12734586 A type of 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. ECO:0000065 CpG island microarray evidence eco ECO:0000069 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 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. PMID:18987809 A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification. MI:0019 eco IPI: co-immunoprecipitation ECO:0000070 If performing GO annotation, the interacting protein is referenced in the evidence_with column. co-immunoprecipitation evidence A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification. ECO:MCC MI:0019 coimmunoprecipitation A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures. IMS eco ECO:0000071 morphological similarity evidence A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures. TAIR:TED eco ECO:0000072 Sos-recruitment assay evidence true A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product. inferred from genomic analysis eco ECO:0000073 This term has been made obsolete with the clean up of experimental genomic evidence branch. experimental genomic evidence true A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product. ECO:MCC A type of physical interaction evidence that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein. MI:0112 eco IPI: split-ubiquitin assay ECO:0000074 The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquitin (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough to reconstitute.TAIR:TED split-ubiquitin assay evidence A type of physical interaction evidence that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein. PMID:15064465 MI:0112 ubiquitin reconstruction A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles. IGES eco ECO:0000075 gene expression similarity evidence A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles. PMID:19958477 A type of physical interaction evidence that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes. MI:0047 eco IPI: far-Western analysis ECO:0000076 The interacting protein is referenced in the evidence_with column. far-Western blotting evidence A type of physical interaction evidence that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes. PMID:18079728 A type of 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. MS-PCR MSP methylation-specific PCR evidence eco ECO:0000077 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 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. PMC:38513 PMID:8790415 A type of DNA detection assay evidence that is based on detection of a specific DNA sequence by hybridization of labeled probes to any immobilized DNA fragment with sequence similarity. Southern blot eco ISS: Southern blotting ECO:0000078 The DNA fragments are prepared through gel electrophoresis then transferred to a filter membrane. southern hybridization evidence A type of DNA detection assay evidence that is based on detection of a specific DNA sequence by hybridization of labeled probes to any immobilized DNA fragment with sequence similarity. PMID:18432697 A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound. MI:0004 eco IDA: affinity chromatography ECO:0000079 "Used when an annotation is made based on affinity chromatography, which is a selective separation technique by which a compound (e.g., an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components, the bound compound is displaced by changing the concentration of protons, salts, or cofactors in the eluent" (from original definition by TAIR:TED). Types of highly specific interaction might include those of antigen and antibody, enzyme and substrate, or receptor and ligand. affinity chromatography evidence A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound. ECO:MCC TAIR:TED MI:0004 affinity chromatography technology A type of similarity that indicates common ancestry. IP eco ECO:0000080 phylogenetic evidence A type of similarity that indicates common ancestry. ECO:MCC PhenoScape:IP IP PhenoScape:IP A type of motif similarity evidence that is based on detection of a targeting sequence in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence. eco ISS: targeting sequence prediction ECO:0000081 targeting sequence prediction evidence A type of motif similarity evidence that is based on detection of a targeting sequence in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence. ECO:RCT TAIR:TED A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand. PCR evidence eco ECO:0000082 This term has been made obsolete because PCR is not evidence. The children have been appropriately placed under other parents. polymerase chain reaction evidence true A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand. OBI:0000415 A type of motif similarity evidence that is based on detection of one, or more, transmembrane domains in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence. eco ISS: transmembrane domain prediction ECO:0000083 transmembrane domain prediction evidence A type of motif similarity evidence that is based on detection of one, or more, transmembrane domains in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence. ECO:RCT TAIR:TED A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes. mgiglio 2009-03-20T11:55:18Z GO_REF:0000025 inferred from genome cluster eco ICL ECO:0000084 Genomic cluster analyses include synteny and operon structure. gene neighbors evidence A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes. ECO:MCC GOC:MG GO_REF:0000025 Operon structure as IGC evidence A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation. CollecTF eco IDA: immunoprecipitation ECO:0000085 Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding. immunoprecipitation evidence A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation. ECO:MCC ECO:SW TAIR:TED A type of 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. AIMS eco ECO:0000086 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 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. PMID:18987810 url:https://www.ncbi.nlm.nih.gov/probe/docs/techpcr/ A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues. eco IDA: immunolocalization ECO:0000087 immunolocalization evidence A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues. ECO:MCC ECO:SN A type of evidence that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system. mgiglio 2009-03-20T12:00:17Z eco ISR inferred from system reconstruction ECO:0000088 The biological system in question might be a multi-step process or pathway or a physical complex comprising several components. The components in the experimental evidence can come from the same species or a mix of species. The experimental evidences may be only partial or weak. biological system reconstruction evidence A type of evidence that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system. ECO:MCC GOC:mg A type of DNA detection assay evidence resulting from the use of restriction enzymes for direct end-labeling of DNA (creating landmarks), followed by high-resolution two-dimensional electrophoresis to visualize the landmarks. SIB:PG ECO:0001125 RLGS evidence restriction landmark genome scanning evidence eco ECO:0000089 restriction landmark genomic scanning evidence A type of DNA detection assay evidence resulting from the use of restriction enzymes for direct end-labeling of DNA (creating landmarks), followed by high-resolution two-dimensional electrophoresis to visualize the landmarks. PMID:8388788 A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy. eco IDA: immunogold labelling ECO:0000090 immunogold labelling evidence A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy. ECO:MCC A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies. eco IDA: immunolocalization of epitope-tagged protein ECO:0000092 epitope-tagged protein immunolocalization evidence A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies. TAIR:TED A type of 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. DNA microarray oligonucleotide microarray evidence SNP array evidence single nucleotide polymorphism array evidence eco ECO:0000093 array-based sequence capture 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. PMID:21049075 eco ECO:0000094 The children of 'biological assay evidence' have been moved under 'direct assay evidence', and this term has been deprecated with no children left. biological assay evidence true true A type of cell growth assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect. mchibucos 2014-10-15T00:58:50Z eco growth curve analysis ECO:0000095 Cell growth aspects can include growth rate and extent of growth. A cell growth curve acts as a natural reporter. cell growth regulation assay evidence A type of cell growth assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect. ECO:SW PomBase:MAH A type of direct assay evidence based on an electrophoretic mobility shift of macromolecules, compounds, and proteins where solutions of protein and nucleic acid are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect protein-nucleic acid interactions. CollecTF MI:0413 EMSA: electrophoretic mobility shift assay eco Gel retardation assay IDA: electrophoretic mobility shift assay ECO:0000096 EMSA is often used for assessing TF-binding with fluorophore labelling. Protein-nucleic acid complexes generally migrate at a slower rate than the corresponding non-bonded nucleic acid. electrophoretic mobility shift assay evidence A type of direct assay evidence based on an electrophoretic mobility shift of macromolecules, compounds, and proteins where solutions of protein and nucleic acid are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect protein-nucleic acid interactions. ECO:KIM ECO:SW PMID:17703195 TAIR:TED MI:0413 electrophoretic mobility shift assay Gel retardation assay PMID:17703195 A type of expression microarray evidence where expression level is quantified by fluroescently-labeled cDNA (reverse transcribed from an unknown RNA sample) hybridized to DNA immobilized on a solid surface. CollecTF ECO:0001041 ECO:0005524 eco DNA microarray RNA microarray ECO:0000097 cDNA to DNA expression microarray evidence A type of expression microarray evidence where expression level is quantified by fluroescently-labeled cDNA (reverse transcribed from an unknown RNA sample) hybridized to DNA immobilized on a solid surface. ECO:RCT A type of nucleic acid hybridization evidence based on localization of a specific segment of DNA or RNA by the application of a complementary strand of nucleic acid to which a reporter molecule is attached. eco IDA: in situ hybridization ECO:0000098 This term has been made obsolete with the clean up of experimental genomic evidence branch. in situ hybridization evidence true true A type of nucleic acid hybridization evidence based on localization of a specific segment of DNA or RNA by the application of a complementary strand of nucleic acid to which a reporter molecule is attached. url:https://www.ncbi.nlm.nih.gov/probe/docs/techish/ A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions. eco ECO:0000100 fractionation evidence A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions. NBK:26936 url:https://www.ncbi.nlm.nih.gov/books/NBK26936/ A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information. Affymetrix array experiment evidence eco ECO:0000101 Affymetrix GeneChip evidence A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information. ERO:0001265 A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules. eco IDA: co-fractionation ECO:0000102 co-fractionation evidence A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules. TAIR:TED A type of expression microarray evidence where expression levels are quantified by hybridization of fluorescently-labeled DNA to cDNA (reverse transcribed from an unknown RNA sample) immobilized on a solid surface. REM evidence RNA expression microarray evidence microarray RNA expression level evidence eco IEP: transcript levels (e.g. microarray data) ECO:0000104 REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that. DNA to cDNA expression microarray evidence A type of expression microarray evidence where expression levels are quantified by hybridization of fluorescently-labeled DNA to cDNA (reverse transcribed from an unknown RNA sample) immobilized on a solid surface. ECO:RCT PMID:15329382 REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that. PMID:15329382 A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels. eco ECO:0000105 Nimblegen array evidence A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels. PMID:15607417 url:https://roche-biochem.jp/pdf/products/microarray/user_guide/SeqCap/SeqCap_UserGuide_Delivery_ver3.0.pdf A type of transcript expression evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples. CollecTF RNA blot evidence northern assay evidence eco IEP: transcript levels (e.g. Northerns) ECO:0000106 northern blot evidence A type of transcript expression evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples. ECO:SW TAIR:TED A type of RNA detection assay evidence where an RNA transcript is reverse transcribed into cDNA and amplified to qualitatively detect gene expression. CollecTF ECO:0000108 reverse transcription polymerase chain reaction transcription evidence RT-PCR eco IEP: transcript levels (e.g. RT-PCR) ECO:0000109 The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate. reverse transcription polymerase chain reaction evidence A type of RNA detection assay evidence where an RNA transcript is reverse transcribed into cDNA and amplified to qualitatively detect gene expression. ECO:SW PMID:11013345 PMID:12901609 A type of nuclease protection assay evidence where mRNA is hybridized with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions, later the remaining probe target hybrids are purified and resolved on denaturing polyacrylamide gel, and quantified by autoradiography. CollecTF ribonuclease protection assay RPA eco IEP: RNA protection assay RNAse protection assay ECO:0000110 RNA protection assay evidence A type of nuclease protection assay evidence where mRNA is hybridized with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions, later the remaining probe target hybrids are purified and resolved on denaturing polyacrylamide gel, and quantified by autoradiography. ECO:SW PMID:23457339 TAIR:TED A type of gel electrophoresis evidence where proteins are separated using gel electrophoresis and then they are blotted on a nitrocellulose or polyvinylidene difluoride (PVDF) membrane, later an antibody with a dye or an enzyme is added to the solution which is able to bind to its specific protein and this product is detected either by chemiluminescent detection technique or fluorescence imaging technique. CollecTF eco IEP: protein levels (e.g. Western blots) Western blot expression analysis protein immunoblot ECO:0000112 Western blot is used for protein detection and analysis. A mixed protein sample is separated through polyacrylamide gel electrophoresis then transferred to a membrane, such as polyvinylidene fluoride (PVDF), and labeled with protein-specific antibodies. western blot evidence A type of gel electrophoresis evidence where proteins are separated using gel electrophoresis and then they are blotted on a nitrocellulose or polyvinylidene difluoride (PVDF) membrane, later an antibody with a dye or an enzyme is added to the solution which is able to bind to its specific protein and this product is detected either by chemiluminescent detection technique or fluorescence imaging technique. ECO:SW PMID:23050259 TAIR:TED A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein. eco IEP: expression library screening ECO:0000114 expression library screen evidence A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein. ECO:MCC TAIR:TED A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue is compared to another cell type or tissue when mRNA from each sample is reverse transcribed, labeled, and hybridized to a cDNA library to compare hybridization patterns. eco IEP: differential hybridization ECO:0000116 Differential hybridization identifies differentially expressed cloned genes. Two different mRNA-derived probes are used to demonstrate RNA expression under a specific condition. differential hybridization evidence A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue is compared to another cell type or tissue when mRNA from each sample is reverse transcribed, labeled, and hybridized to a cDNA library to compare hybridization patterns. PMID:14668817 A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue are compared to another cell type or tissue when denatured ds-cDNA from the two samples are hybridized, and the common sequences are 'subtracted'. eco IEP: subtractive hybridization ECO:0000118 Subtractive hybridization is used for isolation and identification of transcripts involving the removal of any sequences present in the control from the test probe to detect only transcripts present in the sample. The method is PCR-based for the comparison of two cDNA libraries. subtractive hybridization evidence A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue are compared to another cell type or tissue when denatured ds-cDNA from the two samples are hybridized, and the common sequences are 'subtracted'. PMID:11298187 A type of experimental phenotypic evidence in which a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product. eco IMP: analysis of overexpression/ectopic expression phenotype ECO:0000120 over expression analysis evidence A type of experimental phenotypic evidence in which a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product. PMID:22419077 A type of localization evidence where sub-cellular localization of a protein is determined. eco ECO:0000122 protein localization evidence A type of localization evidence where sub-cellular localization of a protein is determined. GO:0008104 url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019937 A type of protein localization evidence resulting from the fusion of a protein of interest to a labeling protein which has enzymatic activity or fluorescence properties. eco ECO:0000124 fusion protein localization evidence A type of protein localization evidence resulting from the fusion of a protein of interest to a labeling protein which has enzymatic activity or fluorescence properties. MI:0240 A type of fusion protein localization evidence resulting from the labeling of a protein of interest with green fluorescent protein (GFP) from the jellyfish Aequorea victoria. GFP fusion protein localization evidence eco IDA: localization of GFP/YFP fusion protein ECO:0000126 green fluorescent protein fusion protein localization evidence A type of fusion protein localization evidence resulting from the labeling of a protein of interest with green fluorescent protein (GFP) from the jellyfish Aequorea victoria. PMID:9759496 A type of fusion protein localization evidence resulting from the labeling of a protein of interest with yellow fluorescent protein (YFP), which was created by mutating green fluorescent protein (GFP) of the Aequorea victoria. YFP fusion protein localization evidence eco IDA: localization of GFP/YFP fusion protein ECO:0000128 yellow fluorescent protein fusion protein localization evidence A type of fusion protein localization evidence resulting from the labeling of a protein of interest with yellow fluorescent protein (YFP), which was created by mutating green fluorescent protein (GFP) of the Aequorea victoria. MI:0368 url:http://www.jbc.org/content/276/31/29188.long A type of fusion protein localization evidence resulting from the targeted insertion of the beta-glucuronidase (GUS) coding gene as a reporter gene for the localization of a particular gene product. GUS fusion protein localization evidence GUS staining evidence eco IDA: localization of GUS fusion protein ECO:0000130 beta-glucuronidase fusion protein localization evidence A type of fusion protein localization evidence resulting from the targeted insertion of the beta-glucuronidase (GUS) coding gene as a reporter gene for the localization of a particular gene product. ECO:RCT A type of fusion protein localization evidence resulting from the targeted insertion of the beta-galactosidase coding gene (lacZ) into a specific gene to create a beta-galactosidase-tagged fusion protein. LacZ fusion protein localization evidence eco ECO:0000132 beta-galactosidase fusion protein localization evidence A type of fusion protein localization evidence resulting from the targeted insertion of the beta-galactosidase coding gene (lacZ) into a specific gene to create a beta-galactosidase-tagged fusion protein. PMID:23681629 A type of direct assay evidence resulting from the activity assessment of transport proteins. eco IDA: transport assay ECO:0000134 transport assay evidence A type of direct assay evidence resulting from the activity assessment of transport proteins. PMID:18401524 A type of affinity evidence resulting from the binding of a molecule to a nucleic acid. eco ECO:0000136 nucleic acid binding evidence A type of affinity evidence resulting from the binding of a molecule to a nucleic acid. GO:0003676 A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer. eco IDA: ribohomopolymer binding assay ECO:0000138 ribohomopolymer binding assay evidence A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer. PMC:102612 A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate. TLC evidence eco IDA: thin layer chromatography ECO:0000140 thin layer chromatography evidence A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate. ECO:MCC A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site. eco ECO:0000142 protein:ion binding evidence A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site. PMID:2377604 A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins. eco IDA: Southwestern analysis ECO:0000144 Southwestern blot evidence A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins. ECO:RCT TAIR:TED A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins. eco IDA: Northwestern analysis ECO:0000146 Northwestern blot evidence A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins. ECO:RCT TAIR:TED eco ECO:0000148 in vitro binding evidence true A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis. eco IDA: in vitro reconstitution assay with recombinant protein ECO:0000150 in vitro transcription reconstitution assay evidence A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis. PMID:9237163 A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system. eco IDA: in vitro reconstitution assay with recombinant protein ECO:0000152 in vitro recombinant protein transcription reconstitution assay evidence A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system. PMID:9237165 A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed. eco IDA: protein expression in heterologous system ECO:0000154 heterologous protein expression evidence A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed. ECO:KAV A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture. eco ECO:0000156 protein separation evidence A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture. ERO:0000526 eco IDA: protein separation and direct sequencing ECO:0000158 protein separation followed by direct sequencing evidence eco IDA: protein separation and fragment identification ECO:0000160 protein separation followed by fragment identification evidence A type of transport assay evidence in which the uptake mechanism of a transporter is investigated in a cell that does not normally express that protein. eco IDA: uptake assay in heterologous system ECO:0000162 The transporter is a recombinant protein. heterologous system uptake evidence A type of transport assay evidence in which the uptake mechanism of a transporter is investigated in a cell that does not normally express that protein. ECO:RCT doi:10.1146/annurev.pp.46.060195.002223 A type of direct assay evidence where electrical properties of cells or tissues are studied. eco ECO:0000164 The scale of electrophysiology assays can range from small, e.g. a single ion channel, to large, e.g. an entire organ such as a heart. electrophysiology assay evidence A type of direct assay evidence where electrical properties of cells or tissues are studied. ECO:KAV A type of voltage clamp recording evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current. eco IDA: two-electrode voltage clamp technique ECO:0000166 two-electrode voltage clamp recording evidence A type of voltage clamp recording evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current. ECO:SN PMID:23529422 A type of direct assay evidence resulting from the detection and quantification of transcribed RNA. eco ECO:0000168 transcription assay evidence A type of direct assay evidence resulting from the detection and quantification of transcribed RNA. MeSH:D014158 url:https://bmcmolbiol.biomedcentral.com/articles/10.1186/1471-2199-15-7 A type of transcription assay evidence in which sequence-specific binding proteins that increase transcription of a specific target gene or genes are identified, quantified, and/or analyzed. eco IDA: transcriptional activation assay ECO:0000170 transcriptional activation assay evidence A type of transcription assay evidence in which sequence-specific binding proteins that increase transcription of a specific target gene or genes are identified, quantified, and/or analyzed. url:http://smcg.ccg.unam.mx/enp-unam/05-TranscripYRegulacion/transcription.pdf A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed. eco IMP: analysis of biochemical trait ECO:0000172 For example, the accumulation of a biosynthetic intermediate. biochemical trait analysis evidence A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed. ECO:RCT A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined. eco IMP: analysis of physiological response ECO:0000174 Examples include: abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions. mutant physiological response evidence A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined. ECO:RCT A type of mutant phenotype evidence in which traits arising from a mutation are visually examined. eco IMP: analysis of visible trait ECO:0000176 mutant visible phenotype evidence A type of mutant phenotype evidence in which traits arising from a mutation are visually examined. ECO:RCT A type of evidence in which the location of the gene within the genome provides insight into its function, or provides evolutionary insight. eco ECO:0000177 This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis. genomic context evidence A type of evidence in which the location of the gene within the genome provides insight into its function, or provides evolutionary insight. PMID:21609955 A type of direct assay evidence resulting from a sample of microorganisms or living tissue grown in a medium. eco ECO:0000178 in vivo assay evidence A type of direct assay evidence resulting from a sample of microorganisms or living tissue grown in a medium. ECO:RCT url:https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=46352 A type of experimental evidence arising from the investigation of an animal model system. eco ECO:0000179 animal model system study evidence true A type of experimental evidence arising from the investigation of an animal model system. ECO:MCC A type of experimental evidence arising from a controlled investigation that uses human subjects. eco ECO:0000180 clinical study evidence A type of experimental evidence arising from a controlled investigation that uses human subjects. ECO:MCC A type of direct assay evidence resulting from a process performed outside the living organism, where the components of an organism have been isolated from their usual biological context, to permit a more detailed or more convenient analysis in an artificial setting. ECO:0005013 eco ECO:0000181 in vitro assay evidence A type of direct assay evidence resulting from a process performed outside the living organism, where the components of an organism have been isolated from their usual biological context, to permit a more detailed or more convenient analysis in an artificial setting. ECO:RCT url:https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=45733 eco ECO:0000182 Use ECO:0001563 (cell growth assay evidence) in place of this term. in vitro culture assay evidence true A type of direct assay evidence resulting from studies in which cytoplasmic and/or nuclear cellular components from resting, nonstimulated cells, are isolated by ultracentrifugation to provide molecular machinery that can be used in reactions in the absence of many of the other cellular components for the purpose of in vitro protein synthesis, transcription, DNA replication, etc. in vitro assay eco ECO:0000183 cell-free assay evidence A type of direct assay evidence resulting from studies in which cytoplasmic and/or nuclear cellular components from resting, nonstimulated cells, are isolated by ultracentrifugation to provide molecular machinery that can be used in reactions in the absence of many of the other cellular components for the purpose of in vitro protein synthesis, transcription, DNA replication, etc. PMID:18453125 A type of specific protein inhibition evidence where the protein under study is an enzyme. eco ECO:0000184 enzyme inhibition evidence A type of specific protein inhibition evidence where the protein under study is an enzyme. ECO:MCC A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment mchibucos 2010-03-18T12:21:31Z ECO:00000057 eco ECO:0000200 Such alignments may be pairwise alignments or multiple alignments. sequence alignment evidence A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment url:http://www.geneontology.org/GO.evidence.shtml A type of sequence similarity evidence in which orthology is established by multiple criteria, including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors. mchibucos 2010-03-18T12:30:06Z ECO:00000060 eco ortholog evidence ECO:0000201 Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor. sequence orthology evidence A type of sequence similarity evidence in which orthology is established by multiple criteria, including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors. url:http://www.geneontology.org/GO.evidence.shtml A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model. mchibucos 2010-03-18T12:32:30Z ECO:00000063 eco ECO:0000202 Used when evidence from any kind of statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Examples of relevant evidence are: Hidden Markov Models, PROSITE motifs, and tools such as tRNASCAN. match to sequence model evidence A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model. ECO:MCC url:http://www.geneontology.org/GO.evidence.shtml An assertion method that does not involve human review. mchibucos 2010-03-18T12:36:04Z ECO:00000067 eco ECO:0000203 An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically. automatic assertion An assertion method that does not involve human review. ECO:MCC An evidence type that is based on an assertion by the author of a paper, which is read by a curator. mchibucos 2010-06-21T11:17:21Z eco ECO:0000204 author statement An evidence type that is based on an assertion by the author of a paper, which is read by a curator. ECO:MCC A type of inferential evidence that is based on a conclusion drawn by a curator. mchibucos 2010-08-18T05:55:12Z eco ECO:0000205 curator inference A type of inferential evidence that is based on a conclusion drawn by a curator. ECO:MCC A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST). mchibucos 2010-08-06T04:48:24Z eco ECO:0000206 BLAST evidence A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST). ECO:MCC A type of BLAST evidence in which nucleotide sequences are aligned. mchibucos 2010-08-06T04:49:58Z eco ECO:0000207 nucleotide BLAST evidence A type of BLAST evidence in which nucleotide sequences are aligned. ECO:MCC A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned. mchibucos 2010-08-06T04:50:45Z eco ECO:0000208 protein BLAST evidence A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned. ECO:MCC A type of BLAST evidence that is used in an automatic assertion. mchibucos 2010-08-06T04:55:21Z eco ECO:0000209 BLAST evidence used in automatic assertion true true A type of BLAST evidence that is used in an automatic assertion. ECO:MCC A type of nucleotide BLAST evidence that is used in an automatic assertion. mchibucos 2010-08-06T05:09:51Z eco ECO:0000210 nucleotide BLAST evidence used in automatic assertion true true A type of nucleotide BLAST evidence that is used in an automatic assertion. ECO:RCT A type of protein BLAST evidence that is used in an automatic assertion. mchibucos 2010-08-06T05:11:04Z eco ECO:0000211 protein BLAST evidence used in automatic assertion true true A type of protein BLAST evidence that is used in an automatic assertion. ECO:RCT A type of evidence that arises out of the integration of more than one line of evidence. mchibucos 2010-08-06T05:24:57Z ECO:0000036 ECO:0000043 eco inferred from in-silico analysis ECO:0000212 A key aspect of this type of evidence is that two or more pieces of information are combined to generate an emergent type of evidence not possible with the constituent pieces of evidence alone. A combinatorial analysis typically involves incorporation of different types of evidence. combinatorial evidence A type of evidence that arises out of the integration of more than one line of evidence. ECO:MCC A type of combinatorial analysis that is used in an automatic assertion. mchibucos 2010-08-06T05:28:33Z eco inferred from in-silico analysis ECO:0000213 Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments. combinatorial evidence used in automatic assertion true true A type of combinatorial analysis that is used in an automatic assertion. ECO:MCC A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene. mchibucos 2010-10-05T11:16:50Z eco ECO:0000214 This type of evidence can be used in support of both positive and "not" GO annotations. It should be used to annotate ancestral genes but not extant ones. biological aspect of descendant evidence A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene. ECO:MCC A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event. mchibucos 2010-10-05T03:41:34Z eco ECO:0000215 Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence. rapid divergence from ancestral sequence evidence A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event. ECO:MCC A type of phylogenetic evidence characterized by the absence of key sequence residues. mchibucos 2010-10-05T03:43:17Z eco ECO:0000216 The loss of certain residues important for function can indicate that a sequence lacks a particular function. phylogenetic determination of loss of key residues evidence A type of phylogenetic evidence characterized by the absence of key sequence residues. ECO:MCC A means by which a statement is made about an entity. mchibucos 2010-11-12T04:17:37Z eco ECO:0000217 assertion method A means by which a statement is made about an entity. ECO:MCC An assertion method that involves human review. mchibucos 2010-11-12T04:20:02Z eco ECO:0000218 A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information. manual assertion An assertion method that involves human review. ECO:MCC A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides. mchibucos 2010-11-15T12:22:40Z eco DNA sequencing ECO:0000219 nucleotide sequencing assay evidence A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides. ECO:MCC DNA sequencing OBI:0000626 A type of experimental evidence where the order of molecules that constitute a biopolymer is determined. mchibucos 2010-11-15T01:44:45Z eco ECO:0000220 sequencing assay evidence A type of experimental evidence where the order of molecules that constitute a biopolymer is determined. ECO:MCC OBI:0600047 A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique. mchibucos 2010-11-15T02:19:34Z eco next generation sequencing evidence ECO:0000221 Typically thousands to millions of reads are produced in parallel. high throughput nucleotide sequencing assay evidence A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique. ECO:MCC A type of high throughput nucleotide sequencing evidence in which sequence is determined through hybridization of adaptor-ligated DNA to a glass slide on which each fragment is simultaneously clonally amplified, followed by progressive rounds of base incorporation with fluorescently-tagged nucleotides, washing, imaging, and cleavage. mchibucos 2010-11-15T02:38:03Z eco Solexa sequencing result ECO:0000222 In Illumina sequencing technology, adapters are ligated onto the ends of randomly fragmented DNA. After single-stranded fragments are bound to the inside surface of a flow cell channel, they undergo in-place bridge PCR amplification. To begin the sequencing cycle, labeled reversible terminators, primers and DNA polymerase are added, followed by laser excitation of the fluorescent label and high resolution scanning. After non-incorporated nucleotides are washed away and the dye is chemically removed, the next cycle repeats with four labeled reversible terminators, primers and DNA polymerase, again followed by imaging. Illumina sequencing evidence A type of high throughput nucleotide sequencing evidence in which sequence is determined through hybridization of adaptor-ligated DNA to a glass slide on which each fragment is simultaneously clonally amplified, followed by progressive rounds of base incorporation with fluorescently-tagged nucleotides, washing, imaging, and cleavage. OBI:0000724 PMID:26000844 Solexa sequencing result OBI:0000724 A type of high throughput nucleotide sequencing evidence in which the sequence for a ssDNA is determined by addition of primers and then nucleotides, one base pair at a time (which generate a specific fluorescence), to the target strand. mchibucos 2010-11-15T03:50:14Z pyrosequencing eco ECO:0000223 454 pyrosequencing technology amplifies individual DNA fragments inside water droplets within an oil solution (emulsion PCR). Within each droplet, a single DNA template is attached to a single primer-coated bead. Each bead is subsequently captured in a picolitre well within the sequencing machine. A luciferase-based readout system is used to identify individual nucleotides added to the nascent DNA. The target strand is usually prepared by fragmentation, adaptor ligation, and amplification by emulsion PCR. 454 pyrosequencing evidence A type of high throughput nucleotide sequencing evidence in which the sequence for a ssDNA is determined by addition of primers and then nucleotides, one base pair at a time (which generate a specific fluorescence), to the target strand. EFO:0005016 pyrosequencing OBI:0000730 A type of high throughput nucleotide sequencing evidence in which sequence is determined through rounds of ligation-based sequencing with fluorescently-labeled Di-base probes and cleavage, after which the template is reset, with a primer offset by one base, for subsequent rounds of ligation. mchibucos 2010-11-15T04:17:41Z eco ECO:0000224 SOLiD sequencing technology is based on sequencing by ligation. After library preparation, emulsion PCR and bead enrichment are performed, including 3' modification of templates on selected beads to allow covalent bonding to a slide. 3' modified beads are attached to a glass slide and primers are added. Four fluorescently labeled di-base probes are added and multiple cycles of ligation, detection and cleavage are performed. The number of cycles determines read length. After a number of ligation cycles, the extension product is removed and another round of ligation cycles is performed with a new primer complimentary to the n-1 position of the template. Five rounds of primer reset are performed for each sequence tag. Samples are prepared by fragmentation of a sample library, adaptor ligation, emulsion PCR, and attachment of resultant beads to glass slides. SOLiD sequencing evidence A type of high throughput nucleotide sequencing evidence in which sequence is determined through rounds of ligation-based sequencing with fluorescently-labeled Di-base probes and cleavage, after which the template is reset, with a primer offset by one base, for subsequent rounds of ligation. OBI:0000706 A type of nucleotide sequencing assay in which DNA sequence is determined by addition of a primed DNA template to a reaction mixture, followed by addition of DNA polymerase, deoxynucleosidetriphosphates (dNTPs - one of which may be radiolabeled), and one of four di-deoxynucleotidetriphosphates (ddNTPs), after which DNA elongation is terminated and the DNA is separated by size and imaged. mchibucos 2010-11-15T04:46:31Z Sanger sequencing dye terminator sequencing eco ECO:0000225 Chain termination sequencing, also called Sanger sequencing after its developer, uses dideoxynucleotide triphosphates (ddNTPs) as DNA chain terminators. Single-stranded DNA template, DNA primer, DNA polymerase, fluorescently or radioactively labeled nucleotides, and one of four ddNTPs are added together in each of four separate sequencing reactions. The synthesized and labeled DNA fragments from each of the four reactions are denatured, separated by size by gel electrophoresis, and visualized by autoradiography or UV light. The ddNTPs lack an OH group so the next dNTP cannot be attached, causing chain termination. chain termination sequencing evidence A type of nucleotide sequencing assay in which DNA sequence is determined by addition of a primed DNA template to a reaction mixture, followed by addition of DNA polymerase, deoxynucleosidetriphosphates (dNTPs - one of which may be radiolabeled), and one of four di-deoxynucleotidetriphosphates (ddNTPs), after which DNA elongation is terminated and the DNA is separated by size and imaged. OBI:0000695 A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence. mchibucos 2010-11-16T01:29:08Z MI:0402 ChIP evidence eco ECO:0000226 Chromatin immunoprecipitation (ChIP) is used to investigate protein-DNA interactions in vivo. DNA and proteins are chemically cross-linked in vivo to form chromatin complexes, followed by cell lysis and DNA shearing. Fragmented DNA-protein complexes are selectively enriched for a protein of interest using a specific antibody (immunoprecipitation). Protein digestion and DNA purification are performed prior to DNA detection via molecular cloning and sequencing, polymerase chain reaction (PCR), microarray analysis (ChIP-on-chip), or direct high-throughput sequencing (ChIP-seq). chromatin immunoprecipitation evidence A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence. ECO:MCC MI:0402 chromatin immunoprecipitation assay A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection. CollecTF mchibucos 2010-11-16T05:02:00Z ChIP-PCR evidence eco ECO:0000227 ChIP-PCR is often used to validate ChIP-chip results and less frequently,ChIP-Seq results. chromatin immunoprecipitation-PCR evidence A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection. ECO:MCC ECO:SW PMID:18388953 A type of chromatin immunoprecipitation evidence in which protein-DNA interactions are investigated at known genomic binding sites through a process of ChIP, DNA purification, and finally quantitative polymerase chain reaction (qPCR) for DNA detection. mchibucos 2010-11-16T05:26:47Z ChIP-qPCR evidence eco ECO:0000228 chromatin immunoprecipitation-qPCR evidence A type of chromatin immunoprecipitation evidence in which protein-DNA interactions are investigated at known genomic binding sites through a process of ChIP, DNA purification, and finally quantitative polymerase chain reaction (qPCR) for DNA detection. url:https://www.diagenode.com/applications/chip-qpcr A type of chromatin immunoprecipitation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins. CollecTF mchibucos 2010-11-16T05:30:41Z ChIP-SEQ evidence ChIP-seq evidence eco ECO:0000229 ChIP-Seq experiments often use the input as a control to eliminate biases. To obtain similar results, ChIP-chip with high-density tiling arrays can be used. chromatin immunoprecipitation-seq evidence A type of chromatin immunoprecipitation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins. ECO:MCC ECO:SW OBI:0000716 PMID:22955991 ChIP-SEQ evidence OBI:0000716 ChIP-seq evidence PMID:22955991 A type of chromatin immunoprecipitation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions. CollecTF mchibucos 2010-11-16T05:43:55Z MI:0225 ChIP-chip evidence ChIP-on-chip evidence eco ECO:0000230 A fixating agent such as formaldehyde is used to cross link proteins and DNA. Sonication is applied for DNA shearing. For transcription factor tagging, an antibody or epitope is employed. After cross-linking is reversed, the DNA is amplified and labeled with a flourophore for microarray which produces a resolution of aproximately 500 bp. chromatin immunoprecipitation-chip evidence A type of chromatin immunoprecipitation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions. ECO:MCC ECO:SW PMID:18388953 PMID:19381927 MI:0225 chromatin immunoprecipitation array A type of 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. CollecTF mchibucos 2010-11-16T05:57:20Z Q-PCR evidence qPCR evidence quantitative PCR evidence quantitative real-time PCR evidence real time polymerase chain reaction evidence real-time PCR evidence real-time quantitative PCR eco qRT-PCR evidence ECO:0000231 Quantitative PCR enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. The dye is activated upon binding double-stranded DNA. Although qRT-PCR is commonly found in literature synonymous to qPCR, it is preferable not to use this synonym as it is the accepted abbreviation for reverse transcription PCR. qPCR should be used instead (ISBN 978-0-470-68386-6 page 173). qPCR can be used to quantitatively determine levels of gene expression. quantitative polymerase chain reaction 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. ECO:MCC ECO:SW A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, 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. mchibucos 2010-11-17T12:27:14Z chromosome conformation capture-based evidence 3C chromosome conformation capture eco ECO:0000232 Chromosome conformation capture technologies are used to study the structural properties and spatial organization of chromosomes inside cells. All types of chromosome conformation capture technology involve five primary steps: cross-linking of DNA in vivo, restriction digestion, intramolecular ligation, reversing cross-linkages, and DNA enrichment and quantitation. The last step is different for each type of chromosome conformation capture technology, and may include PCR (3C), inverse PCR (4C), or ligation-mediated amplification (5C). Methods for product quantitation can include agarose gel detection or real-time quantitative PCR in the case of 3C, or high-throughput sequencing or microarray analysis for 4C and 5C. chromosome conformation-based evidence A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, 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. ECO:MCC 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. mchibucos 2010-11-17T12:46:15Z 3C chromosome conformation capture evidence chromosome conformation capture-PCR evidence eco ECO:0000233 3C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C differs only in the fifth step, which involves performing either standard polymerase chain reaction (PCR) or quantitative PCR (qPCR) for product quantitation. 3C evidence 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. ECO:MCC 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. mchibucos 2010-11-19T01:20:28Z chromosome conformation capture on chip circularized 3C circularized chromosome conformation capture evidence eco ECO:0000234 4C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 4C differs only in the fifth step, which involves inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation. 4C evidence 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. ECO:MCC PMID:17033624 A type of chromosome conformation-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation. mchibucos 2010-11-19T01:22:20Z 5C carbon-copy 3C carbon-copy chromosome conformation capture evidence eco ECO:0000235 5C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 5C differs only in the fifth step, which involves ligation-mediated amplification (LMA) followed by product quantitation. 5C evidence A type of chromosome conformation-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation. ECO:MCC A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step. mchibucos 2010-11-19T03:00:47Z 3C 3C-PCR eco ECO:0000236 See 3C evidence. 3C evidence was initially developed using PCR. chromosome conformation capture-PCR evidence true A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step. ECO:MCC A type of 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. mchibucos 2010-11-19T03:06:47Z 3C-quantitative PCR 3C-real-time PCR chromosome conformation capture-qPCR evidence eco ECO:0000237 3C-qPCR evidence 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. ECO:MCC PMID:17641637 PMID:26025624 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. mchibucos 2010-11-19T04:24:03Z eco ECO:0000238 Hi-C is used to study the structural properties and spatial organization of chromosomes inside cells. Hi-C is similar to other types of chromosome conformation capture technology, but involves the addition of biotinylated nucleotides during the second or fourth step and enrichment for ligated fragments using immunoprecipitation after the fourth step. Hi-C evidence A type of chromosome conformation-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. ECO:MCC 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. mchibucos 2010-11-30T03:22:25Z 3C sequencing circularized 3C sequencing circularized 3C-seq eco chromosome conformation capture sequencing evidence ECO:0000239 3C-seq is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C-seq differs only in the fifth step, which involves inverse polymerase chain reaction (PCR) on a circularized 3C library prior to product quantitation. 3C-seq evidence 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. ECO:MCC PMID:23411633 A type of experimental phenotypic evidence in which the phenotype of an organism is observed after the disruption of a structural feature. mchibucos 2010-12-06T12:24:16Z eco ECO:0000240 anatomical perturbation evidence A type of experimental phenotypic evidence in which the phenotype of an organism is observed after the disruption of a structural feature. ECO:MCC A type of experimental phenotypic evidence in which the phenotype of an organism is observed after modification of the extra-organismal context. mchibucos 2010-12-06T12:33:58Z eco mechanical constraint evidence ECO:0000241 Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth. environmental perturbation evidence A type of experimental phenotypic evidence in which the phenotype of an organism is observed after modification of the extra-organismal context. ECO:MCC A type of anatomical perturbation that is based on disruption of tissue. mchibucos 2010-12-06T12:33:58Z ablated tissue evidence eco ECO:0000242 A tissue ablation experiment involves observing the phenotype of an entity whose tissues have been disrupted through genetic or biochemical manipulation, physical destruction, or some other means. tissue ablation evidence A type of anatomical perturbation that is based on disruption of tissue. ECO:MCC A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure. mchibucos 2010-12-06T12:33:58Z eco ECO:0000243 tissue grafting evidence A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure. ECO:MCC A type of combinatorial analysis that is used in a manual assertion. mchibucos 2010-12-09T02:02:12Z eco inferred from in-silico analysis ECO:0000244 Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments. combinatorial evidence used in manual assertion true true A type of combinatorial analysis that is used in a manual assertion. ECO:MCC A type of computational combinatorial analysis that is used in a manual assertion. mchibucos 2010-12-09T02:37:54Z GOECO:RCA RCA inferred from reviewed computational analysis eco ECO:0000245 computational combinatorial evidence used in manual assertion http://geneontology.org/page/rca-inferred-reviewed-computational-analysis true true A type of computational combinatorial analysis that is used in a manual assertion. ECO:MCC GOECO:RCA inferred from reviewed computational analysis RCA GOECO:RCA inferred from reviewed computational analysis GOECO:RCA A type of computational combinatorial analysis that is used in an automatic assertion. mchibucos 2010-12-09T02:37:54Z eco ECO:0000246 computational combinatorial evidence used in automatic assertion true true A type of computational combinatorial analysis that is used in an automatic assertion. ECO:MCC A type of sequence alignment evidence that is used in a manual assertion. mchibucos 2010-12-09T05:12:27Z GOECO:ISA ISA inferred from sequence alignment eco ECO:0000247 sequence alignment evidence used in manual assertion http://geneontology.org/page/isa-inferred-sequence-alignment true true A type of sequence alignment evidence that is used in a manual assertion. ECO:RCT GOECO:ISA inferred from sequence alignment ISA GOECO:ISA inferred from sequence alignment GOECO:ISA A type of sequence alignment evidence that is used in an automatic assertion. mchibucos 2010-12-09T05:12:27Z eco ECO:0000248 sequence alignment evidence used in automatic assertion true true A type of sequence alignment evidence that is used in an automatic assertion. ECO:RCT A type of sequence similarity evidence that is used in an automatic assertion. mchibucos 2010-12-09T05:22:30Z eco ECO:0000249 sequence similarity evidence used in automatic assertion true true A type of sequence similarity evidence that is used in an automatic assertion. ECO:RCT A type of sequence similarity evidence that is used in a manual assertion. mchibucos 2010-12-09T05:22:30Z GOECO:ISS ISS inferred from sequence or structural similarity eco ECO:0000250 sequence similarity evidence used in manual assertion http://geneontology.org/page/iss-inferred-sequence-or-structural-similarity true true A type of sequence similarity evidence that is used in a manual assertion. ECO:MCC GOECO:ISS inferred from sequence or structural similarity ISS GOECO:ISS inferred from sequence or structural similarity GOECO:ISS A type of similarity evidence that is used in an automatic assertion. mchibucos 2010-12-09T05:28:12Z IS eco inferred from similarity ECO:0000251 similarity evidence used in automatic assertion true true A type of similarity evidence that is used in an automatic assertion. ECO:RCT A type of similarity evidence that is used in a manual assertion. mchibucos 2010-12-09T05:28:12Z IS eco inferred from similarity ECO:0000252 similarity evidence used in manual assertion true true A type of similarity evidence that is used in a manual assertion. ECO:RCT A type of genetic similarity evidence that is used in a manual assertion. mchibucos 2010-12-10T01:42:44Z IGTS eco inferred from genetic similarity ECO:0000253 genetic similarity evidence used in manual assertion true true A type of genetic similarity evidence that is used in a manual assertion. ECO:RCT A type of genetic similarity evidence that is used in an automatic assertion. mchibucos 2010-12-10T01:42:44Z IGTS eco inferred from genetic similarity ECO:0000254 genetic similarity evidence used in automatic assertion true true A type of genetic similarity evidence that is used in an automatic assertion. ECO:RCT A type of match to sequence model evidence that is used in a manual assertion. mchibucos 2010-12-10T02:26:35Z GOECO:ISM GO_REF:0000011 ISM inferred from sequence model eco ECO:0000255 match to sequence model evidence used in manual assertion http://geneontology.org/page/ism-inferred-sequence-model true true A type of match to sequence model evidence that is used in a manual assertion. ECO:RCT GOECO:ISM inferred from sequence model GO_REF:0000011 Hidden Markov Models (TIGR) ISM GOECO:ISM inferred from sequence model GOECO:ISM A type of match to sequence model evidence that is used in an automatic assertion. mchibucos 2010-12-10T02:26:35Z GO_REF:0000002 GO_REF:0000107 eco ECO:0000256 match to sequence model evidence used in automatic assertion true true A type of match to sequence model evidence that is used in an automatic assertion. ECO:RCT GO_REF:0000002 Gene Ontology annotation through association of InterPro records with GO terms. GO_REF:0000107 Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl A type of motif similarity evidence that is used in a manual assertion. mchibucos 2010-12-10T02:44:34Z eco ISS: recognized domains ECO:0000257 motif similarity evidence used in manual assertion true true A type of motif similarity evidence that is used in a manual assertion. ECO:RCT A type of motif similarity evidence that is used in an automatic assertion. mchibucos 2010-12-10T02:44:34Z eco ISS: recognized domains ECO:0000258 motif similarity evidence used in automatic assertion true true A type of motif similarity evidence that is used in an automatic assertion. ECO:RCT A type of match to InterPro member signature evidence that is used in an automatic assertion. mchibucos 2010-12-10T02:54:51Z eco ECO:0000259 match to InterPro member signature evidence used in automatic assertion true true A type of match to InterPro member signature evidence that is used in an automatic assertion. ECO:RCT A type of match to InterPro member signature evidence that is used in a manual assertion. mchibucos 2010-12-10T02:54:51Z eco ECO:0000260 match to InterPro member signature evidence used in manual assertion true true A type of match to InterPro member signature evidence that is used in a manual assertion. ECO:RCT A type of targeting sequence prediction that is used in an automatic assertion. mchibucos 2010-12-10T03:02:49Z eco ISS: targeting sequence prediction ECO:0000261 targeting sequence prediction evidence used in automatic assertion true true A type of targeting sequence prediction that is used in an automatic assertion. ECO:RCT A type of targeting sequence prediction that is used in a manual assertion. mchibucos 2010-12-10T03:02:49Z eco ISS: targeting sequence prediction ECO:0000262 targeting sequence prediction evidence used in manual assertion true true A type of targeting sequence prediction that is used in a manual assertion. ECO:RCT A type of transmembrane domain prediction that is used in an automatic assertion. mchibucos 2010-12-10T03:28:35Z eco ISS: transmembrane domain prediction ECO:0000263 transmembrane domain prediction evidence used in automatic assertion true true A type of transmembrane domain prediction that is used in an automatic assertion. ECO:RCT A type of transmembrane domain prediction that is used in a manual assertion. mchibucos 2010-12-10T03:28:35Z eco ISS: transmembrane domain prediction ECO:0000264 transmembrane domain prediction evidence used in manual assertion true true A type of transmembrane domain prediction that is used in a manual assertion. ECO:RCT A type of sequence orthology evidence that is used in an automatic assertion. mchibucos 2010-12-10T03:39:41Z GO_REF:0000019 GO_REF:0000020 GO_REF:0000035 GO_REF:0000049 eco Ortholog evidence ortholog evidence ECO:0000265 sequence orthology evidence used in automatic assertion true true A type of sequence orthology evidence that is used in an automatic assertion. ECO:RCT GO_REF:0000019 Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara GO_REF:0000020 Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins. GO_REF:0000035 Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara GO_REF:0000049 Automatic transfer of experimentally verified manual GO annotation data to fungal orthologs using Ensembl Compara A type of sequence orthology evidence that is used in a manual assertion. mchibucos 2010-12-10T03:39:41Z GOECO:ISO ISO inferred from sequence orthology eco Ortholog evidence ortholog evidence ECO:0000266 sequence orthology evidence used in manual assertion http://geneontology.org/page/iso-inferred-sequence-orthology true true A type of sequence orthology evidence that is used in a manual assertion. ECO:MCC GOECO:ISO inferred from sequence orthology ISO GOECO:ISO inferred from sequence orthology GOECO:ISO A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate. CollecTF mchibucos 2010-12-14T01:57:13Z MI:0411 ELISA evidence enzyme-linked immunosorbent assay eco ECO:0000267 ELISA is sometimes used in the study of transcriptional regulation to identify a produced protein, especially secreted protein. enzyme-linked immunoabsorbent assay evidence A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate. ECO:MCC ECO:SW PMID:23949770 MI:0411 enzyme linked immunosorbent assay A type of direct assay evidence in which cells or particles are characterized by passing them through a light source and monitoring the resultant light scatter or fluorochrome excitation. mchibucos 2010-12-14T02:07:08Z FCM eco ECO:0000268 flow cytometry evidence A type of direct assay evidence in which cells or particles are characterized by passing them through a light source and monitoring the resultant light scatter or fluorochrome excitation. ECO:MCC A type of experimental evidence that is used in a manual assertion. mchibucos 2010-12-20T05:36:49Z GOECO:EXP EXP inferred from experiment eco ECO:0000269 experimental evidence used in manual assertion http://geneontology.org/page/exp-inferred-experiment true true A type of experimental evidence that is used in a manual assertion. ECO:MCC GOECO:EXP inferred from experiment EXP GOECO:EXP inferred from experiment GOECO:EXP A type of expression pattern evidence that is used in a manual assertion. mchibucos 2010-12-20T05:46:39Z GOECO:IEP IEP inferred from expression pattern eco ECO:0000270 expression evidence used in manual assertion http://geneontology.org/page/iep-inferred-expression-pattern true true A type of expression pattern evidence that is used in a manual assertion. ECO:MCC GOECO:IEP inferred from expression pattern IEP GOECO:IEP inferred from expression pattern GOECO:IEP mchibucos 2010-12-20T05:51:58Z eco ECO:0000271 This general 'array experiment' term should not be used - replace with the specific type of array (e.g. ECO:0000273, ECO:0000276, ECO:0000285, etc.) array experiment evidence used in manual assertion true A type of Affymetrix GeneChip evidence that is used in a manual assertion. mchibucos 2010-12-20T05:53:36Z Affymetrix array experiment evidence eco ECO:0000272 Affymetrix GeneChip evidence used in manual assertion true true A type of Affymetrix GeneChip evidence that is used in a manual assertion. ECO:MCC A type of cDNA to DNA expression microarray evidence that is used in a manual assertion. mchibucos 2010-12-20T05:55:49Z ECO:0001178 ECO:0005525 eco DNA microarray|RNA microarray ECO:0000273 cDNA to DNA expression microarray evidence used in manual assertion true true A type of cDNA to DNA expression microarray evidence that is used in a manual assertion. ECO:MCC A type of differential methylation hybridization evidence that is used in a manual assertion. mchibucos 2010-12-20T05:58:44Z CpG island microarray evidence CpG island microarray evidence used in manual assertion eco ECO:0000274 differential methylation hybridization evidence used in manual assertion true true A type of differential methylation hybridization evidence that is used in a manual assertion. ECO:RCT A type of expression microarray evidence that is used in a manual assertion. mchibucos 2010-12-20T06:01:26Z eco differential gene expression evidence from microarray experiment ECO:0000275 expression microarray evidence used in manual assertion true true A type of expression microarray evidence that is used in a manual assertion. ECO:MCC A type of cRNA to DNA expression microarray evidence that is used in a manual assertion. mchibucos 2010-12-20T06:03:28Z genomic microarray evidence genomic microarray evidence used in manual assertion eco ECO:0000276 cRNA to DNA expression microarray evidence used in manual assertion true true A type of cRNA to DNA expression microarray evidence that is used in a manual assertion. ECO:RCT A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion. mchibucos 2010-12-20T06:05:20Z eco ECO:0000277 Nimblegen array evidence used in manual assertion true true A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion. ECO:MCC A type of array-based sequence capture evidence that is used in a manual assertion. mchibucos 2010-12-20T06:09:45Z DNA microarray oligonucleotide microarray evidence oligonucleotide microarray evidence used in manual assertion eco SNP array evidence single nucleotide polymorphism array evidence ECO:0000278 array-based sequence capture evidence used in manual assertion true true A type of array-based sequence capture evidence that is used in a manual assertion. ECO:MCC A type of Western blot assay that is used in a manual assertion. mchibucos 2010-12-20T06:20:01Z eco IEP: protein levels (e.g. Western blots) Western blot expression analysis protein immunoblot ECO:0000279 western blot evidence used in manual assertion true true A type of Western blot assay that is used in a manual assertion. ECO:MCC A type of protein expression level analysis that is used in a manual assertion. mchibucos 2010-12-20T06:21:54Z eco ECO:0000280 protein expression level evidence used in manual assertion true true A type of protein expression level analysis that is used in a manual assertion. ECO:MCC A type of expression library screen evidence that is used in a manual assertion. mchibucos 2010-12-20T06:24:05Z eco IEP: expression library screening ECO:0000281 expression library screen evidence used in manual assertion true true A type of expression library screen evidence that is used in a manual assertion. ECO:MCC A type of heterologous protein expression analysis that is used in a manual assertion. mchibucos 2010-12-20T06:27:04Z eco IDA: protein expression in heterologous system ECO:0000282 heterologous protein expression evidence used in manual assertion true true A type of heterologous protein expression analysis that is used in a manual assertion. ECO:MCC A type of protein expression spatial pattern analysis that is used in a manual assertion. mchibucos 2010-12-20T06:31:44Z eco ECO:0000283 spatial pattern of protein expression evidence used in manual assertion true true A type of protein expression spatial pattern analysis that is used in a manual assertion. ECO:MCC A type of protein expression analysis that is used in a manual assertion. mchibucos 2010-12-20T06:33:46Z eco ECO:0000284 protein expression evidence used in manual assertion true true true A type of protein expression analysis that is used in a manual assertion. ECO:MCC A type of DNA to cDNA expression microarray evidence that is used in a manual assertion. mchibucos 2010-12-20T06:41:33Z REM evidence RNA expression microarray evidence microarray RNA expression level evidence eco IEP: transcript levels (e.g. microarray data) ECO:0000285 DNA to cDNA expression microarray evidence used in manual assertion true true A type of DNA to cDNA expression microarray evidence that is used in a manual assertion. ECO:MCC A type of differential hybridization experiment that is used in a manual assertion. mchibucos 2010-12-20T06:55:14Z eco IEP: differential hybridization ECO:0000287 differential hybridization evidence used in manual assertion true true A type of differential hybridization experiment that is used in a manual assertion. ECO:MCC A type of RNA protection assay that is used in a manual assertion. mchibucos 2010-12-20T06:57:33Z ribonuclease protection assay eco IEP: RNA protection assay|RPA RNAse protection assay ECO:0000288 RNA protection assay evidence used in manual assertion true true A type of RNA protection assay that is used in a manual assertion. ECO:MCC A type of spatial pattern of transcript expression analysis that is used in a manual assertion. mchibucos 2010-12-20T06:59:18Z eco ECO:0000289 spatial pattern of transcript expression evidence used in manual assertion true true A type of spatial pattern of transcript expression analysis that is used in a manual assertion. ECO:MCC A type of subtractive hybridization experiment that is used in a manual assertion. mchibucos 2010-12-20T07:00:48Z eco IEP: subtractive hybridization ECO:0000290 subtractive hybridization evidence used in manual assertion true true A type of subtractive hybridization experiment that is used in a manual assertion. ECO:MCC A type of transcript expression evidence that is used in a manual assertion. mchibucos 2010-12-20T07:02:08Z ECO:0000286 transcript expression level evidence eco ECO:0000291 transcript expression evidence used in manual assertion true true A type of transcript expression evidence that is used in a manual assertion. ECO:MCC A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell. mchibucos 2011-01-10T03:36:25Z anti-sense eco ECO:0000292 Morpholino oligonucleotides modify gene expression by blocking access of other molecules to specific, approximately 25-base-long regions of the base-pairing surfaces of ribonucleic acid (RNA). To achieve this anti-sense knockdown technique, delivery of the morpholino can be achieved via microinjection, electroporation, or another method. morpholino experiment evidence A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell. ECO:MCC A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand. mchibucos 2011-01-10T04:23:50Z MI:0657 SELEX evidence in vitro selection evidence eco in vitro evolution evidence ECO:0000293 SELEX begins with the synthesis of a large oligonucleotide library, either single-stranded DNA or RNA, which consists of random fixed-length sequences flanked by constant 5' and 3' ends that serve as primers. The library is exposed to a target ligand, typically a protein or small organic compound. Unbound sequences are removed, typically with affinity chromatography. Bound sequences are eluted and the nucleic acid is extracted, followed by PCR amplification (RNA is first reverse transcribed). PCR product is converted to single stranded (DNA) or transcribed (RNA). Oligonucleotides are bound to the ligand again and the process is repeated with increasing elution stringency. After several rounds of the process, recovered oligonucleotides are sequenced and analyzed to reveal the binding specificity of the protein. systematic evolution of ligands by exponential amplification evidence A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand. ECO:MCC url:http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment MI:0657 systematic evolution of ligands by exponential enrichment A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey). mchibucos 2011-01-10T06:16:20Z B1H evidence eco ECO:0000294 Bacterial one-hybrid assay is a method for screening a library of candidate proteins (prey plasmid) for the ability to bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to reporter genes (bait plasmid). Transformation of a bacterial host with two different plasmids is required: One is designed to express the "bait". The other plasmid contains a "prey" which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes. bacterial one-hybrid evidence A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey). ECO:MCC A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules. mchibucos 2011-01-11T12:54:50Z ECO:0000357 WTSS whole transcriptome shotgun sequencing differential gene expression evidence from RNA-seq experiment eco RNA sequencing ECO:0000295 Total RNA is isolated from cells and mRNA is purified by targeting the 3' polyadenylated (poly(A)) tail with poly(T) oligos covalently attached to a substrate. Next, cDNA fragments are generated either by hydrolysis of RNA into 200-300 base oligonucleotides, preceded by reverse transcription, or by reverse transcription initiated by random primers. The cDNA second strand is synthesized, fragments are adapter ligated and high-throughput sequencing is performed by Roche 454, Illumina, ABI-SOLiD, or another HT sequencing technology. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed. RNA-seq evidence A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules. ECO:MCC whole transcriptome shotgun sequencing PMID:18611170 A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked. mchibucos 2011-01-11T03:28:49Z eco ECO:0000298 In the embryos of some organisms, inhibition of cytokinesis blocks neither the cell cycle nor the unfolding of the developmental program. As such, embryonic morphology can be frozen, allowing analysis of the developmental fate of each cell present at the time of cleavage arrest. cleavage arrested development evidence A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked. ECO:MCC A type of cleavage arrested development that arises after treatment with cytochalasin. mchibucos 2011-01-11T03:30:29Z eco ECO:0000299 Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments. cytochalasin experiment evidence A type of cleavage arrested development that arises after treatment with cytochalasin. ECO:MCC A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker. mchibucos 2011-01-11T03:48:50Z GFP immunolocalization evidence eco ECO:0000300 This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript". green fluorescent protein immunolocalization evidence A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker. ECO:MCC A type of immunolocalization evidence that was generated using LacZ protein as a marker. mchibucos 2011-01-11T04:06:40Z LacZ protein immunolocalization evidence eco ECO:0000301 This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript". beta-galactosidase protein immunolocalization evidence A type of immunolocalization evidence that was generated using LacZ protein as a marker. ECO:MCC A type of author statement that is used in a manual assertion. mchibucos 2011-01-20T02:26:47Z eco ECO:0000302 author statement used in manual assertion true true A type of author statement that is used in a manual assertion. ECO:MCC A type of author statement without traceable support that is used in a manual assertion. mchibucos 2011-01-20T02:29:50Z GOECO:NAS NAS eco non-traceable author statement ECO:0000303 author statement without traceable support used in manual assertion http://geneontology.org/page/nas-non-traceable-author-statement true true A type of author statement without traceable support that is used in a manual assertion. ECO:MCC GOECO:NAS non-traceable author statement NAS GOECO:NAS non-traceable author statement GOECO:NAS A type of author statement supported by traceable reference that is used in a manual assertion. mchibucos 2011-01-20T02:31:03Z GOECO:TAS TAS eco traceable author statement ECO:0000304 author statement supported by traceable reference used in manual assertion http://geneontology.org/page/tas-traceable-author-statement true true A type of author statement supported by traceable reference that is used in a manual assertion. ECO:MCC GOECO:TAS traceable author statement TAS GOECO:TAS traceable author statement GOECO:TAS A type of curator inference that is used in a manual assertion. mchibucos 2011-01-20T02:33:32Z GOECO:IC IC inferred by curator eco ECO:0000305 curator inference used in manual assertion http://geneontology.org/page/ic-inferred-curator true true A type of curator inference that is used in a manual assertion. ECO:MCC GOECO:IC inferred by curator IC GOECO:IC inferred by curator GOECO:IC A type of inference from background scientific knowledge that is used in a manual assertion. mchibucos 2011-01-20T02:35:11Z eco ECO:0000306 inference from background scientific knowledge used in manual assertion true true A type of inference from background scientific knowledge that is used in a manual assertion. ECO:MCC A type of no biological data found that is used in a manual assertion. mchibucos 2011-01-20T02:43:18Z GOECO:ND ND no biological data available eco ECO:0000307 no biological data found used in manual assertion http://geneontology.org/page/nd-no-biological-data-available true true A type of no biological data found that is used in a manual assertion. ECO:MCC GOECO:ND no biological data available ND GOECO:ND no biological data available GOECO:ND A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene. mchibucos 2011-02-04T05:41:26Z eco ECO:0000308 First, a characteristic of the most recent common ancestor (MRCA) is inferred from experimental evidence in descendants; this is followed by inferring a characteristic of a descendant of the MRCA. This type of evidence can be used in support of both positive and "not" GO annotations. biological aspect of ancestor evidence A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene. ECO:MCC A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system. mchibucos 2011-02-17T01:33:09Z CAGE eco ECO:0000309 Complementary DNA (cDNA) is synthesized from microgram quantities of mRNA using first-strand cDNA primer (oligo dT12-18) and reverse transcriptase in the presence of trehalose and sorbitol, followed by selection of full-length cDNA with biotinylated cap-trapper. Linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI, which creates a two base overhang. After amplification, sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed. cap analysis of gene expression evidence A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system. ECO:MCC CAGE PMID:16489339 A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching. mchibucos 2011-02-17T01:33:34Z eco nanoCAGE ECO:0000310 NanoCAGE captures the 5' ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5' full length cDNAs is extended upon hybridization of the riboguanosine-tailed template switching oligonucleotides to these extra cytosines. In semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers, which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template switching, semisuppressive PCR, and EcoP151 cleavage, 25-bp tags are ligated to bar code-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. NanoCAGE requires as little as 10 nanograms of total RNA. nano-cap analysis of gene expression evidence A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching. ECO:MCC nanoCAGE PMID:20543846 A type of evidence that is based on work performed by a person or group prior to a use by a different person or group. mchibucos 2011-03-02T05:24:13Z eco ECO:0000311 imported information A type of evidence that is based on work performed by a person or group prior to a use by a different person or group. ECO:MCC A type of imported information that is used in a manual assertion. mchibucos 2011-03-02T05:29:44Z eco ECO:0000312 imported information used in manual assertion true true A type of imported information that is used in a manual assertion. ECO:MCC A type of imported information that is used in an automatic assertion. mchibucos 2011-03-02T05:33:43Z eco ECO:0000313 imported information used in automatic assertion true true A type of imported information that is used in an automatic assertion. ECO:MCC A type of direct assay evidence that is used in a manual assertion. mchibucos 2011-10-28T04:59:31Z GOECO:IDA inferred from direct assay eco IDA ECO:0000314 direct assay evidence used in manual assertion http://geneontology.org/page/ida-inferred-direct-assay true true A type of direct assay evidence that is used in a manual assertion. ECO:MCC GOECO:IDA inferred from direct assay inferred from direct assay GOECO:IDA IDA GOECO:IDA A type of mutant phenotype evidence that is used in a manual assertion. mchibucos 2011-10-28T05:12:49Z GOECO:IMP eco IMP inferred from mutant phenotype ECO:0000315 mutant phenotype evidence used in manual assertion http://geneontology.org/page/imp-inferred-mutant-phenotype true true A type of mutant phenotype evidence that is used in a manual assertion. ECO:MCC GOECO:IMP inferred from mutant phenotype IMP GOECO:IMP inferred from mutant phenotype GOECO:IMP A type of genetic interaction experiment evidence that is used in a manual assertion. mchibucos 2011-10-28T05:14:42Z GOECO:IGI IGI inferred from genetic interaction eco ECO:0000316 genetic interaction evidence used in manual assertion http://geneontology.org/page/igi-inferred-genetic-interaction true true A type of genetic interaction experiment evidence that is used in a manual assertion. ECO:MCC GOECO:IGI inferred from genetic interaction IGI GOECO:IGI inferred from genetic interaction GOECO:IGI A type of genomic context evidence that is used in a manual assertion. mchibucos 2011-10-28T05:22:53Z GOECO:IGC IGC inferred from genomic context eco ECO:0000317 genomic context evidence used in manual assertion http://geneontology.org/page/igc-inferred-genomic-context true true A type of genomic context evidence that is used in a manual assertion. ECO:MCC GOECO:IGC inferred from genomic context IGC GOECO:IGC inferred from genomic context GOECO:IGC A type of biological aspect of ancestor evidence that is used in a manual assertion. mchibucos 2011-10-28T05:23:51Z GOECO:IBA IBA inferred from biological aspect of ancestor eco ECO:0000318 biological aspect of ancestor evidence used in manual assertion http://geneontology.org/page/iba-inferred-biological-aspect-ancestor true true A type of biological aspect of ancestor evidence that is used in a manual assertion. ECO:MCC GOECO:IBA inferred from biological aspect of ancestor IBA GOECO:IBA inferred from biological aspect of ancestor GOECO:IBA A type of biological aspect of descendant evidence that is used in a manual assertion. mchibucos 2011-10-28T05:25:09Z GOECO:IBD IBD inferred from biological aspect of descendant eco ECO:0000319 biological aspect of descendant evidence used in manual assertion http://geneontology.org/page/ibd-inferred-biological-aspect-descendent true true A type of biological aspect of descendant evidence that is used in a manual assertion. ECO:MCC GOECO:IBD inferred from biological aspect of descendant IBD GOECO:IBD inferred from biological aspect of descendant GOECO:IBD A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion. mchibucos 2011-10-28T05:25:48Z GOECO:IKR GOECO:IMR IKR IMR inferred from key residues inferred from missing residues eco ECO:0000320 phylogenetic determination of loss of key residues evidence used in manual assertion http://geneontology.org/page/ikr-inferred-key-residues true true A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion. ECO:MCC GOECO:IKR inferred from key residues GOECO:IMR inferred from missing residues IKR GOECO:IKR IMR GOECO:IKR inferred from key residues GOECO:IKR inferred from missing residues GOECO:IKR A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion. mchibucos 2011-10-28T05:26:42Z GOECO:IRD IRD inferred from rapid divergence eco ECO:0000321 rapid divergence from ancestral sequence evidence used in manual assertion http://geneontology.org/page/ird-inferred-rapid-divergence true true A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion. ECO:MCC GOECO:IRD inferred from rapid divergence IRD GOECO:IRD inferred from rapid divergence GOECO:IRD Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion. mchibucos 2011-12-13T12:04:48Z GO_REF:0000037 GO_REF:0000039 GO_REF:0000041 eco ECO:0000322 imported manually asserted information used in automatic assertion Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion. ECO:MCC GO_REF:0000037 Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries. GO_REF:0000039 Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries. GO_REF:0000041 IEA (UniProt UniPathway) A type of imported information used in automatic assertion that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion. mchibucos 2011-12-13T02:06:25Z GO_REF:0000038 GO_REF:0000040 eco ECO:0000323 imported automatically asserted information used in automatic assertion A type of imported information used in automatic assertion that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion. ECO:MCC GO_REF:0000038 Gene Ontology annotation based on automatic assignment of UniProtKB keywords in UniProtKB/TrEMBL entries. GO_REF:0000040 Gene Ontology annotation based on the automatic assignment of UniProtKB Subcellular Location terms in UniProtKB/TrEMBL entries. A type of direct assay evidence in which an image is created and analyzed. mchibucos 2012-02-23T12:01:43Z ECO:0001122 ECO:0005024 ECO:MCC radiologic test evidence eco ECO:0000324 imaging assay evidence A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase. mchibucos 2012-05-16T11:46:27Z chromatographic evidence eco ECO:0000325 chromatography evidence A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase. ECO:MCC A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript. mchibucos 2012-06-08T11:03:59Z eco ECO:0000326 transcript splice pattern evidence A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript. ECO:MCC A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features. mchibucos 2012-06-08T11:11:24Z eco ECO:0000327 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child. whole transcript splice pattern evidence A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features. ECO:MCC A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript. mchibucos 2012-06-08T11:21:57Z eco ECO:0000328 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child. coding sequence splice pattern evidence A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript. ECO:MCC A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion. mchibucos 2012-06-08T11:40:03Z eco ECO:0000329 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child. whole transcript splice pattern evidence used in manual assertion true true A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion. ECO:MCC A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion. mchibucos 2012-06-08T11:43:47Z eco ECO:0000330 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child. coding sequence splice pattern evidence used in manual assertion true true A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion. ECO:MCC A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion. mchibucos 2012-06-08T11:48:09Z eco ECO:0000331 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child. coding sequence splice pattern evidence used in automatic assertion true true A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion. ECO:MCC A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion. mchibucos 2012-06-08T11:49:17Z eco ECO:0000332 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child. whole transcript splice pattern evidence used in automatic assertion true true A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion. ECO:MCC A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility. mchibucos 2012-07-31T02:56:43Z SDS-PAGE evidence eco ECO:0000333 Electrophoretic mobility is a function of both the length and charge of a protein. The protein sample is linearized with sodium dodecyl sulfate (SDS), an anionic detergent. Typically, polypeptides bound with SDS possess an even distribution of charge per unit mass, and subsequent fractionation is by size. sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility. ECO:MCC PubMed:4861258 url:http://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html url:http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Protein/protein18.html A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined. mchibucos 2012-07-31T03:19:32Z eco ECO:0000334 An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system. particle size and count assay evidence A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined. ECO:MCC A type of direct assay evidence where the quantity of a substance used as part of an assay is measured. mchibucos 2012-07-31T03:52:46Z eco ECO:0000335 Two examples of substance quantification assay are (i) measuring how much of a radiolabelled compound is taken up by a cell and (ii) measuring how much of a substrate is turned over by a given enzyme. substance quantification evidence A type of direct assay evidence where the quantity of a substance used as part of an assay is measured. ECO:MCC A type of cell proliferation assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed usually by means of a fluorescent marker and flow cytometric analysis. mchibucos 2012-08-24T12:03:58Z fitness profiling eco ECO:0000336 competitive growth assay evidence A type of cell proliferation assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed usually by means of a fluorescent marker and flow cytometric analysis. GOC:MAH PMID:14718172 PMID:20537132 fitness profiling GOC:MAH PMID:20537132 A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field. mchibucos 2012-08-24T12:11:51Z ECO:0005026 eco ECO:0000337 Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch. gel electrophoresis evidence A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field. ECO:MCC wikipedia:Gel_electrophoresis A type of gel electrophoresis evidence in which large DNA molecules are separated on agarose gel by alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous. mchibucos 2012-08-24T12:34:01Z PFGE eco ECO:0000338 pulsed-field gel electrophoresis evidence A type of gel electrophoresis evidence in which large DNA molecules are separated on agarose gel by alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous. PMID:6373014 A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide. mchibucos 2012-08-24T12:42:37Z 2-D agarose gel electrophoresis eco ECO:0000339 The first dimension gel is intentionally run at low voltage in low percentage agarose to separate DNA molecules in proportion to their mass. The second dimension is run at high voltage in a gel of higher agarose concentration in the presence of ethidium bromide so that the mobility of a non-linear molecule is drastically influenced by its shape. two-dimensional agarose gel electrophoresis evidence A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide. PMID:16118435 PMID:8594382 A type of experimental evidence in which retention of an introduced plasmid is determined when a mitotically stable plasmid (or minichromosome) is introduced into cells, which are grown without selection for several generations. mchibucos 2012-08-24T01:27:58Z minichromosome maintenance assay evidence eco ECO:0000340 Loss per generation is determined by comparing colony numbers on selective and non-selective media. plasmid maintenance assay evidence true A type of experimental evidence in which retention of an introduced plasmid is determined when a mitotically stable plasmid (or minichromosome) is introduced into cells, which are grown without selection for several generations. ECO:MCC PMID:6323245 minichromosome maintenance assay evidence PMID:6323245 A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody. mchibucos 2012-08-24T01:48:24Z eco ECO:0000341 specific protein inhibition by antibody evidence A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody. ECO:MCC A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence. mchibucos 2013-04-03T04:22:05Z eco ECO:0000342 RNA-seq alignment intron location evidence is used by NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq). Exon-exon boundaries (or intron locations) of a RefSeq transcript, as determined by aligning the transcript to a reference chromosome, are compared to intron locations supported by RNAseq data. Support of intron position by RNA-seq alignment evidence A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence. ECO:MCC A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript. mchibucos 2013-04-03T04:41:48Z eco ECO:0000343 Full support entails that all exon pairs represented in the transcript are supported. For example, for a transcript containing five exons, if liver RNA-seq reads support all four introns but brain RNA-seq supports only three introns, then the liver data fully support the transcript exons whereas the brain data do not. Full support of intron position by RNA-seq alignment evidence A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript. ECO:MCC A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript. mchibucos 2013-04-03T04:50:46Z eco ECO:0000344 Partial support can occur in two ways. First, one or more exon-exon pair (intron) is not supported by any RNA-seq sample included in the analysis. Second, no single RNA-seq sample provides support for all exon-exon pairs (introns) represented in a transcript, but all represented exons are supported by at least one sample. Partial support of intron position by RNA-seq alignment evidence A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript. ECO:MCC mchibucos 2013-04-03T05:10:34Z eco ECO:0000345 single exon transcript confirmation via alignment evidence A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion. mchibucos 2013-04-04T04:37:35Z eco ECO:0000346 Support of intron position by RNA-seq alignment evidence used in manual assertion true true A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:MCC A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. mchibucos 2013-04-04T04:38:45Z eco ECO:0000347 Support of intron position by RNA-seq alignment evidence used in automatic assertion true true A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:MCC A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. mchibucos 2013-04-04T04:40:19Z eco ECO:0000348 Full support of intron position by RNA-seq alignment evidence used in automatic assertion true true A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:MCC A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion. mchibucos 2013-04-04T04:41:34Z eco ECO:0000349 Full support of intron position by RNA-seq alignment evidence used in manual assertion true true A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:MCC A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. mchibucos 2013-04-04T04:42:53Z eco ECO:0000350 Partial support of intron position by RNA-seq alignment evidence used in automatic assertion true true A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:MCC A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion. mchibucos 2013-04-04T04:43:56Z eco ECO:0000351 Partial support of intron position by RNA-seq alignment evidence used in manual assertion true true A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:MCC A type of evidence that is used in an manual assertion. mchibucos eco ECO:0000352 evidence used in manual assertion true true A type of evidence that is used in an manual assertion. ECO:MCC A type of physical interaction evidence that is used in a manual assertion. mchibucos 2013-10-31T21:01:27Z GOECO:IPI IPI inferred from physical interaction eco ECO:0000353 physical interaction evidence used in manual assertion http://geneontology.org/page/ipi-inferred-physical-interaction true true A type of physical interaction evidence that is used in a manual assertion. ECO:MCC GOECO:IPI inferred from physical interaction IPI GOECO:IPI inferred from physical interaction GOECO:IPI A type of gene neighbors evidence that is used in a manual assertion. mchibucos 2013-11-19T13:37:24Z inferred from genome cluster GO_REF:0000025 eco ICL ECO:0000354 gene neighbors evidence used in manual assertion true true A type of gene neighbors evidence that is used in a manual assertion. ECO:MCC GO_REF:0000025 operon structure as IGC evidence A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony. mchibucos 2014-04-22T17:02:31Z eco ECO:0000355 Example of use: "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor." PMID: 7013637. Northcutt RG. (1981) Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. phylogenetic distribution evidence A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony. ECO:MCC PMID:21238344 A type of transcript expression evidence resulting from a microarray analysis with the use of the Gene Set Enrichment Analysis (GSEA) method or the Fisher's-Exact (FE) method to assess the differential expression. mchibucos 2014-09-26T16:25:47Z eco ECO:0000358 differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) A type of transcript expression evidence resulting from a microarray analysis with the use of the Gene Set Enrichment Analysis (GSEA) method or the Fisher's-Exact (FE) method to assess the differential expression. PMID:19725948 A type of transcript expression evidence resulting from the use of the Gene Set Enrichment Analysis (GSEA) method or Fisher's-Exact (FE) method to assess an RNA-seq dataset for differential gene expression. mchibucos 2014-09-26T16:26:48Z eco ECO:0000359 differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) A type of transcript expression evidence resulting from the use of the Gene Set Enrichment Analysis (GSEA) method or Fisher's-Exact (FE) method to assess an RNA-seq dataset for differential gene expression. PMC:2881125 mchibucos 2014-09-26T16:39:11Z eco ECO:0000360 biological target-disease association via drug A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means. mchibucos 2015-07-14T11:19:37Z eco ECO:0000361 Inference is the process of deriving logical conclusions from premises known or assumed to be true, or alternatively, arriving at conclusions via some non-logical means of observation of patterns of facts, which can result in identifying new meanings and contexts for understanding. Given the evidence provided by a set of premises, deductive reasoning involves drawing conclusions that necessarily follow, i.e. are certain, whereas inductive reasoning generates conclusions that are likely to be, but are not necessarily, true. inferential evidence A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means. ECO:MCC A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is computationally derived. mchibucos 2015-07-14T11:24:27Z eco ECO:0000362 evidence based on computational logical inference A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is computationally derived. ECO:MCC GOC:MC A type of evidence based on computational logical inference that is used in automatic assertion. mchibucos 2015-07-14T11:35:08Z GO_REF:0000108 eco ECO:0000363 evidence based on computational logical inference used in automatic assertion true true A type of evidence based on computational logical inference that is used in automatic assertion. ECO:MCC GO_REF:0000108 Automatic assignment of GO terms using logical inference, based on on inter-ontology links A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion. mchibucos 2015-07-14T11:44:19Z eco ECO:0000364 evidence based on logical inference from manual annotation used in automatic assertion A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion. ECO:MCC A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion. mchibucos 2015-07-14T11:45:25Z eco ECO:0000366 evidence based on logical inference from automatic annotation used in automatic assertion A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion. ECO:MCC A type of evidence that is used in an automatic assertion. cjm GOECO:IEA GO_REF:0000003 GO_REF:0000004 GO_REF:0000023 IEA inferred from electronic annotation eco ECO:0000501 evidence used in automatic assertion http://geneontology.org/page/automatically-assigned-evidence-codes true true A type of evidence that is used in an automatic assertion. ECO:cjm GOECO:IEA inferred from electronic annotation GO_REF:0000003 Gene Ontology annotation based on Enzyme Commission mapping. GO_REF:0000004 Gene Ontology annotation based on Swiss-Prot keyword mapping. GO_REF:0000023 Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping. IEA GOECO:IEA inferred from electronic annotation GOECO:IEA A type of cell proliferation assay evidence resulting from the growth of cells in a micro-environment that mimics real tissue and establishes physiological cell-cell and cell-substrate interactions that regulate proliferation and differentiation. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001001 3D cell culture evidence A type of cell proliferation assay evidence resulting from the growth of cells in a micro-environment that mimics real tissue and establishes physiological cell-cell and cell-substrate interactions that regulate proliferation and differentiation. PMID:21042962 url:http://volttecnologia.com.br/wp-content/uploads/2016/03/Drug-discovery.pdf A type of cell-based assay evidence resulting from labeling cells with [3H]arachidonic acid and subsequently determining the release of the arachidonic acid by the cells. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001002 [3H]arachidonic acid release assay evidence A type of cell-based assay evidence resulting from labeling cells with [3H]arachidonic acid and subsequently determining the release of the arachidonic acid by the cells. ISBN:0323152295 PMID:20693009 A type of DNA synthesis cell proliferation assay evidence resulting from the measurement of cell proliferation rate by determining the incorporation of [3H]-thymidine into cellular nucleic acids. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001003 [3H]-thymidine incorporation assay evidence A type of DNA synthesis cell proliferation assay evidence resulting from the measurement of cell proliferation rate by determining the incorporation of [3H]-thymidine into cellular nucleic acids. OBI:0000669 url:http://www.scientistsolutions.com/forum/cell-culture-and-tissue-culture-proliferationapoptosis/3h-thymidine-incorporation-assay-rat-1a A type of cytotoxicity assay evidence resulting from the measurement of the amount of radioactive 51Cr released in the supernatant of a sample of 51Cr pre-labeled cells via cytolysis by effector cells (cytotoxic T-cells). SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001004 51Cr release assay evidence A type of cytotoxicity assay evidence resulting from the measurement of the amount of radioactive 51Cr released in the supernatant of a sample of 51Cr pre-labeled cells via cytolysis by effector cells (cytotoxic T-cells). PMC:3929704 url:http://www4.mpbio.com/ecom/docs/proddata.nsf/5f64ffd4f38c2fda8525645d00769d68/53d2a75653615bab852568cb00572ff3?OpenDocument A type of apoptotic assay evidence resulting from the use of 7-aminoactinomycin D (7-AAD) to distinguish viable, apoptotic, and dead cells, using the fact that permeability of the cell membrane, and fluorescence intensity, is low in early apoptotic cells and high in late apoptotic and dead cells. SIB:PG mchibucos 2014-03-16T11:30:54Z 7-AAD staining evidence 7-amino-actinomycin D staining evidence eco ECO:0001005 7-aminoactinomycin staining evidence A type of apoptotic assay evidence resulting from the use of 7-aminoactinomycin D (7-AAD) to distinguish viable, apoptotic, and dead cells, using the fact that permeability of the cell membrane, and fluorescence intensity, is low in early apoptotic cells and high in late apoptotic and dead cells. ECO:RCT A type of cell-based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001006 adhesion assay evidence A type of cell-based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells. PMID:15576904 PMID:21909903 A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host. SIB:PG mchibucos 2014-03-16T11:30:54Z Adoptive immunotherapy passive immunization eco ECO:0001007 adoptive cell transfer evidence A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host. ECO:SN url:http://jco.ascopubs.org/content/23/10/2346.full.pdf+html url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf A type of cell viability assay evidence resulting from the continuous measurement of fluorescence intensity from the viable cells, where a cell permeable compound, resazurin (the active ingredient of alamarBlue), is reduced to fluorescent resorufin. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001008 alamarBlue assay evidence A type of cell viability assay evidence resulting from the continuous measurement of fluorescence intensity from the viable cells, where a cell permeable compound, resazurin (the active ingredient of alamarBlue), is reduced to fluorescent resorufin. PMC:3478843 url:https://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/cell-profilteration-assay-protocols/cell-viability-with-alamarblue.html A type of anatomical perturbation evidence where an organ or tissue is transplanted from one individual to another of the same species with a different genotype. SIB:PG mchibucos 2014-03-16T11:30:54Z Allotransplantation allografting tissue grafting eco ECO:0001009 allograft transplantation experiment evidence A type of anatomical perturbation evidence where an organ or tissue is transplanted from one individual to another of the same species with a different genotype. ECO:SN url:http://www.nature.com/subjects/allograft url:http://www.organdonor.gov/about/terms_and_topics/ A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001010 anion-exchange chromatography evidence A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules. ECO:SN PMID:20978968 url:http://www.bio-rad.com/en-us/applications-technologies/anion-exchange-chromatography url:http://www.uta.edu/faculty/sawasthi/Enzymology-4351-5324/Class%20Syllabus%20Enzymology/Ion%20Exchange%20Chromatography-1.pdf A type of apoptotic assay evidence resulting from the addition and subsequent binding of Annexin V to phosphatidylserine in cells to detect if they are viable, apoptotic, or necrotic. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001011 annexin-V staining evidence A type of apoptotic assay evidence resulting from the addition and subsequent binding of Annexin V to phosphatidylserine in cells to detect if they are viable, apoptotic, or necrotic. PMC:3169266 A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001012 behavioral assay evidence A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning. PMID:24462904 A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001013 blocking monoclonal antibody evidence A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies. PMID:11292349 url:http://www.sciencedirect.com/science/article/pii/S0140673600034966 A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001014 blocking peptide evidence A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets. ECO:RCT SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001015 blocking polyclonal antibody evidence A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001016 blood test evidence A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components. ECO:SN url:https://www.nhlbi.nih.gov/health/health-topics/topics/bdt A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the number of cells that migrate from the upper compartment of a chamber (separated by a micro-porous membrane) to the lower compartment, in which chemotactic agents are present. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001017 Boyden chamber assay evidence A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the number of cells that migrate from the upper compartment of a chamber (separated by a micro-porous membrane) to the lower compartment, in which chemotactic agents are present. PMID:13872176 PMID:15576901 A type of nucleotide analog incorporation evidence resulting from the incorporation of bromodeoxyuridine (BrdU) as a thymidine analog into nuclear DNA, resulting in a label that can be tracked using antibody probes. SIB:PG mchibucos 2014-03-16T11:30:54Z ECO:0005010 cell proliferation marker detection assay evidence 5-bromo-2'-deoxyuridine incorporation assay evidence BUdR incorporation assay evidence BrdU incorporation assay evidence BrdUrd incorporation assay evidence eco ECO:0001018 bromodeoxyuridine incorporation assay evidence A type of nucleotide analog incorporation evidence resulting from the incorporation of bromodeoxyuridine (BrdU) as a thymidine analog into nuclear DNA, resulting in a label that can be tracked using antibody probes. PMID:23690005 A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001019 caspase assay evidence A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis. PMID:18314058 PMID:25086023 A type of cell-based assay evidence resulting from the quantification of a sample of cells. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001020 cell counting evidence A type of cell-based assay evidence resulting from the quantification of a sample of cells. ECO:RCT A type of cell-based assay evidence resulting from the quantification of cell permeability. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001021 cell permeability assay evidence A type of cell-based assay evidence resulting from the quantification of cell permeability. PMID:16962665 A type of staining evidence resulting from monitoring division by the use of carboxyfluorescein diacetate succinimidyl ester (CFSE) to label intracellular molecules with carboxyfluorescein; when a labeled cell divides, the number of carboxyfluorescein-tagged molecules is split. SIB:PG mchibucos 2014-03-16T11:30:54Z CFDA-SE staining evidence CFSE-staining evidence eco ECO:0001022 carboxyfluorescein diacetate succinimidyl ester staining evidence A type of staining evidence resulting from monitoring division by the use of carboxyfluorescein diacetate succinimidyl ester (CFSE) to label intracellular molecules with carboxyfluorescein; when a labeled cell divides, the number of carboxyfluorescein-tagged molecules is split. PMC:3185625 A type of protein detection assay evidence resulting from a complex (a chemiluminescent compound, protein and a steroidal hapten) utilized as a labeled antigen, which emits light when treated with hydrogen peroxide and copper acetate at a high pH. SIB:PG mchibucos 2014-03-16T11:30:54Z CLIA evidence eco ECO:0001023 chemiluminescence-linked immunoassay evidence A type of protein detection assay evidence resulting from a complex (a chemiluminescent compound, protein and a steroidal hapten) utilized as a labeled antigen, which emits light when treated with hydrogen peroxide and copper acetate at a high pH. PMID:659901 A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001024 chimeric protein evidence A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product. PMID:22588898 PMID:25832756 A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001025 co-electrophoresis evidence A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions. PMID:7668395 A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001026 co-localization evidence A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location. PMC:3074624 A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001027 colony counting evidence A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish. PMID:16558698 PMID:23457446 A type of physical interaction evidence resulting from the separation of a mixture of molecules under the influence of a force such as artificial gravity, where molecules sedimenting together are assumed to interact. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001028 co-sedimentation assay evidence A type of physical interaction evidence resulting from the separation of a mixture of molecules under the influence of a force such as artificial gravity, where molecules sedimenting together are assumed to interact. MI:0027 A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001029 comet assay evidence A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration. OBI:0302736 PMID:10737956 A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001030 conditional knockout evidence A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal. PMC:3572410 A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001031 conditional knockin evidence A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation. PMID:16832820 A type of experimental phenotypic evidence resulting from a constitutively active mutant (CAM), resulting in mutant proteins that remain active in the absence of upstream signals. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001032 constitutively active mutant evidence A type of experimental phenotypic evidence resulting from a constitutively active mutant (CAM), resulting in mutant proteins that remain active in the absence of upstream signals. PMID:12217490 A type of protein binding evidence resulting from the identification of two interacting proteins (that exist in close proximity) by linking through covalent bonds followed by identification SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001033 cross-linking evidence A type of protein binding evidence resulting from the identification of two interacting proteins (that exist in close proximity) by linking through covalent bonds followed by identification PMID:15530987 PMID:19241040 A type of structure determination evidence resulting from the use of a narrow beam of x-rays to identify molecular structures by creating a diffraction pattern. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001034 crystallography evidence A type of structure determination evidence resulting from the use of a narrow beam of x-rays to identify molecular structures by creating a diffraction pattern. MI:0114 A type of histochemistry evidence resulting from localizing chemical components of cells and organelles on histological sections. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001035 cytochemistry evidence A type of histochemistry evidence resulting from localizing chemical components of cells and organelles on histological sections. PMID:11597006 A type of apoptotic assay evidence resulting from the identification of an accumulation of cytochrome C in the cytoplasm after its release from the mitochondria, an early event in apoptosis. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001036 cytochrome C release assay evidence A type of apoptotic assay evidence resulting from the identification of an accumulation of cytochrome C in the cytoplasm after its release from the mitochondria, an early event in apoptosis. PMID:10914021 PMID:12815469 A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence. SIB:PG mchibucos 2014-03-16T11:30:54Z DAPI staining evidence diaminophenylindole staining eco ECO:0001037 4',6-diamidino-2-phenylindole staining evidence A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence. PMID:8580206 url:https://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/protocols/dapi-imaging-protocol.html A type of experimental phenotypic evidence resulting from a mutation in which there is a removal of one or more contiguous nucleotides. SIB:PG mchibucos 2014-03-16T11:30:54Z ECO:0005510 eco ECO:0001038 deletion mutation evidence A type of experimental phenotypic evidence resulting from a mutation in which there is a removal of one or more contiguous nucleotides. SO:0000159 A type of apoptotic assay evidence resulting from the visualization via gel electrophoresis of the fragmented DNA (DNA ladder) which is the result of apoptotic DNA fragmentation. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001039 DNA laddering assay evidence A type of apoptotic assay evidence resulting from the visualization via gel electrophoresis of the fragmented DNA (DNA ladder) which is the result of apoptotic DNA fragmentation. PMC:4401164 A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments. CollecTF SIB:PG mchibucos 2014-03-16T11:30:54Z eco RNA dot blot ECO:0001040 RNA dot blot assay evidence A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments. ECO:SW PMID:21424648 A type of experimental phenotypic evidence resulting from the analysis of a mutated gene producing mutant polypeptides that disrupt the activity of the wild-type genes. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001042 dominant-negative mutant evidence A type of experimental phenotypic evidence resulting from the analysis of a mutated gene producing mutant polypeptides that disrupt the activity of the wild-type genes. PMC:2217636 PMID:8018332 A type of Edman degradation evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:59:00Z eco ECO:0001043 Edman degradation evidence used in manual assertion true true A type of Edman degradation evidence that is used in a manual assertion. ECO:MCC A type of protein detection assay evidence resulting from labeling a termonal amino acid residue and cleaving it from a peptide by sequentially removing one residue at a time from the amino end of the peptide, without disrupting the bonds. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001044 Edman degradation evidence A type of protein detection assay evidence resulting from labeling a termonal amino acid residue and cleaving it from a peptide by sequentially removing one residue at a time from the amino end of the peptide, without disrupting the bonds. OBI:0000705 doi:10.3891/acta.chem.scand.04-0283 A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001045 eTag assay evidence true A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters. PMID:15137949 A type of physical interaction evidence resulting from a mixture of two molecules passed through a nitrocellulose filter, where one may be immobilized on the filter, and if the immobilized molecule is capable of binding to the other, it will be retained on the filter as well. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001046 filter binding assay evidence A type of physical interaction evidence resulting from a mixture of two molecules passed through a nitrocellulose filter, where one may be immobilized on the filter, and if the immobilized molecule is capable of binding to the other, it will be retained on the filter as well. PMID:23028069 A type of nucleic acid localization evidence and in situ hybridization evidence resulting from the use of fluorescent probes to detect complementary sequences of nucleic acids. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001047 fluorescence in situ hybridization evidence A type of nucleic acid localization evidence and in situ hybridization evidence resulting from the use of fluorescent probes to detect complementary sequences of nucleic acids. PMC:346675 PMID:6812046 A type of physical interaction evidence resulting from the measurement of the proximity of two fluorophores, where the energy from an excited molecular fluorophore to another fluorophore can only occur within ~10nm. SIB:PG mchibucos 2014-03-16T11:30:54Z FRET eco ECO:0001048 fluorescence resonance energy transfer evidence A type of physical interaction evidence resulting from the measurement of the proximity of two fluorophores, where the energy from an excited molecular fluorophore to another fluorophore can only occur within ~10nm. PMID:11516318 PMID:15696158 A type of chromatography evidence resulting from the exclusion of proteins based on molecular size by filtration through a porous matrix (swollen gel), from which larger molecules are excluded. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001049 gel-filtration evidence A type of chromatography evidence resulting from the exclusion of proteins based on molecular size by filtration through a porous matrix (swollen gel), from which larger molecules are excluded. CHMO:0001011 doi:10.1038/nmeth0506-410 A type of histology evidence resulting from the identification of chemical components in cells and tissues. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001050 histochemistry evidence A type of histology evidence resulting from the identification of chemical components in cells and tissues. MMO:0000497 A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001051 histology evidence A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues. OBI:0600020 A type of chromatography evidence resulting from the separation of molecules in a solute by forcing the solvent containing the sample through a column packed with nonporous particles at high pressure. mchibucos 2014-03-16T11:30:54Z HPLC evidence eco ECO:0001052 high-performance liquid chromatography evidence A type of chromatography evidence resulting from the separation of molecules in a solute by forcing the solvent containing the sample through a column packed with nonporous particles at high pressure. PMID:16376355 A type of protein detection assay evidence resulting from the use of antibodies linked to coloring agents to localize structures in cell cultures to identify proteins. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001053 immunocytochemistry evidence A type of protein detection assay evidence resulting from the use of antibodies linked to coloring agents to localize structures in cell cultures to identify proteins. MI:1200 OBI:0001986 A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001054 immunodepletion evidence A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample. BAO:0002505 A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001055 immunohistochemistry evidence A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections. OBI:0001986 A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001056 induced mutation evidence A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation. OBI:0001154 A type of acetylation assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001057 in vitro acetylation assay evidence A type of acetylation assay evidence used in an in vitro experiment. ECO:SN SIB:PG url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml A type of cleavage assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001058 in vitro cleavage assay evidence A type of cleavage assay evidence used in an in vitro experiment. PMID:21121091 A type of deubiquitination assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001059 in vitro deubiquitination assay evidence A type of deubiquitination assay evidence used in an in vitro experiment. ECO:SN PMID:19692941 SIB:PG A type of deacetylation assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001060 in vitro deacetylation assay evidence A type of deacetylation assay evidence used in an in vitro experiment. ECO:SN SIB:PG url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml A type of defarnesylation assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001061 in vitro defarnesylation assay evidence A type of defarnesylation assay evidence used in an in vitro experiment. ECO:SN PMID:16126733 SIB:PG A type of demethylation assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001062 in vitro demethylation assay evidence A type of demethylation assay evidence used in an in vitro experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Demethylation A type of desumoylation assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001063 in vitro desumoylation assay evidence A type of desumoylation assay evidence used in an in vitro experiment. ECO:SN SIB:PG url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/ A type of farnesylation assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001064 in vitro farnesylation assay evidence A type of farnesylation assay evidence used in an in vitro experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Farnesyltransferase A type of methylation assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001065 in vitro methylation assay evidence A type of methylation assay evidence used in an in vitro experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Methylation A type of palmitoylation assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001066 in vitro palmitoylation assay evidence A type of palmitoylation assay evidence used in an in vitro experiment. ECO:SN PMID:17077383 SIB:PG A type of phosphatase assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001067 in vitro phosphatase assay evidence A type of phosphatase assay evidence used in an in vitro experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Phosphatase A type of protein kinase assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001068 in vitro protein kinase assay evidence A type of protein kinase assay evidence used in an in vitro experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Protein_kinase url:http://en.wikipedia.org/wiki/Protein_phosphorylation A type of polyADP-ribosylation assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001069 in vitro polyADP-ribosylation assay evidence A type of polyADP-ribosylation assay evidence used in an in vitro experiment. ECO:SN PMID:21870253 SIB:PG A type of sumoylation assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001070 in vitro sumoylation assay evidence A type of sumoylation assay evidence used in an in vitro experiment. ECO:SN SIB:PG url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/ A type of transcription assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001071 in vitro transcription assay evidence A type of transcription assay evidence used in an in vitro experiment. ECO:SN ECO:SW PMID:21125481 SIB:PG A type of translation assay evidence used in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001072 in vitro translation assay evidence A type of translation assay evidence used in an in vitro experiment. ECO:SN PMID:18230759 SIB:PG A type of ubiquitination assay evidenceused in an in vitro experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001073 in vitro ubiquitination assay evidence A type of ubiquitination assay evidenceused in an in vitro experiment. ECO:SN PMID:19692941 SIB:PG A type of acetylation assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001074 in vivo acetylation assay evidence A type of acetylation assay evidence used in an in vivo experiment. ECO:SN SIB:PG url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml A type of cleavage assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001075 in vivo cleavage assay evidence A type of cleavage assay evidence used in an in vivo experiment. ECO:SN PMID:22154596 A type of deacetylation assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001076 in vivo deacetylation assay evidence A type of deacetylation assay evidence used in an in vivo experiment. ECO:SN SIB:PG url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml A type of defarnesylation assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001077 in vivo defarnesylation assay evidence A type of defarnesylation assay evidence used in an in vivo experiment. ECO:SN PMID:15556768 PMID:16507103 SIB:PG A type of demethylation assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001078 in vivo demethylation assay evidence A type of demethylation assay evidence used in an in vivo experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Demethylation A type of deubiquitination assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001079 in vivo deubiquitination assay evidence A type of deubiquitination assay evidence used in an in vivo experiment. ECO:SN PMID:19692941 SIB:PG A type of desumoylation assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001080 in vivo desumoylation assay evidence A type of desumoylation assay evidence used in an in vivo experiment. ECO:SN SIB:PG url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/ A type of farnesylation assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001081 in vivo farnesylation assay evidence A type of farnesylation assay evidence used in an in vivo experiment. ECO:SN PMID:9030603 SIB:PG A type of methylation assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001082 in vivo methylation assay evidence A type of methylation assay evidence used in an in vivo experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Methylation A type of palmitoylation assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001083 in vivo palmitoylation assay evidence A type of palmitoylation assay evidence used in an in vivo experiment. ECO:SN PMID:10329400 SIB:PG A type of phosphatase assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001084 in vivo phosphatase assay evidence A type of phosphatase assay evidence used in an in vivo experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Phosphatase A type of protein kinase assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001085 in vivo protein kinase assay evidence A type of protein kinase assay evidence used in an in vivo experiment. ECO:SN SIB:PG url:http://en.wikipedia.org/wiki/Protein_kinase url:http://en.wikipedia.org/wiki/Protein_phosphorylation A type of sumoylation assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001086 in vivo sumoylation assay evidence A type of sumoylation assay evidence used in an in vivo experiment. ECO:SN SIB:PG url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/ A type of transcription assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001087 in vivo transcription assay evidence A type of transcription assay evidence used in an in vivo experiment. ECO:SN PMID:12181418 SIB:PG A type of translation assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001088 in vivo translation assay evidence A type of translation assay evidence used in an in vivo experiment. ECO:SN PMID:24901308 SIB:PG A type of ubiquitination assay evidence used in an in vivo experiment. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001089 in vivo ubiquitination assay evidence A type of ubiquitination assay evidence used in an in vivo experiment. ECO:SN PMID:19692941 SIB:PG A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001090 knockin evidence A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence. PMID:18077807 PMID:21800101 A type of genetic transformation evidence resulting from the removal of a particular gene (or genes), disrupting the function and allowing for functional analysis. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001091 knockout evidence A type of genetic transformation evidence resulting from the removal of a particular gene (or genes), disrupting the function and allowing for functional analysis. PMC:2782548 A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001092 lipid binding assay evidence A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid. PMID:22848065 PMID:23681540 A type of physical interaction evidence resulting from the analysis of protein-protein interactions by use of a luciferase enzyme fused to a particular protein (or proteins), which are coexpressed with epitope-tagged partners in mammalian cells. SIB:PG mchibucos 2014-03-16T11:30:54Z LUMIER assay eco ECO:0001093 luminescence-based mammalian interactome mapping assay evidence A type of physical interaction evidence resulting from the analysis of protein-protein interactions by use of a luciferase enzyme fused to a particular protein (or proteins), which are coexpressed with epitope-tagged partners in mammalian cells. MI:0729 PMID:15761153 SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001094 macroscopy evidence A type of hybrid interaction evidence resulting from the analysis of proteins of interest attached to two portions of the transcriptional activator, and in interaction bring the two portions together to increase expression of the reporter gene. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001095 mammalian 2-hybrid assay evidence A type of hybrid interaction evidence resulting from the analysis of proteins of interest attached to two portions of the transcriptional activator, and in interaction bring the two portions together to increase expression of the reporter gene. ECO:RCT PMID:9043710 A type of spectrometry evidence resulting from identifying the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001096 mass spectrometry evidence A type of spectrometry evidence resulting from identifying the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles. OBI:0000470 A type of imaging assay evidence resulting from the use of technology to visualize and provide information about the body to diagnose, treat, or monitor medical conditions. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001097 medical imaging evidence A type of imaging assay evidence resulting from the use of technology to visualize and provide information about the body to diagnose, treat, or monitor medical conditions. url:http://www.fda.gov/Radiation-EmittingProducts/RadiationEmittingProductsandProcedures/MedicalImaging/ucm2005914.htm A type of direct assay evidence where a microscope was used to view a sample. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001098 microscopy evidence A type of direct assay evidence where a microscope was used to view a sample. ECO:MCC A type of cell-based assay evidence to measure cell motility in which a "wound" is created in a cell monolayer and the migration of the cells is captured by imaging at regular intervals during cell migration to close the wound. SIB:PG mchibucos 2014-03-16T11:30:54Z ECO:0001135 wound healing assay evidence eco ECO:0001099 motility wound healing assay evidence A type of apoptotic assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) in combination with phenazine methyl sulfate (PMS) as an intermediate electron acceptor reagent to produce a soluble formazan dye in viable cells. SIB:PG mchibucos 2014-03-16T11:30:54Z 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium eco ECO:0001100 MTS assay evidence A type of apoptotic assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) in combination with phenazine methyl sulfate (PMS) as an intermediate electron acceptor reagent to produce a soluble formazan dye in viable cells. NBK:144065 PMID:1867954 A type of apoptotic assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to its insoluble purple formazan dye in viable cells and measures cell viability / metabolic activity. SIB:PG mchibucos 2014-03-16T11:30:54Z 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide eco ECO:0001101 MTT assay evidence A type of apoptotic assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to its insoluble purple formazan dye in viable cells and measures cell viability / metabolic activity. NBK:144065 PMID:6606682 A type of protein detection assay evidence resulting from determination of analyte concentration by fluorescent bead sets attached to an antibody (to a specific analyte) with a fluorescent reporter dye label attached to a second antibody (to a specific analyte). SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001102 multiplex bead-based immunoassay evidence A type of protein detection assay evidence resulting from determination of analyte concentration by fluorescent bead sets attached to an antibody (to a specific analyte) with a fluorescent reporter dye label attached to a second antibody (to a specific analyte). PMC:1534009 A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001103 natural variation mutant evidence A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits. ECO:RCT A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001104 nuclear fragmentation evidence A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death. PMID:16738861 A type of structure determination evidence resulting from the use of an MRI to provide chemical information about tissue metabolites. SIB:PG mchibucos 2014-03-16T11:30:54Z NMR spectroscopy eco ECO:0001105 nuclear magnetic resonance spectroscopy evidence A type of structure determination evidence resulting from the use of an MRI to provide chemical information about tissue metabolites. PMID:16428685 A type of RNA detection assay evidence resulting from the detection and quantitation of specific RNAs (from a sample of total cellular RNA) that are bound by antisense RNA or DNA probes and therefore protected from nucleases. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001106 nuclease protection assay evidence A type of RNA detection assay evidence resulting from the detection and quantitation of specific RNAs (from a sample of total cellular RNA) that are bound by antisense RNA or DNA probes and therefore protected from nucleases. PMID:17486122 PMID:18428580 A type of DNA synthesis cell proliferation assay evidence resulting from the analysis and measurement of the incorporation of fluorescently labeled nucleotide analog(s) into the DNA. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001107 nucleotide analog incorporation assay evidence A type of DNA synthesis cell proliferation assay evidence resulting from the analysis and measurement of the incorporation of fluorescently labeled nucleotide analog(s) into the DNA. PMC:3149870 A type of protein binding evidence resulting from the panning of a phage library where the individual phage displayed a different peptide or protein by fusion to coat proteins on the capsid. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001108 phage display evidence A type of protein binding evidence resulting from the panning of a phage library where the individual phage displayed a different peptide or protein by fusion to coat proteins on the capsid. MI:0084 PMID:11680867 A type of protein assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001109 phosphoamino acid analysis evidence A type of protein assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis. PMID:11680867 PMID:18429115 SIB:PG mchibucos 2014-03-16T11:30:54Z phosphopeptide affinity enrichment evidence eco ECO:0001110 peptide affinity enrichment evidence A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001111 physical examination evidence A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample. ECO:RCT A type of protein assay evidence resulting from protein-bound peptides detected from a collection of peptides arranged as an array and incubated with the partner protein in order to map protein-protein interaction sites. SIB:PG mchibucos 2014-03-16T11:30:54Z phosphopeptide array evidence eco ECO:0001112 peptide array evidence A type of protein assay evidence resulting from protein-bound peptides detected from a collection of peptides arranged as an array and incubated with the partner protein in order to map protein-protein interaction sites. PMID:21243154 A type of experimental phenotypic evidence resulting from the change in a single nucleotide. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001113 point mutation evidence A type of experimental phenotypic evidence resulting from the change in a single nucleotide. SO:1000008 A type of staining evidence resulting from the binding and labeling of DNA (during apoptosis, when there is a loss of nuclear DNA content) with propidium iodide (PI) to identify the cells from which it originated. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001114 propidium iodide staining evidence A type of staining evidence resulting from the binding and labeling of DNA (during apoptosis, when there is a loss of nuclear DNA content) with propidium iodide (PI) to identify the cells from which it originated. PMID:17406435 A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001115 fluorescence evidence A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore. url:http://www.nature.com/subjects/biological-fluorescence A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001116 protein dot blot assay evidence A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged. doi:10.1007/978-94-009-0951-9_24 A type of protein detection assay evidence resulting from proteins immobilized to prepare protein chips, or microwells, that can be utilized to determine presence of proteins, monitor differential expression profiles, and/or study protein interactions. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001117 protein microarray evidence A type of protein detection assay evidence resulting from proteins immobilized to prepare protein chips, or microwells, that can be utilized to determine presence of proteins, monitor differential expression profiles, and/or study protein interactions. PMC:1828913 A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001118 protein sequencing assay evidence A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein. ERO:0001287 A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001119 quantitative mass spectrometry evidence A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes. PMID:22665296 A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant. SIB:PG mchibucos 2014-03-16T11:30:54Z radioassay radioisotopic assay eco ECO:0001120 radioisotope assay evidence A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant. ISBN:978-3-642-50036-7 A type of protein detection assay evidence resulting from the use of a radioligand to measure the binding of a substance to a specific antibody or other receptor system. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001121 radioimmunoassay evidence A type of protein detection assay evidence resulting from the use of a radioligand to measure the binding of a substance to a specific antibody or other receptor system. MeSH:D011863 A type of direct assay evidence from the analysis of the real-time interaction between an analyte in solution and its interactant linked to the surface of the resonant mirror. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001123 resonant mirror biosensor evidence A type of direct assay evidence from the analysis of the real-time interaction between an analyte in solution and its interactant linked to the surface of the resonant mirror. PMID:19151938 A type of DNA detection assay evidence resulting from homologous DNA fragments digested by restriction enzymes, and the resulting restriction fragments are sorted by length to illustrate differences. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001124 restriction fragment detection evidence A type of DNA detection assay evidence resulting from homologous DNA fragments digested by restriction enzymes, and the resulting restriction fragments are sorted by length to illustrate differences. doi:10.1007/978-94-009-0951-9_24 url:http://www.ncbi.nlm.nih.gov/probe/docs/techrflp/ A type of spectrometry evidence resulting from the evaluation of a molecule in a fluid by its ability to alter the transmission of light at specific wavelengths. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001126 spectrophotometry evidence A type of spectrometry evidence resulting from the evaluation of a molecule in a fluid by its ability to alter the transmission of light at specific wavelengths. MMO:0000173 A type of physical interaction evidence based on real-time, rapid plasmon generation on the interface between a planar surface and vacuum that measures changes in refractive index close to the sensor surface when an analyte and its immobilized ligand bind to observe and characterize molecular interaction. SIB:PG mchibucos 2014-03-16T11:30:54Z SPR evidence eco ECO:0001127 Plasmons are generated by an incident light beam. surface plasmon resonance evidence A type of physical interaction evidence based on real-time, rapid plasmon generation on the interface between a planar surface and vacuum that measures changes in refractive index close to the sensor surface when an analyte and its immobilized ligand bind to observe and characterize molecular interaction. ECO:SW PMID:11578932 PMID:19151937 PMID:8574707 SPR evidence PMID:11578932 A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001128 syngeneic transplantation experiment evidence A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin. PMID:18469352 A type of enzyme assay evidence resulting from the analysis of tumor necrosis factor (TNF)-a converting enzyme (TACE), which releases a soluble TNF-a from the membrane-bound precursor protein. SIB:PG mchibucos 2014-03-16T11:30:54Z Tumor necrosis factor - alpha converting enzyme activity assay eco ECO:0001129 TACE activity assay evidence A type of enzyme assay evidence resulting from the analysis of tumor necrosis factor (TNF)-a converting enzyme (TACE), which releases a soluble TNF-a from the membrane-bound precursor protein. PMC:1808921 A type of cytochemistry evidence resulting from the analysis of section(s) of a paraffin block containing embedded tissues cores arranged in an array pattern. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001130 tissue microarray evidence A type of cytochemistry evidence resulting from the analysis of section(s) of a paraffin block containing embedded tissues cores arranged in an array pattern. PMID:11770905 A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001131 transgenic organism evidence A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification. OBI:1000048 A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001132 tryptic phosphopeptide mapping assay evidence A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate. PMID:18429120 A type of apoptotic assay evidence resulting from the visualization of DNA fragmentation by detection of exposed 3'-OH ends, localized by terminal deoxynucleotidyl transferase (TdT) which then catalyzes the addition of labeled dUTPs. SIB:PG mchibucos 2014-03-16T11:30:54Z TUNEL assay evidence TdT-mediated dUTP-biotin nick end labeling assay terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence eco ECO:0001133 terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence A type of apoptotic assay evidence resulting from the visualization of DNA fragmentation by detection of exposed 3'-OH ends, localized by terminal deoxynucleotidyl transferase (TdT) which then catalyzes the addition of labeled dUTPs. PMID:22566045 A type of direct assay evidence resulting from the analysis of a urine sample. SIB:PG mchibucos 2014-03-16T11:30:54Z eco ECO:0001134 urine test evidence A type of direct assay evidence resulting from the analysis of a urine sample. ECO:RCT A type of cell proliferation assay evidence resulting from the assessment of metabolic activity from a water-soluble tetrazolium salt WST-1 being reduced outside the cell (by reacting with mitochondrial succinate-tetrazolium reductase) to form a formazan dye. SIB:PG mchibucos 2014-03-16T11:30:54Z ECO:0005009 metabolic cell proliferation assay evidence eco ECO:0001136 WST-1 assay evidence A type of cell proliferation assay evidence resulting from the assessment of metabolic activity from a water-soluble tetrazolium salt WST-1 being reduced outside the cell (by reacting with mitochondrial succinate-tetrazolium reductase) to form a formazan dye. PMID:18417231 A type of anatomical perturbation evidence where live cells, tissues, or organs from a non-human animal source are transplanted, implanted or infused into a human recipient. SIB:PG mchibucos 2014-03-16T11:30:54Z Xenograft transplantation Xenografting Xenotransplantation tissue grafting eco ECO:0001137 xenotransplantation experiment evidence A type of anatomical perturbation evidence where live cells, tissues, or organs from a non-human animal source are transplanted, implanted or infused into a human recipient. ECO:SN url:http://ilarjournal.oxfordjournals.org/content/37/1/16.full.pdf+html url:http://www.fda.gov/BiologicsBloodVaccines/Xenotransplantation/ A type of 3D cell culture evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:18:35Z eco ECO:0001138 3D cell culture evidence used in manual assertion true true A type of 3D cell culture evidence that is used in a manual assertion. ECO:MCC A type of 51Cr release assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:20:55Z eco ECO:0001139 51Cr release assay evidence used in manual assertion true true A type of 51Cr release assay evidence that is used in a manual assertion. ECO:MCC A type of 7-aminoactinomycin staining evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:22:01Z 7-AAD staining evidence 7-amino-actinomycin D staining evidence eco ECO:0001140 7-aminoactinomycin staining evidence used in manual assertion true true A type of 7-aminoactinomycin staining evidence that is used in a manual assertion. ECO:MCC A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:31:52Z eco ECO:0001141 [3H]-thymidine incorporation assay evidence used in manual assertion true true A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion. ECO:MCC A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:32:44Z eco ECO:0001142 [3H]arachidonic acid release assay evidence used in manual assertion true true A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion. ECO:MCC A type of adhesion assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:33:38Z eco ECO:0001143 adhesion assay evidence used in manual assertion true true A type of adhesion assay evidence that is used in a manual assertion. ECO:MCC A type of adoptive cell transfer evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:36:19Z Adoptive immunotherapy passive immunization eco ECO:0001144 adoptive cell transfer evidence used in manual assertion true true A type of adoptive cell transfer evidence that is used in a manual assertion. ECO:MCC A type of alamarBlue assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:37:21Z eco ECO:0001145 alamarBlue assay evidence used in manual assertion true true A type of alamarBlue assay evidence that is used in a manual assertion. ECO:MCC A type of allograft transplantation experiment evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:38:22Z Allotransplantation allografting eco tissue grafting ECO:0001146 allograft transplantation experiment evidence used in manual assertion true true A type of allograft transplantation experiment evidence that is used in a manual assertion. ECO:MCC A type of anion-exchange chromatography evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:44:30Z eco ECO:0001147 anion-exchange chromatography evidence used in manual assertion true true A type of anion-exchange chromatography evidence that is used in a manual assertion. ECO:MCC A type of annexin-V staining evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:52:01Z eco ECO:0001148 annexin-V staining evidence used in manual assertion true true A type of annexin-V staining evidence that is used in a manual assertion. ECO:MCC A type of behavioral assay evidence used that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:53:38Z eco ECO:0001149 behavioral assay evidence used in manual assertion true true A type of behavioral assay evidence used that is used in a manual assertion. ECO:MCC A type of blocking monoclonal antibody evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:54:44Z eco ECO:0001150 blocking monoclonal antibody evidence used in manual assertion true true A type of blocking monoclonal antibody evidence that is used in a manual assertion. ECO:MCC A type of blocking peptide evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T15:55:33Z eco ECO:0001151 blocking peptide evidence used in manual assertion true true A type of blocking peptide evidence that is used in a manual assertion. ECO:MCC A type of blocking polyclonal antibody evidence tthat is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:01:39Z eco ECO:0001152 blocking polyclonal antibody evidence used in manual assertion true true A type of blocking polyclonal antibody evidence tthat is used in a manual assertion. ECO:MCC A type of blood test evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:02:47Z eco ECO:0001153 blood test evidence used in manual assertion true true A type of blood test evidence that is used in a manual assertion. ECO:MCC A type of Boyden chamber assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:03:53Z eco ECO:0001154 Boyden chamber assay evidence used in manual assertion true true A type of Boyden chamber assay evidence that is used in a manual assertion. ECO:MCC A type of bromodeoxyuridine incorporation assay evidence used in manual assertion. SIB:PG mchibucos 2014-03-17T16:04:49Z 5-bromo-2'-deoxyuridine incorporation assay evidence BUdR incorporation assay evidence BrdU incorporation assay evidence BrdUrd incorporation assay evidence eco ECO:0001155 bromodeoxyuridine incorporation assay evidence used in manual assertion true true A type of bromodeoxyuridine incorporation assay evidence used in manual assertion. ECO:MCC A type of caspase assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:06:06Z eco ECO:0001156 caspase assay evidence used in manual assertion true true A type of caspase assay evidence that is used in a manual assertion. ECO:MCC A type of cell counting evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:07:13Z eco ECO:0001157 cell counting evidence used in manual assertion true true A type of cell counting evidence that is used in a manual assertion. ECO:MCC A type of cell permeability assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:07:58Z eco ECO:0001158 cell permeability assay evidence used in manual assertion true true A type of cell permeability assay evidence that is used in a manual assertion. ECO:MCC A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:08:54Z CFDA-SE staining evidence CFSE-staining evidence eco ECO:0001159 carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion true true A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion. ECO:MCC A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:09:55Z CLIA evidence eco ECO:0001160 chemiluminescence-linked immunoassay evidence used in manual assertion true true A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion. ECO:MCC A type of chimeric protein evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:10:40Z eco ECO:0001161 chimeric protein evidence used in manual assertion true true A type of chimeric protein evidence that is used in a manual assertion. ECO:MCC A type of co-electrophoresis evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:11:22Z eco ECO:0001162 co-electrophoresis evidence used in manual assertion true true A type of co-electrophoresis evidence that is used in a manual assertion. ECO:MCC A type of co-localization evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:12:04Z eco ECO:0001163 co-localization evidence used in manual assertion true true A type of co-localization evidence that is used in a manual assertion. ECO:MCC A type of co-sedimentation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:12:55Z eco ECO:0001164 co-sedimentation assay evidence used in manual assertion true true A type of co-sedimentation assay evidence that is used in a manual assertion. ECO:MCC A type of colony counting evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:14:57Z eco ECO:0001165 colony counting evidence used in manual assertion true true A type of colony counting evidence that is used in a manual assertion. ECO:MCC A type of comet assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:16:01Z eco ECO:0001166 comet assay evidence used in manual assertion true true A type of comet assay evidence that is used in a manual assertion. ECO:MCC A type of conditional knockin evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:17:22Z eco ECO:0001167 conditional knockin evidence used in manual assertion true true A type of conditional knockin evidence that is used in a manual assertion. ECO:MCC A type of conditional knockout evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:17:58Z eco ECO:0001168 conditional knockout evidence used in manual assertion true true A type of conditional knockout evidence that is used in a manual assertion. ECO:MCC A type of constitutively active mutant evidence that is used a in manual assertion. SIB:PG mchibucos 2014-03-17T16:20:23Z eco ECO:0001169 constitutively active mutant evidence used in manual assertion true true A type of constitutively active mutant evidence that is used a in manual assertion. ECO:MCC A type of cross-linking evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:21:29Z eco ECO:0001170 cross-linking evidence used in manual assertion true true A type of cross-linking evidence that is used in a manual assertion. ECO:MCC A type of crystallography evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:22:20Z eco ECO:0001171 crystallography evidence used in manual assertion true true A type of crystallography evidence that is used in a manual assertion. ECO:MCC A type of cytochemistry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:23:10Z eco ECO:0001172 cytochemistry evidence used in manual assertion true true A type of cytochemistry evidence that is used in a manual assertion. ECO:MCC A type of cytochrome C release assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:23:53Z eco ECO:0001173 cytochrome C release assay evidence used in manual assertion true true A type of cytochrome C release assay evidence that is used in a manual assertion. ECO:MCC A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:25:03Z DAPI staining evidence eco ECO:0001174 4',6-diamidino-2-phenylindole staining evidence used in manual assertion true true A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion. ECO:MCC A type of deletion evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:25:54Z eco ECO:0001175 deletion mutation evidence used in manual assertion true true A type of deletion evidence that is used in a manual assertion. ECO:MCC A type of DNA laddering assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:26:46Z eco ECO:0001176 DNA laddering assay evidence used in manual assertion true true A type of DNA laddering assay evidence that is used in a manual assertion. ECO:MCC A type of RNA dot blot assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:45:52Z RNA dot blot evidence eco ECO:0001177 RNA dot blot assay evidence used in manual assertion true true A type of RNA dot blot assay evidence that is used in a manual assertion. ECO:MCC A type of dominant-negative mutant evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:47:44Z eco ECO:0001179 dominant-negative mutant evidence used in manual assertion true true A type of dominant-negative mutant evidence that is used in a manual assertion. ECO:MCC A type of eTag assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T16:59:39Z eco ECO:0001180 eTag assay evidence used in manual assertion true true A type of eTag assay evidence that is used in a manual assertion. ECO:MCC A type of filter binding assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:03:28Z eco ECO:0001181 filter binding assay evidence used in manual assertion true true A type of filter binding assay evidence that is used in a manual assertion. ECO:MCC A type of fluorescence in situ hybridization evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:04:20Z eco ECO:0001182 fluorescence in situ hybridization evidence used in manual assertion true true true A type of fluorescence in situ hybridization evidence that is used in a manual assertion. ECO:MCC A type of fluorescence resonance energy transfer evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:05:22Z FRET evidence eco ECO:0001183 fluorescence resonance energy transfer evidence used in manual assertion true true A type of fluorescence resonance energy transfer evidence that is used in a manual assertion. ECO:MCC A type of gel-filtration evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:06:14Z eco ECO:0001184 gel-filtration evidence used in manual assertion true true A type of gel-filtration evidence that is used in a manual assertion. ECO:MCC A type of histochemistry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:07:19Z eco ECO:0001185 histochemistry evidence used in manual assertion true true A type of histochemistry evidence that is used in a manual assertion. ECO:MCC A type of immunocytochemistry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:12:39Z eco ECO:0001186 immunocytochemistry evidence used in manual assertion true true A type of immunocytochemistry evidence that is used in a manual assertion. ECO:MCC A type of histology evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:09:50Z eco ECO:0001187 histology evidence used in manual assertion true true A type of histology evidence that is used in a manual assertion. ECO:MCC A type of immunodepletion evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:16:19Z eco ECO:0001188 immunodepletion evidence used in manual assertion true true A type of immunodepletion evidence that is used in a manual assertion. ECO:MCC A type of immunohistochemistry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:17:22Z eco ECO:0001189 immunohistochemistry evidence used in manual assertion true true A type of immunohistochemistry evidence that is used in a manual assertion. ECO:MCC A type of in vitro acetylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:19:24Z eco ECO:0001190 in vitro acetylation assay evidence used in manual assertion true true A type of in vitro acetylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro cleavage assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:21:22Z eco ECO:0001191 in vitro cleavage assay evidence used in manual assertion true true A type of in vitro cleavage assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro deacetylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:23:42Z eco ECO:0001192 in vitro deacetylation assay evidence used in manual assertion true true A type of in vitro deacetylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro defarnesylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:25:45Z eco ECO:0001193 in vitro defarnesylation assay evidence used in manual assertion true true A type of in vitro defarnesylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro demethylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:27:00Z eco ECO:0001194 in vitro demethylation assay evidence used in manual assertion true true A type of in vitro demethylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro desumoylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:29:01Z eco ECO:0001195 in vitro desumoylation assay evidence used in manual assertion true true A type of in vitro desumoylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro deubiquitination assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:29:48Z eco ECO:0001196 in vitro deubiquitination assay evidence used in manual assertion true true A type of in vitro deubiquitination assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro farnesylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:30:50Z eco ECO:0001197 in vitro farnesylation assay evidence used in manual assertion true true A type of in vitro farnesylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro methylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:31:54Z eco ECO:0001198 in vitro methylation assay evidence used in manual assertion true true A type of in vitro methylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro palmitoylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:32:57Z eco ECO:0001199 in vitro palmitoylation assay evidence used in manual assertion true true A type of in vitro palmitoylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro phosphatase assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:34:16Z eco ECO:0001200 in vitro phosphatase assay evidence used in manual assertion true true A type of in vitro phosphatase assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:34:57Z eco ECO:0001201 in vitro polyADP-ribosylation assay evidence used in manual assertion true true A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro protein kinase assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:39:57Z eco ECO:0001202 in vitro protein kinase assay evidence used in manual assertion true true A type of in vitro protein kinase assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro sumoylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:41:25Z eco ECO:0001203 in vitro sumoylation assay evidence used in manual assertion true true A type of in vitro sumoylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro transcription assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:44:40Z eco ECO:0001204 in vitro transcription assay evidence used in manual assertion true true A type of in vitro transcription assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro translation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:46:30Z eco ECO:0001205 in vitro translation assay evidence used in manual assertion true true A type of in vitro translation assay evidence that is used in a manual assertion. ECO:MCC A type of in vitro ubiquitination assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:47:18Z eco ECO:0001206 in vitro ubiquitination assay evidence used in manual assertion true true A type of in vitro ubiquitination assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo acetylation assay evidence that is used in manual assertion. SIB:PG mchibucos 2014-03-17T17:48:56Z eco ECO:0001207 in vivo acetylation assay evidence used in manual assertion true true A type of in vivo acetylation assay evidence that is used in manual assertion. ECO:MCC A type of in vivo cleavage assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:49:43Z eco ECO:0001208 in vivo cleavage assay evidence used in manual assertion true true A type of in vivo cleavage assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo deacetylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:50:47Z eco ECO:0001209 in vivo deacetylation assay evidence used in manual assertion true true A type of in vivo deacetylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo defarnesylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:52:41Z eco ECO:0001210 in vivo defarnesylation assay evidence used in manual assertion true true A type of in vivo defarnesylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo demethylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:53:40Z eco ECO:0001211 in vivo demethylation assay evidence used in manual assertion true true A type of in vivo demethylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo desumoylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:54:36Z eco ECO:0001212 in vivo desumoylation assay evidence used in manual assertion true true A type of in vivo desumoylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo deubiquitination assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:56:28Z eco ECO:0001213 in vivo deubiquitination assay evidence used in manual assertion true true A type of in vivo deubiquitination assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo farnesylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T17:57:18Z eco ECO:0001214 in vivo farnesylation assay evidence used in manual assertion true true A type of in vivo farnesylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo methylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:03:16Z eco ECO:0001215 in vivo methylation assay evidence used in manual assertion true true A type of in vivo methylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo palmitoylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:04:07Z eco ECO:0001216 in vivo palmitoylation assay evidence used in manual assertion true true A type of in vivo palmitoylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo phosphatase assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:06:08Z eco ECO:0001217 in vivo phosphatase assay evidence used in manual assertion true true A type of in vivo phosphatase assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo protein kinase assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:07:58Z eco ECO:0001218 in vivo protein kinase assay evidence used in manual assertion true true A type of in vivo protein kinase assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo sumoylation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:09:49Z eco ECO:0001219 in vivo sumoylation assay evidence used in manual assertion true true A type of in vivo sumoylation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo transcription assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:11:20Z eco ECO:0001220 in vivo transcription assay evidence used in manual assertion true true A type of in vivo transcription assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo translation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:42:50Z eco ECO:0001221 in vivo translation assay evidence used in manual assertion true true A type of in vivo translation assay evidence that is used in a manual assertion. ECO:MCC A type of in vivo ubiquitination assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:44:11Z eco ECO:0001222 in vivo ubiquitination assay evidence used in manual assertion true true A type of in vivo ubiquitination assay evidence that is used in a manual assertion. ECO:MCC A type of induced mutation evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:45:56Z eco ECO:0001223 induced mutation evidence used in manual assertion true true A type of induced mutation evidence that is used in a manual assertion. ECO:MCC A type of knockin evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:49:35Z eco ECO:0001224 knockin evidence used in manual assertion true true A type of knockin evidence that is used in a manual assertion. ECO:MCC A type of knockout evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:51:31Z eco ECO:0001225 knockout evidence used in manual assertion true true A type of knockout evidence that is used in a manual assertion. ECO:MCC A type of lipid binding assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:52:19Z eco ECO:0001226 lipid binding assay evidence used in manual assertion true true A type of lipid binding assay evidence that is used in a manual assertion. ECO:MCC A type of LUMIER assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:55:16Z LUMIER assay evidence eco ECO:0001227 luminescence-based mammalian interactome mapping assay evidence used in manual assertion true true A type of LUMIER assay evidence that is used in a manual assertion. ECO:MCC A type of macroscopy evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:56:21Z eco ECO:0001228 macroscopy evidence used in manual assertion true true A type of macroscopy evidence that is used in a manual assertion. ECO:MCC A type of mammalian 2-hybrid assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:57:25Z eco ECO:0001229 mammalian 2-hybrid assay evidence used in manual assertion true true A type of mammalian 2-hybrid assay evidence that is used in a manual assertion. ECO:MCC A type of mass spectrometry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T18:59:50Z eco ECO:0001230 mass spectrometry evidence used in manual assertion true true A type of mass spectrometry evidence that is used in a manual assertion. ECO:MCC A type of medical imaging evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:04:43Z eco ECO:0001231 medical imaging evidence used in manual assertion true true A type of medical imaging evidence that is used in a manual assertion. ECO:MCC A type of microscopy evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:05:37Z eco ECO:0001232 microscopy evidence used in manual assertion true true A type of microscopy evidence that is used in a manual assertion. ECO:MCC A type of motility wound healing assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:08:13Z ECO:0001262 wound healing assay evidence used in manual assertion eco ECO:0001233 motility wound healing assay evidence used in manual assertion true true A type of motility wound healing assay evidence that is used in a manual assertion. ECO:MCC A type of MTS assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:08:51Z eco 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium ECO:0001234 MTS assay evidence used in manual assertion true true A type of MTS assay evidence that is used in a manual assertion. ECO:MCC A type of MTT assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:13:17Z eco 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide ECO:0001235 MTT assay evidence used in manual assertion true true A type of MTT assay evidence that is used in a manual assertion. ECO:MCC A type of multiplex bead-based immunoassay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:14:03Z eco ECO:0001236 multiplex bead-based immunoassay evidence used in manual assertion true true A type of multiplex bead-based immunoassay evidence that is used in a manual assertion. ECO:MCC A type of natural variation mutant evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:15:48Z eco ECO:0001237 natural variation mutant evidence used in manual assertion true true A type of natural variation mutant evidence that is used in a manual assertion. ECO:MCC A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:18:50Z NMR spectroscopy evidence eco ECO:0001238 nuclear magnetic resonance spectroscopy evidence used in manual assertion true true A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion. ECO:MCC A type of nuclear fragmentation evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:19:55Z eco ECO:0001239 nuclear fragmentation evidence used in manual assertion true true A type of nuclear fragmentation evidence that is used in a manual assertion. ECO:MCC A type of nuclease protection assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:23:41Z eco ECO:0001240 nuclease protection assay evidence used in manual assertion true true A type of nuclease protection assay evidence that is used in a manual assertion. ECO:MCC A type of nucleotide analog incorporation assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:25:17Z eco ECO:0001241 nucleotide analog incorporation assay evidence used in manual assertion true true A type of nucleotide analog incorporation assay evidence that is used in a manual assertion. ECO:MCC A type of phage display evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:27:17Z eco ECO:0001242 phage display evidence used in manual assertion true true A type of phage display evidence that is used in a manual assertion. ECO:MCC A type of phosphoamino acid analysis evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:28:59Z eco ECO:0001243 phosphoamino acid analysis evidence used in manual assertion true true A type of phosphoamino acid analysis evidence that is used in a manual assertion. ECO:MCC A type of peptide affinity enrichment evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T19:30:13Z eco phosphopeptide affinity enrichment evidence ECO:0001244 peptide affinity enrichment evidence used in manual assertion true true A type of peptide affinity enrichment evidence that is used in a manual assertion. ECO:MCC A type of peptide array evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:16:45Z eco phosphopeptide array evidence ECO:0001245 peptide array evidence used in manual assertion true true A type of peptide array evidence that is used in a manual assertion. ECO:MCC A type of physical examination evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:17:27Z eco ECO:0001246 physical examination evidence used in manual assertion true true A type of physical examination evidence that is used in a manual assertion. ECO:MCC A type of point mutation evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:18:10Z eco ECO:0001247 point mutation evidence used in manual assertion true true A type of point mutation evidence that is used in a manual assertion. ECO:MCC A type of propidium iodide staining evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:18:58Z eco ECO:0001248 propidium iodide staining evidence used in manual assertion true true A type of propidium iodide staining evidence that is used in a manual assertion. ECO:MCC A type of protein detection by fluorescence evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:19:35Z eco ECO:0001249 fluorescence evidence used in manual assertion true true A type of protein detection by fluorescence evidence that is used in a manual assertion. ECO:MCC A type of protein dot blot assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:20:30Z eco ECO:0001250 protein dot blot assay evidence used in manual assertion true true A type of protein dot blot assay evidence that is used in a manual assertion. ECO:MCC A type of protein microarray evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:21:11Z eco ECO:0001251 protein microarray evidence used in manual assertion true true A type of protein microarray evidence that is used in a manual assertion. ECO:MCC A type of protein sequencing assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:22:08Z eco ECO:0001252 protein sequencing assay evidence used in manual assertion true true A type of protein sequencing assay evidence that is used in a manual assertion. ECO:MCC A type of quantitative mass spectrometry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:23:15Z eco ECO:0001253 quantitative mass spectrometry evidence used in manual assertion true true A type of quantitative mass spectrometry evidence that is used in a manual assertion. ECO:MCC A type of radioisotope assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:27:05Z radioassay evidence radioisotopic assay evidence eco ECO:0001254 radioisotope assay evidence used in manual assertion true true A type of radioisotope assay evidence that is used in a manual assertion. ECO:MCC A type of radioimmunoassay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:28:04Z eco ECO:0001255 radioimmunoassay evidence used in manual assertion true true A type of radioimmunoassay evidence that is used in a manual assertion. ECO:MCC A type of imaging assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:00Z eco radiologic test evidence ECO:0001256 imaging assay evidence used in manual assertion true true A type of imaging assay evidence that is used in a manual assertion. ECO:MCC A type of restriction fragment detection evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:05Z eco ECO:0001257 restriction fragment detection evidence used in manual assertion true true A type of restriction fragment detection evidence that is used in a manual assertion. ECO:MCC A type of spectrophotometry evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:09Z eco ECO:0001258 spectrophotometry evidence used in manual assertion true true A type of spectrophotometry evidence that is used in a manual assertion. ECO:MCC A type of syngeneic transplantation experiment evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:13Z eco ECO:0001259 syngeneic transplantation experiment evidence used in manual assertion true true A type of syngeneic transplantation experiment evidence that is used in a manual assertion. ECO:MCC A type of xenotransplantation experiment evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:18Z xenograft transplantation evidence xenografting evidence xenotransplantation evidence eco tissue grafting ECO:0001260 xenotransplantation experiment evidence used in manual assertion true true A type of xenotransplantation experiment evidence that is used in a manual assertion. ECO:MCC A type of WST-1 assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:22Z metabolic cell proliferation assay evidence eco ECO:0001261 WST-1 assay evidence used in manual assertion true true A type of WST-1 assay evidence that is used in a manual assertion. ECO:MCC A type of urine test evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:30Z eco ECO:0001263 urine test evidence used in manual assertion true true A type of urine test evidence that is used in a manual assertion. ECO:MCC A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:34Z TUNEL assay evidence TdT-mediated dUTP-biotin nick end labeling assay evidence terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence eco ECO:0001264 terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion true true A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence assay evidence that is used in a manual assertion. ECO:MCC A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:38Z eco ECO:0001265 tryptic phosphopeptide mapping assay evidence used in manual assertion true true A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion. ECO:MCC A type of transgenic organism evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:41Z eco ECO:0001266 transgenic organism evidence used in manual assertion true true A type of transgenic organism evidence that is used in a manual assertion. ECO:MCC A type of tissue microarray evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:45Z eco ECO:0001267 tissue microarray evidence used in manual assertion true true A type of tissue microarray evidence that is used in a manual assertion. ECO:MCC A type of TACE activity assay evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:49Z Tumor necrosis factor - alpha converting enzyme activity assay evidence eco ECO:0001268 TACE activity assay evidence used in manual assertion true true A type of TACE activity assay evidence that is used in a manual assertion. ECO:MCC A type of surface plasmon resonance evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:54Z SPR evidence eco ECO:0001269 surface plasmon resonance evidence used in manual assertion true true A type of surface plasmon resonance evidence that is used in a manual assertion. ECO:MCC A type of restriction landmark genome scanning evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:29:58Z RLGS evidence restriction landmark genome scanning evidence eco ECO:0001270 restriction landmark genomic scanning evidence used in manual assertion true true A type of restriction landmark genome scanning evidence that is used in a manual assertion. ECO:MCC A type of resonant mirror biosensor evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T20:30:02Z eco ECO:0001271 resonant mirror biosensor evidence used in manual assertion true true A type of resonant mirror biosensor evidence that is used in a manual assertion. ECO:MCC A type of high-performance liquid chromatography evidence that is used in a manual assertion. mchibucos 2014-03-16T20:49:54Z HPLC evidence eco ECO:0001272 high-performance liquid chromatography evidence used in manual assertion true true A type of high-performance liquid chromatography evidence that is used in a manual assertion. ECO:MCC A type of ectopic expression evidence that is used in a manual assertion. SIB:PG mchibucos 2014-03-17T22:34:56Z eco IMP: analysis of overexpression/ectopic expression phenotype ECO:0001273 ectopic expression evidence used in manual assertion true true A type of ectopic expression evidence that is used in a manual assertion. ECO:MCC A type of direct assay evidence in which the sub-cellular location of a protein or nucleic acid sequence is determined. ECO_ExpGenomicCleanup jbmunro 2018-05-17T12:00:00Z eco ECO:0001533 localization evidence 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. ECO_ExpGenomicCleanup jbmunro 2018-05-17T12:00:00Z eco ECO:0001534 nucleic acid localization evidence A type of direct assay evidence where acetylated residues are detected in a protein. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001546 acetylation assay evidence A type of direct assay evidence where acetylated residues are detected in a protein. SIB:PG url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml A type of direct assay evidence where the cleavage of a protein into protein fragments by a protease is detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001547 cleavage assay evidence A type of direct assay evidence where the cleavage of a protein into protein fragments by a protease is detected. PMID:21121091 PMID:22154596 A type of direct assay evidence where the removal of acetyl groups are detected in a protein. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001548 deacetylation assay evidence A type of direct assay evidence where the removal of acetyl groups are detected in a protein. SIB:PG url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml A type of direct assay evidence where the removal of farnesyl groups from a protein is detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001549 defarnesylation assay evidence A type of direct assay evidence where the removal of farnesyl groups from a protein is detected. PMID:15556768 PMID:16126733 PMID:16507103 SIB:PG A type of direct assay evidence where the removal of methyl groups from a substrate (RNA/DNA or protein) is detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001550 demethylation assay evidence A type of direct assay evidence where the removal of methyl groups from a substrate (RNA/DNA or protein) is detected. SIB:PG url:http://en.wikipedia.org/wiki/Demethylation A type of direct assay evidence where the removal of sumo groups from a protein is detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001551 desumoylation assay evidence A type of direct assay evidence where the removal of sumo groups from a protein is detected. SIB:PG url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/ A type of direct assay evidence where the removal of ubiquitin groups from a protein is detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001552 deubiquitination assay evidence A type of direct assay evidence where the removal of ubiquitin groups from a protein is detected. PMID:19692941 SIB:PG A type of direct assay evidence where farnesylated residues in proteins are detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001553 farnesylation assay evidence A type of direct assay evidence where farnesylated residues in proteins are detected. PMID:9030603 SIB:PG url:http://en.wikipedia.org/wiki/Farnesyltransferase A type of direct assay evidence where methylated residues of a substarte (RNA/DNA or protein) are detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001554 methylation assay evidence A type of direct assay evidence where methylated residues of a substarte (RNA/DNA or protein) are detected. SIB:PG url:http://en.wikipedia.org/wiki/Methylation A type of direct assay evidence where palmitoylated residues in a protein are detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001555 palmitoylation assay evidence A type of direct assay evidence where palmitoylated residues in a protein are detected. PMID:10329400 PMID:17077383 SIB:PG A type of direct assay evidence where the removal of phosphatase groups from a protein is detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001556 phosphatase assay evidence A type of direct assay evidence where the removal of phosphatase groups from a protein is detected. SIB:PG url:http://en.wikipedia.org/wiki/Phosphatase A type of direct assay evidence where ADP-ribosylated residues in proteins are detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001557 polyADP-ribosylation assay evidence A type of direct assay evidence where ADP-ribosylated residues in proteins are detected. PMID:21870253 PMID:2820766 SIB:PG A type of direct assay evidence where phosphorylated residues in proteins are detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001558 protein kinase assay evidence A type of direct assay evidence where phosphorylated residues in proteins are detected. SIB:PG url:http://en.wikipedia.org/wiki/Protein_kinase url:http://en.wikipedia.org/wiki/Protein_phosphorylation A type of direct assay evidence where sumoylated residues on a protein are detected. ECO_AssayCleanup jbmunro 2017-11-30T14:00:00Z eco ECO:0001559 sumoylation assay evidence A type of direct assay evidence where sumoylated residues on a protein are detected. SIB:PG url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/ A type of direct assay evidence where de novo protein synthesis is detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001561 translation assay evidence A type of direct assay evidence where de novo protein synthesis is detected. PMID:18230759 PMID:24901308 SIB:PG A type of direct assay evidence where ubiquitinated residues on a protein are detected. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001562 ubiquitination assay evidence A type of direct assay evidence where ubiquitinated residues on a protein are detected. PMID:19692941 SIB:PG A type of direct assay evidence where biological cell development, i.e. an increase in cell mass and size are measured. ECO_AssayCleanup mchibucos / jbmunro 2017-11-30T14:00:00Z eco ECO:0001563 cell growth assay evidence A type of direct assay evidence where biological cell development, i.e. an increase in cell mass and size are measured. GO:0016049 PMID:11057898 A type of direct assay evidence resulting from the study of cells. jbmunro 2017-11-30T14:00:00Z eco ECO:0001565 cell-based assay evidence A type of protein-binding evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites. swolfish 2015-06-05T14:36:00Z PBM evidence eco ECO:0001601 protein-binding microarray evidence A type of protein-binding evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites. PMID:22146299 A type of cell-based assay evidence in which living cells are stained with a vital stain, i.e. dye that can be used on living cells without causing cell death. swolfish 2015-06-08T11:51:37Z eco vital staining evidence ECO:0001603 cell staining evidence A type of cell-based assay evidence in which living cells are stained with a vital stain, i.e. dye that can be used on living cells without causing cell death. GOC:MAH vital staining evidence GOC:MAH A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing. CollecTF swolfish 2015-10-29T15:53:45Z eco SEAP reporter assay Secreted Embryonic Alkaline Phosphatase reporter assay ECO:0001801 Alkaline phosphatase reporter assay produces a hybrid protein with alkaline phosphatase activity following transportation across the cellular membrane. alkaline phosphatase reporter gene assay evidence A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing. ECO:SW PMID:11823238 A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium. CollecTF swolfish 2015-10-29T15:57:10Z ECO:0000297 LacZ transcript localization evidence beta-gal reporter gene assay beta-galactosidase assay evidence eco lacZ reporter gene assay ECO:0001802 The assay is often performed using a plasmid borne construction on a lacZ strain. beta-galactosidase reporter gene assay evidence A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium. ECO:SW PMID:20439410 A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic. CollecTF swolfish 2015-10-29T16:06:42Z CAT reporter gene assay eco ECO:0001803 The amount of acetylated chloramphenicol is directly proportional to the amount of CAT enzyme present. chloramphenicol acetyltransferase reporter gene assay evidence A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic. ECO:SW PMID:1630936 CAT reporter gene assay PMID:1630936 A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection. CollecTF swolfish 2015-10-29T16:11:02Z GUS reporter gene assay eco ECO:0001804 beta-glucuronidase reporter gene assay evidence A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection. ECO:SW A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence. CollecTF swolfish 2015-10-29T16:15:39Z eco ECO:0001805 luciferase reporter gene assay evidence A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence. ECO:SW PMID:17623934 A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data. CollecTF swolfish 2015-10-29T16:37:36Z ChIP-exo eco ECO:0001806 chromatin immunoprecipitation- exonuclease evidence A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data. ECO:SW PMID:25249628 ChIP-exo PMID:25249628 A type of electrophoretic mobility shift that is used in a manual assertion. swolfish 2015-11-03T12:13:17Z EMSA evidence IDA: electrophoretic mobility shift assay eco gel retardation assay ECO:0001807 electrophoretic mobility shift assay evidence used in manual assertion true true A type of electrophoretic mobility shift that is used in a manual assertion. ECO:SW A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion. swolfish 2015-11-03T12:22:46Z eco ECO:0001808 reverse transcription polymerase chain reaction evidence used in manual assertion true true A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion. ECO:SW A type of chromatography evidence where immobilized promoter DNA is labeled and bound to a matrix through which a protein mixture is poured and then eluted to purify specific DNA binding proteins. CollecTF swolfish 2015-11-03T13:48:49Z eco DNA affinity purification ECO:0001809 Biotinylation is commonly used for labeling and beads are commonly used as the matrix. Bound protein will remain attached to the beads. Results can be detected through gel electrophoresis and then sequenced by mass-spectrometry. This technique can be used to demonstrate binding of a purified protein, or to purify the binding protein from crude extract or protein mixture. DNA affinity chromatography evidence A type of chromatography evidence where immobilized promoter DNA is labeled and bound to a matrix through which a protein mixture is poured and then eluted to purify specific DNA binding proteins. ECO:SW PMID:11694305 PMID:11725488 A type of nucleic acid binding evidence where proteins that have been bound to DNA protect a binding site from enzymatic cleavage with DNAse, thereby detecting protein-DNA interactions. CollecTF swolfish 2015-11-03T13:55:15Z eco DNase protection ECO:0001810 In DNAse footingprinting amplified DNA combined with TF and DNAse is electrophoresed for fragment comparison with a non-TF control sample. TF-bound fragments do not appear in the gel. Such fragments can be isolated, purified, and sequenced. This technique is often used to identify the binding motif of a TF resolving the protected region to 50-100 bp which can be further examined for TF-binding sites. DNAse footprinting evidence A type of nucleic acid binding evidence where proteins that have been bound to DNA protect a binding site from enzymatic cleavage with DNAse, thereby detecting protein-DNA interactions. ECO:SW PMID:212715 PMID:22194258 A type of fluorescence evidence based on rapid and quantitative analysis of diverse molecular interactions, enzyme activities, and nucleic acid hybridization which uses a fluorophore to measure the binding constants and kinetics of reactions that cause a change in the rotational time of the molecules. CollecTF swolfish 2015-11-03T14:01:36Z FA eco FP Fluorescence polarization ECO:0001811 The degree of polarization of a fluorophore is inversely related to its molecular rotation. When the fluorophore is bound to a small molecule, the rate at which it tumbles can decrease significantly from when it is bound tightly to a large protein. If the fluorophore is attached to the larger protein in a binding pair, the difference in polarization between bound and unbound states will be smaller and less accurate. The degree of binding is calculated by using the difference in anisotropy of the partially bound, free, and fully bound states measured by titrating the two binding partners. Fluorescence polarixation assays are homogeneous. fluorescence anisotropy evidence A type of fluorescence evidence based on rapid and quantitative analysis of diverse molecular interactions, enzyme activities, and nucleic acid hybridization which uses a fluorophore to measure the binding constants and kinetics of reactions that cause a change in the rotational time of the molecules. ECO:SW PMID:20232898 FP PMCID:3277431 PMID:20232898 Fluorescence polarization PMCID:3277431 PMID:20232898 A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing. CollecTF swolfish 2015-11-03T14:05:37Z genomic SELEX eco ECO:0001812 The reported sequences should always be verified for presence in the genome sequence. genomic systematic evolution of ligands by exponential amplification evidence A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing. ECO:SW PMID:20541015 PMID:21720957 genomic SELEX PMID:20541015 A type of nuclear magnetic resonance spectroscopy evidence based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum. CollecTF swolfish 2015-11-03T14:11:06Z HSQC eco ECO:0001813 Chemical shifts in the spectrum indicating binding can be detected from analysis of a protein spectrum in the presence or absence of its cognate DNA binding site. heteronuclear single quantum coherence spectroscopy evidence A type of nuclear magnetic resonance spectroscopy evidence based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum. ECO:SW PMID:19856946 HSQC PMID:19856946 A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA. CollecTF swolfish 2015-11-03T14:24:04Z eco MPE Fe(II) footprinting MPE-EDTA Fe(II) footprinting Methidiumpropyl-EDTA Fe(II) footprinting ECO:0001814 methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA. ECO:SW PMID:6225070 MPE Fe(II) footprinting PMID:6225070 MPE-EDTA Fe(II) footprinting PMID:6225070 Methidiumpropyl-EDTA Fe(II) footprinting PMID:6225070 A type of nucleic acid binding evidence where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts. CollecTF swolfish 2015-11-04T08:37:51Z 1,10-Phenanthroline-copper footprinting eco OP-Cu Complex ECO:0001815 copper-phenanthroline footprinting evidence A type of nucleic acid binding evidence where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts. ECO:SW PMID:11691942 1,10-Phenanthroline-copper footprinting PMID:1384472 OP-Cu Complex PMID:1384472 A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light. CollecTF swolfish 2015-11-04T08:58:42Z ECO:0000296 GFP reporter gene assay green fluorescent protein transcript localization evidence eco GFP promoter fusion green fluorescent protein promoter fusion ECO:0001816 green fluorescent protein reporter gene assay evidence A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light. ECO:SW PMID:11989662 GFP reporter gene assay PMID:11989662 A type of protein binding evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions. CollecTF swolfish 2015-11-04T09:05:56Z GST pull-down assay eco ECO:0001817 The recombinant protein can also be eluted following the pull-down and analyzed further with qPCR or sequencing. glutathione S-transferase pull-down assay evidence A type of protein binding evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions. ECO:SW PMID:26096507 GST pull-down assay PMID:26096507 A type of nucleic acid binding evidence used to identify protein-binding sites on the DNA molecule where DNA that has been bound to protein is digested with hydroxyl radical produced by reduction of hydrogen peroxide with iron (II), followed by separating the cleavage products on a denaturing electrophoresis gel. CollecTF swolfish 2015-11-04T09:20:26Z eco ECO:0001818 hydroxyl-radical footprinting evidence A type of nucleic acid binding evidence used to identify protein-binding sites on the DNA molecule where DNA that has been bound to protein is digested with hydroxyl radical produced by reduction of hydrogen peroxide with iron (II), followed by separating the cleavage products on a denaturing electrophoresis gel. ECO:SW PMID:18546600 PMID:19378159 PMID:3090544 A type of transcript expression evidence used to determine expression levels of mRNA where a radiolabeled synthetic oligonucleotide primer is annealed to mRNA at the transcription start site of a gene and the mRNA is extended with reverse transcriptase producing cDNA which is electrophoresed on a polyacrylamide gel and autoradiographed, and the band size is proportional to the initial RNA. CollecTF swolfish 2015-11-04T09:33:18Z eco ECO:0001819 The most commonly used radiolabel is 32P. primer extension assay evidence A type of transcript expression evidence used to determine expression levels of mRNA where a radiolabeled synthetic oligonucleotide primer is annealed to mRNA at the transcription start site of a gene and the mRNA is extended with reverse transcriptase producing cDNA which is electrophoresed on a polyacrylamide gel and autoradiographed, and the band size is proportional to the initial RNA. ECO:SW PMID:23378648 A type of 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. CollecTF swolfish 2015-11-04T09:48:38Z 3’ RACE-PCR 5’ RACE-PCR RACE PCR eco ECO:0001820 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 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. ECO:SW PMID:17498297 PMID:7685466 RACE PCR PMI:17498297 CollecTF swolfish 2015-11-04T10:15:57Z eco ECO:0001821 Use ECO:0000295 (RNA-seq evidence) in place of this term. RNA sequencing assay evidence true A type of knockout evidence based on the survival of an organism in a particular environment where a gene for an enzyme or regulator is knocked out and results are used as a natural reporter. CollecTF swolfish 2015-11-04T10:48:59Z eco ECO:0001822 survival rate analysis evidence A type of knockout evidence based on the survival of an organism in a particular environment where a gene for an enzyme or regulator is knocked out and results are used as a natural reporter. ECO:SW A type of crystallography evidence where a purified sample at high concentration is crystallised and the crystals are exposed to an x ray beam to obtain three dimensional molecular structure of proteins and biological macromolecules. CollecTF swolfish 2015-11-04T10:56:22Z eco ECO:0001823 X-ray crystallography can be used for a crystal used to probe at the tridimensional structure of proteins. In some cases, it is possible to co-crystallize the protein bound to its DNA binding site, providing detail on the particular arrangement of the two components. x-ray crystallography evidence A type of crystallography evidence where a purified sample at high concentration is crystallised and the crystals are exposed to an x ray beam to obtain three dimensional molecular structure of proteins and biological macromolecules. ECO:SW PMID:23135450 PMID:24648090 A type of affinity evidence used to identify DNA binding sites in eukaryotes where Escherichia coli DNA adenine methyltransferase (Dam) is fused to a transcription factor, co-factor, chromatin-associated protein, or nuclear-associated protein, followed by a methyl-dependent PCR to localize methyltransferase in the region of the binding site. CollecTF swolfish 2015-11-05T15:56:13Z DamID eco ECO:0001824 The methylation tag is detected with methylation-sensitive restriction enzymes, DpnI and DpnII. DNA adenine methyltransferase identification evidence true A type of affinity evidence used to identify DNA binding sites in eukaryotes where Escherichia coli DNA adenine methyltransferase (Dam) is fused to a transcription factor, co-factor, chromatin-associated protein, or nuclear-associated protein, followed by a methyl-dependent PCR to localize methyltransferase in the region of the binding site. ECO:SW PMID:16938559 PMID:17545983 PMID:19588092 DamID PMID:19588092 A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction. CollecTF swolfish 2015-11-05T16:06:20Z ITC eco ECO:0001825 When ITC is used to study TF, the temperature of two identical cells containing a known concentration of TF is monitored. After the ligand is added to the cells in precisely measured aliquots, the temperature difference in each cell is observed to determine target binding. This value can be used to compute the energetics of the reaction and hence, binding affinity of the TF for the DNA fragment. The thermodynamic profile that is measured includes the values of binding constant (K(a)), stoichiometry (n), and the enthalpy of binding (DeltaH(b)). isothermal titration calorimetry evidence true A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction. ECO:SW PMID:10527727 ITC PMID:10527727 A type of nucleic acid binding evidence where DNA is non-specifically fragmented with ultraviolet light while protein-bound regions are protected from UV damage and strand breakage patterns are analyzed by PAGE and sequenced to detect protein-DNA contacts. CollecTF swolfish 2015-11-05T16:13:36Z eco UV footprinting ultraviolet footprinting ECO:0001826 ultraviolet light footprinting evidence A type of nucleic acid binding evidence where DNA is non-specifically fragmented with ultraviolet light while protein-bound regions are protected from UV damage and strand breakage patterns are analyzed by PAGE and sequenced to detect protein-DNA contacts. ECO:SW PMID:2842760 PMID:7602584 A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel. CollecTF swolfish 2015-11-05T16:16:27Z methylation interference footprinting evidence eco ECO:0001827 methylation interference footprinting evidence A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel. ECO:SW PMID:1583685 A type of inference from background scientific knowledge used in manual assertion where a visual inspection of promoter region is made to identify putative binding sites. swolfish 2015-11-10T14:40:16Z eco ECO:0001828 visual sequence inspection evidence A type of inference from background scientific knowledge used in manual assertion where a visual inspection of promoter region is made to identify putative binding sites. ECO:SW A type of reporter gene assay evidence used to locate and isolate Fur sites where a plasmid library is created and cloned into a cell line with a ferric uptake regulator (Fur)-repressed reporter and the Fur protein is titrated away from its binding site on the reporter, after which the cell is isolated and plasmid extracted for further sequence analysis. CollecTF swolfish 2015-11-10T14:55:36Z FURTA eco Fluorescence polarization ECO:0001829 ferric uptake regulator titration assay evidence A type of reporter gene assay evidence used to locate and isolate Fur sites where a plasmid library is created and cloned into a cell line with a ferric uptake regulator (Fur)-repressed reporter and the Fur protein is titrated away from its binding site on the reporter, after which the cell is isolated and plasmid extracted for further sequence analysis. ECO:SW PMID:10713425 PMID:7642488 PMID:8107138 FURTA PMID:10713425 Fluorescence polarization PMID:15689115 A type of cell-based assay evidence resulting from analyzing the ability of cells to survive or live successfully. snadendla 2015-02-13T12:08:01Z eco ECO:0005004 cell viability assay evidence A type of cell-based assay evidence resulting from analyzing the ability of cells to survive or live successfully. NBK:144065 A type of cell-based assay evidence resulting from the measurement of the number of cells, which is a reflection of the balance between cell division and cell loss through cell differentiation or cell death. snadendla 2015-02-11T16:27:13Z eco ECO:0005007 cell proliferation assay evidence A type of cell-based assay evidence resulting from the measurement of the number of cells, which is a reflection of the balance between cell division and cell loss through cell differentiation or cell death. ECO:RCT GO:0008283 PMID:11057898 A type of cell proliferation assay evidence resulting from the measure of DNA synthesis in the presece of a label. snadendla 2015-02-11T16:30:10Z eco ECO:0005008 DNA synthesis cell proliferation assay evidence A type of cell proliferation assay evidence resulting from the measure of DNA synthesis in the presece of a label. PMC:3908118 A type of cell viability assay evidence resulting from the analysis of ATP concentration (by measuring light intensity) when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions and molecular oxygen. snadendla 2015-02-11T16:47:30Z eco ECO:0005011 ATP bioluminescence assay evidence A type of cell viability assay evidence resulting from the analysis of ATP concentration (by measuring light intensity) when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions and molecular oxygen. PMID:15344559 A type of cell-based assay evidence resulting from the ability of an agent to induce cellular necrosis or apoptosis and the subsequent analysis of cell death mechanism. snadendla 2015-02-12T11:39:35Z eco ECO:0005012 cytotoxicity assay evidence snadendla 2015-02-12T13:26:55Z eco ECO:0005014 Use children of ECO:0001565 (cell-based assay evidence) in place of this term. in vitro cell based assay evidence true A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image. snadendla 2015-02-19T11:48:57Z eco ECO:0005019 staining evidence A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image. ECO:RCT A type of cell-based assay evidence resulting from the evaluation of chemotactic ability (i.e. the movement, or lack of movement, in response to a chemical stimulus) of prokaryotic or eukaryotic cells. snadendla 2015-02-19T13:10:20Z eco ECO:0005021 chemotaxis assay evidence A type of cell-based assay evidence resulting from the evaluation of chemotactic ability (i.e. the movement, or lack of movement, in response to a chemical stimulus) of prokaryotic or eukaryotic cells. PMC:3667641 A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA. snadendla 2015-03-16T15:33:50Z eco ECO:0005027 genetic transformation evidence A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA. ECO:RCT A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures. snadendla 2015-03-20T12:16:17Z eco ECO:0005031 structure determination evidence A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures. ECO:RCT A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image. snadendla 2015-03-20T12:21:48Z eco ECO:0005033 electron microscopy evidence A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image. ECO:RCT A type of cell-based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis. snadendla 2015-04-07T21:58:24Z eco ECO:0005034 apoptotic assay evidence A type of cell-based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis. ECO:RCT A type of polyADP-ribosylation assay evidence used in an in vivo experiment. snadendla 2015-06-15T15:35:05Z eco ECO:0005500 in vivo polyADP-ribosylation assay evidence A type of polyADP-ribosylation assay evidence used in an in vivo experiment. ECO:SN PMID:2820766 SIB:PG A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion. snadendla 2015-06-15T15:37:23Z eco ECO:0005501 in vivo polyADP-ribosylation assay evidence used in manual assertion true true A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion. ECO:SN A type of direct assay evidence derived by studying an organ, tissues, or cells taken from an organism and studied in an external environment with the minimum alteration of natural conditions. snadendla 2015-06-26T11:46:15Z eco ECO:0005502 ex vivo assay evidence A type of direct assay evidence derived by studying an organ, tissues, or cells taken from an organism and studied in an external environment with the minimum alteration of natural conditions. ECO:SN PMID:16305312 url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf A type of gel electrophoresis evidence that involves one dimension electrophoresis where biomolecules are electrophoresed on a low percentage polyacrylamide gel to be separated in proportion to their mass or isoelectric point, followed by high voltage electrophoresis on a higher percentage gel in the presence of ethidium bromide to alter non-linear molecular shape. CollecTF snadendla 2015-10-01T16:23:20Z 2D PAGE 2D-PAGE eco ECO:0005503 Two-dimensional polyacrylamide gel electrophoresis is commonly employed to establish a proteome for an organism and demonstrate expression changes. two-dimensional polyacrylamide gel electrophoresis evidence A type of gel electrophoresis evidence that involves one dimension electrophoresis where biomolecules are electrophoresed on a low percentage polyacrylamide gel to be separated in proportion to their mass or isoelectric point, followed by high voltage electrophoresis on a higher percentage gel in the presence of ethidium bromide to alter non-linear molecular shape. ECO:SW url:http://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html A type of experimental evidence resulting from the use of a spectrometer. snadendla 2015-08-14T15:48:08Z eco ECO:0005504 spectrometry evidence A type of experimental evidence resulting from the use of a spectrometer. ECO:RCT A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression. CollecTF snadendla 2015-10-09T13:51:52Z eco ECO:0005505 Regular expression is a computational tool used for determining whether a given genome contains a DNA region resembling a transcription factor binding motif. For example A/T=W indicates A or T may be present in a column of the alignment. (PMID: 20708667). regular expression motif search evidence A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression. ECO:SW PMID:17337630 A type of point mutation evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another. snadendla 2015-09-18T16:52:34Z eco ECO:0005506 missense mutation evidence A type of point mutation evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another. SO:0001583 A type of point mutation evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon. snadendla 2015-09-18T16:55:32Z eco ECO:0005507 nonsense mutation evidence A type of point mutation evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon. url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations A type of point mutation evidence resulting from the change of a DNA nucleotide that does not cause any changes in the amino acid sequence. snadendla 2015-09-18T17:01:12Z eco ECO:0005508 silent mutation evidence A type of point mutation evidence resulting from the change of a DNA nucleotide that does not cause any changes in the amino acid sequence. url:http://www.sciencemag.org/news/2006/12/sound-silent-mutation A type of experimental phenotypic evidence resulting from a mutation in which there is an insertion of an additional nucleotide, or nucleotides. snadendla 2015-09-18T17:02:03Z eco ECO:0005509 insertion mutation evidence A type of experimental phenotypic evidence resulting from a mutation in which there is an insertion of an additional nucleotide, or nucleotides. GO:0070705 A type of experimental phenotypic evidence resulting from a mutation in which inserted nucleotide(s) have a sequence identical to, or derived from, adjacent nucleotides. snadendla 2015-09-18T17:03:25Z eco ECO:0005511 duplication mutation evidence A type of experimental phenotypic evidence resulting from a mutation in which inserted nucleotide(s) have a sequence identical to, or derived from, adjacent nucleotides. SO:1000035 A type of experimental phenotypic evidence resulting from any mutation that causes a shift in bases and therefore changes the code for the amino acids. snadendla 2015-09-18T17:05:49Z eco ECO:0005512 frameshift mutation evidence A type of experimental phenotypic evidence resulting from any mutation that causes a shift in bases and therefore changes the code for the amino acids. url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations A type of experimental phenotypic evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated. snadendla 2015-09-18T17:06:34Z eco ECO:0005513 repeat expansion mutation evidence A type of experimental phenotypic evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated. PMID:9397685 url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations A type of experimental phenotypic evidence resulting from a mutation in which there is a change in nucleotides at a splice site snadendla 2015-09-18T17:07:29Z eco ECO:0005514 splice site mutation evidence A type of experimental phenotypic evidence resulting from a mutation in which there is a change in nucleotides at a splice site ECO:RCT A type of experimental phenotypic evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome snadendla 2015-09-18T17:08:01Z eco ECO:0005515 translocation mutation evidence A type of experimental phenotypic evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome ECO:RCT A type of experimental evidence resulting from the detection and analysis of molecular markers. snadendla 2015-09-24T15:54:21Z eco ECO:0005516 molecule detection assay evidence A type of experimental evidence resulting from the detection and analysis of molecular markers. ECO:RCT A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins. snadendla 2015-09-25T14:27:40Z eco ECO:0005517 protein detection assay evidence A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins. ECO:RCT A type of molecule detection assay evidence resulting from the detection of specific RNAs. snadendla 2015-09-25T14:43:53Z eco ECO:0005518 RNA detection assay evidence true A type of molecule detection assay evidence resulting from the detection of specific RNAs. ECO:RCT A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA. snadendla 2015-09-25T19:33:25Z eco ECO:0005519 DNA detection assay evidence A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA. ECO:RCT A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels. CollecTF snadendla 2015-09-28T16:01:01Z IRIS SRIB Spectral Reflectance Imaging Biosensor eco ECO:0005520 Differences in the optical path lengths between a surface layer and a buried silica layer can be measured very precisely allowing optical height information to be converted to accumulated mass on the surface. For the purpose of TF-binding site identification, IRIS is coupled with DNA-arrays with immobilized potential binding regions exposed to the protein of interest and eluted. Protein-bound fragments exhibit changes in reflectance that can be used to gauge binding quantitatively. interferometric reflectance imaging sensor evidence A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels. ECO:SW PMID:21587155 PMID:24271115 A type of nuclease protection assay evidence where RNA is hybridized with complementary DNA probes and exposed to S1 nuclease for unbound RNA degradation after which the intact RNA is run on a gel for probe size determination and RNA identification to detect and map specific RNAs in a complex mixture of total cellular RNA. CollecTF snadendla 2015-09-28T17:16:56Z eco ECO:0005521 S1 nuclease protection assay evidence A type of nuclease protection assay evidence where RNA is hybridized with complementary DNA probes and exposed to S1 nuclease for unbound RNA degradation after which the intact RNA is run on a gel for probe size determination and RNA identification to detect and map specific RNAs in a complex mixture of total cellular RNA. ECO:SW PMID:21390683 A type of DNA detection assay evidence resulting from evaluation of the relative abundance of target sequences hybridizing to DNA samples that are immobilized on a nitrocellulose or nylon membrane. snadendla 2015-09-30T10:03:03Z eco ECO:0005522 DNA dot blot assay evidence A type of DNA detection assay evidence resulting from evaluation of the relative abundance of target sequences hybridizing to DNA samples that are immobilized on a nitrocellulose or nylon membrane. PMID:18265189 A type of DNA dot blot assay evidence that is used in a manual assertion. snadendla 2015-09-30T10:04:00Z eco ECO:0005523 DNA dot blot assay evidence used in manual assertion true true A type of DNA dot blot assay evidence that is used in a manual assertion. ECO:SN ECO:SW A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology. CollecTF snadendla 2015-09-30T10:51:56Z MALDI-TOF Mass Spectrometry MALDI-TOF-MS eco ECO:0005526 MALDI-TOF MS is commonly used for protein identification in constructing a proteome where protein fingerprints obtained by microbial cells are compared with a database of reference spectra by means of various algorithms integrated in systems recently made commercially available. matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology. ECO:SW PMID:21964792 PMID:25354905 A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion. snadendla 2015-09-30T10:58:51Z MALDI-TOF mass spectrometry evidence MALDI-TOF-MS evidence eco ECO:0005527 matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion true true A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion. ECO:SN ECO:SW A type of experimental phenotypic evidence based on target-specified mutagenesis for the characterization of various gene and protein interactions, structures, and functions where oligonucleotide primers are used to alter a nucleotide sequence. CollecTF snadendla 2015-09-30T11:34:41Z site directed mutagenesis eco ECO:0005528 Site-directed mutagenesis is often performed in tandem with EMSA. It is often implemented only in conserved motif positions or serially through all positions of a site. site-directed mutagenesis evidence A type of experimental phenotypic evidence based on target-specified mutagenesis for the characterization of various gene and protein interactions, structures, and functions where oligonucleotide primers are used to alter a nucleotide sequence. ECO:SW PMID:21204030 PMID:24011050 PMID:3541892 A type of experimental phenotypic evidence where radiation or a DNA-damaging agent in vivo, or PCR with degenerate primers in vitro are used for non-targeted mutagenesis. CollecTF snadendla 2015-09-30T11:55:03Z eco ECO:0005529 Random mutagenesis is not often used in TF-binding site determination; however, it is sometimes used to investigate the effect of mutations in TF binding domains in conjunction with expression assays. Random mutations can also be introduced via chemicals, error-prone PCR (EP-PCR), degenerate oligonucleotides-Pfu(DOP), UV irradiation, mutator strains, nucleotide analogs, or DNA recombination. random mutagenesis evidence A type of experimental phenotypic evidence where radiation or a DNA-damaging agent in vivo, or PCR with degenerate primers in vitro are used for non-targeted mutagenesis. ECO:SW PMID:15153637 PMID:18265275 A type of random mutagenesis evidence that is used in a manual assertion. snadendla 2015-09-30T11:57:00Z eco ECO:0005530 random mutagenesis evidence used in manual assertion true true A type of multiple sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs. CollecTF snadendla 2015-09-30T15:04:45Z eco ECO:0005531 Relationship type between sequences (e.g. orthologs from multiple genomes or co-expressed genes in the same genome) is not necessarily assumed. The local multiple sequence alignment is typically ungapped. A common application of motif discovery is to infer the binding motif of a given transcription factor (TF). This can be based on the results of a whole-genome expression analysis, assuming that co-expressed genes are co-regulated by the same TF, from peaks in ChIP-seq experiments with the TF, or from the comparative genomics analysis of the promoter regions of orthologs. motif discovery evidence A type of multiple sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs. ECO:SW PMID:10812473 PMID:16845028 PMID:8211139 Relationship type between sequences (e.g. orthologs from multiple genomes or co-expressed genes in the same genome) is not necessarily assumed. The local multiple sequence alignment is typically ungapped. A common application of motif discovery is to infer the binding motif of a given transcription factor (TF). This can be based on the results of a whole-genome expression analysis, assuming that co-expressed genes are co-regulated by the same TF, from peaks in ChIP-seq experiments with the TF, or from the comparative genomics analysis of the promoter regions of orthologs. PMID:19892760 PMID:23032607 A type of motif similarity evidence where the motif is represented by a consensus sequence which incorporates the most frequent nucleotide at each position acting as a generic representative for the sequences in the alignment, and is compared to the genetic sequence for a perfect or imperfect match. CollecTF snadendla 2015-10-09T14:12:54Z eco ECO:0005532 This technique is used to identify transcription factor binding sites by searching a bacterial genome for DNA regions resembling a given TF-binding motif. PMID: 17085555. consensus search evidence A type of motif similarity evidence where the motif is represented by a consensus sequence which incorporates the most frequent nucleotide at each position acting as a generic representative for the sequences in the alignment, and is compared to the genetic sequence for a perfect or imperfect match. ECO:SW PMID:15130839 A type of motif discovery evidence based on a set of algorithms that infer motifs in non-coding DNA sequences from the conservation of functional regulatory sites through evolution at a higher rate than their local surroundings for the identification of an evolutionary 'footprint'. CollecTF snadendla 2015-09-30T16:23:02Z eco ECO:0005533 The name derives to experimental footprinting techniques where transcription factor (TF)-binding sites are identified by sequencing the region of DNA protected from biochemical agents by the bound TF. This technique is used to identify or verify transcription factor-binding motifs, most commonly in the Eukaryota (PMID: 11997340). phylogenetic footprinting evidence A type of motif discovery evidence based on a set of algorithms that infer motifs in non-coding DNA sequences from the conservation of functional regulatory sites through evolution at a higher rate than their local surroundings for the identification of an evolutionary 'footprint'. ECO:SW PMID:16477324 PMID:3199442 A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes. CollecTF snadendla 2015-10-09T14:30:38Z eco ECO:0005534 This technique is used to predict transcription factor binding sites in gene promoter regions by identifying conserved DNA regions across multiple genomes. PMID: 22305460. Orthology is a typical comparative criterion used. comparative genomics motif search evidence A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes. ECO:SW PMID:10854408 A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences. CollecTF snadendla 2015-10-01T11:58:36Z eco ECO:0005535 Machine learning algorithms include, but are not limited to artificial neural networks, random-forest, k-means clustering, hidden Markov models. This suite of methods can be used to identify or verify transcription factor-binding sites in genomic sequences (PMID: 15703297). machine learning prediction of motif instance evidence A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences. ECO:SW PMID:17117497 PMID:2014171 A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis. CollecTF snadendla 2015-10-09T15:04:35Z PSSM motif search PSSM eco ECO:0005536 This technique is used to predict transcription factor binding sites in gene promoter regions by using a position weight matrix approach. (PMID: 15604457). position-specific scoring matrix motif search evidence A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis. ECO:SW PMID:10812473 A type of reporter gene assay evidence based on the fusion of the xylE gene to a specific promoter for the expression of catechol 2,3-dioxygenase that converts the colorless catechol substrate to yellow 2-hydroxymuconic semialdehyde for identification of the expression of a particular gene. CollecTF snadendla 2015-10-28T15:31:28Z eco ECO:0005537 xylE reporter gene assay evidence A type of reporter gene assay evidence based on the fusion of the xylE gene to a specific promoter for the expression of catechol 2,3-dioxygenase that converts the colorless catechol substrate to yellow 2-hydroxymuconic semialdehyde for identification of the expression of a particular gene. ECO:SW PMID:2592344 snadendla 2015-11-17T15:15:50Z eco ECO:0005538 computationally derived logical inference true snadendla 2015-11-17T15:17:47Z eco ECO:0005539 computationally derived logical inference used in automatic assertion true snadendla 2015-11-17T15:24:42Z eco ECO:0005540 computationally derived logical inference from automatic assertion used in automatic assertion true snadendla 2015-11-17T15:32:03Z eco ECO:0005541 computationally derived logical inference from manual assertion used in automatic assertion true A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion. snadendla 2015-12-16T15:32:41Z eco ECO:0005542 Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof. biological system reconstruction evidence by experimental evidence from single species used in manual assertion true true A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion. ECO:SN PMID:19450514 A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion. snadendla 2015-12-16T15:45:01Z eco ECO:0005543 Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. The evidence may originate from a combination of several experiments. biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion true true A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion. ECO:SN PMID:22232657 A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion. snadendla 2015-12-18T16:20:49Z eco ECO:0005544 Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments. biological system reconstruction evidence based on orthology evidence used in manual assertion true A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion. ECO:SN A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by orthology from an existing experimentally supported model to a process, pathway or complex in another species. snadendla 2015-12-16T15:57:37Z eco ECO:0005545 Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments. biological system reconstruction evidence based on orthology evidence A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by orthology from an existing experimentally supported model to a process, pathway or complex in another species. ECO:SN PMID:15660128 A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion. snadendla 2015-12-16T16:05:15Z eco ECO:0005546 Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments. biological system reconstruction evidence based on paralogy evidence used in manual assertion true A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion. ECO:SN PMID:15660128 A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion. snadendla 2015-12-16T16:07:42Z eco ECO:0005547 Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components. biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion true true A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion. ECO:SN PMID:17876790 A type of biological system reconstruction based solely on background scientific knowledge of that biological system. snadendla 2015-12-18T15:32:15Z eco ECO:0005548 The available knowledge is usually a combination of partial or weak experimental evidence where either some components are missing or no physical interaction evidence can be found but the system is inferred by similarity to related systems in taxonomically-disparate organisms with experimental evidence. Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components. biological system reconstruction evidence based on inference from background scientific knowledge A type of biological system reconstruction based solely on background scientific knowledge of that biological system. ECO:SN PMID:17876790 A type of biological system reconstruction where the evidence is inferred by homology based on conservation of sequence, function, and composition from an existing experimentally supported model to a process, pathway, or complex. snadendla 2015-12-18T15:49:46Z eco ECO:0005549 Inference may be based on paralogy and/or orthology of the genome-encoded components and is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments in the same or another species. biological system reconstruction evidence based on homology evidence A type of biological system reconstruction where the evidence is inferred by homology based on conservation of sequence, function, and composition from an existing experimentally supported model to a process, pathway, or complex. ECO:SN PMID:15660128 A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by paralogy from an existing experimentally supported model to a process, pathway, or complex in the same species. snadendla 2015-12-18T16:24:08Z eco ECO:0005550 Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments. biological system reconstruction evidence based on paralogy evidence A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by paralogy from an existing experimentally supported model to a process, pathway, or complex in the same species. ECO:SN PMID:15660128 A type of biological system reconstruction evidence that uses experimental evidence as support. snadendla 2015-12-18T16:34:13Z eco ECO:0005551 biological system reconstruction evidence by experimental evidence A type of biological system reconstruction evidence that uses experimental evidence as support. ECO:SN PMID:19450514 PMID:22232657 A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment. snadendla 2015-12-18T16:35:13Z eco ECO:0005552 Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. The evidence may originate from a combination of several experiments. biological system reconstruction evidence by experimental evidence from mixed species A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment. ECO:SN PMID:22232657 A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species. snadendla 2015-12-18T16:36:44Z eco ECO:0005553 Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof. biological system reconstruction evidence by experimental evidence from single species A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species. ECO:SN A type of sequence alignment evidence where two sequences are aligned to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid). snadendla 2016-02-08T14:30:46Z eco ECO:0005554 pairwise sequence alignment evidence A type of sequence alignment evidence where two sequences are aligned to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid). ECO:SN url:http://www.ebi.ac.uk/Tools/psa/ A type of sequence alignment evidence where three or more biological sequences (protein or nucleic acid) of similar length are aligned to infer homology and the evolutionary relationships between the sequences studied. CollecTF snadendla 2016-02-08T14:31:24Z eco ECO:0005555 multiple sequence alignment evidence A type of sequence alignment evidence where three or more biological sequences (protein or nucleic acid) of similar length are aligned to infer homology and the evolutionary relationships between the sequences studied. ECO:SN url:http://www.ebi.ac.uk/Tools/msa/ A type of multiple sequence alignment evidence that is used in a manual assertion. snadendla 2016-02-08T14:59:18Z eco ECO:0005556 multiple sequence alignment evidence used in manual assertion true true A type of multiple sequence alignment evidence that is used in a manual assertion. ECO:SN A type of multiple sequence alignment evidence that is used in an automatic assertion. snadendla 2016-02-08T15:00:50Z eco ECO:0005557 multiple sequence alignment evidence used in automatic assertion true true A type of multiple sequence alignment evidence that is used in an automatic assertion. ECO:SN A type of motif discovery evidence that is used in a manual assertion. snadendla 2016-02-08T15:07:47Z eco ECO:0005558 motif discovery evidence used in manual assertion true true A type of motif discovery evidence that is used in a manual assertion. ECO:SN A type of motif discovery evidence that is used in an automatic assertion. snadendla 2016-02-08T15:08:19Z eco ECO:0005559 motif discovery evidence used in automatic assertion true true A type of motif discovery evidence that is used in an automatic assertion. ECO:SN A type of pairwise sequence alignment evidence that is used in a manual assertion. snadendla 2016-02-08T15:17:05Z eco ECO:0005560 pairwise sequence alignment evidence used in manual assertion true true A type of pairwise sequence alignment evidence that is used in a manual assertion. ECO:SN A type of pairwise sequence alignment evidence that is used in an automatic evidence. snadendla 2016-02-08T15:17:52Z eco ECO:0005561 pairwise sequence alignment evidence used in automatic assertion true true A type of pairwise sequence alignment evidence that is used in an automatic evidence. ECO:SN A type of protein kinase assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated kinase substrate. snadendla 2016-02-09T12:05:29Z eco ECO:0005562 in-gel protein kinase assay evidence A type of protein kinase assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated kinase substrate. PMID:12372853 A type of voltage clamp recording evidence that involves recording trace of the current (pA) going through the analyzed ion channels determined from voltage clamp current recording. snadendla 2016-02-09T12:40:03Z eco ECO:0005563 macroscopic current trace evidence A type of voltage clamp recording evidence that involves recording trace of the current (pA) going through the analyzed ion channels determined from voltage clamp current recording. ECO:SN PMID:17938230 url:http://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch03.pdf A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane. snadendla 2016-02-09T12:43:07Z eco ECO:0005564 current density evidence A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane. ECO:SN url:http://circres.ahajournals.org/content/102/11/1298.full url:http://www.bem.fi/book/04/04.htm snadendla 2016-02-09T12:45:42Z eco ECO:0005565 single channel conductance evidence true A type of electrophysiology assay evidence that involves the measurement of the current that persists after the fast and slow inactivation of the analyzed channels. snadendla 2016-02-09T12:46:54Z eco ECO:0005566 sustained current evidence A type of electrophysiology assay evidence that involves the measurement of the current that persists after the fast and slow inactivation of the analyzed channels. ECO:SN url:http://www.nature.com/ncomms/journal/v3/n2/full/ncomms1717.html snadendla 2016-02-09T12:48:17Z eco ECO:0005567 steady state activation curve evidence true snadendla 2016-02-09T12:50:45Z eco ECO:0005568 steady state inactivation curve evidence true snadendla 2016-02-09T12:57:16Z eco ECO:0005569 window current trace evidence true A type of electrophysiology assay evidence in which the amount of current remaining after a series of depolarization at different frequencies described as the normalized current related to the time course. snadendla 2016-02-09T12:58:18Z eco ECO:0005570 use dependence of inactivation evidence A type of electrophysiology assay evidence in which the amount of current remaining after a series of depolarization at different frequencies described as the normalized current related to the time course. ECO:SN url:http://circres.ahajournals.org/content/89/8/700.full A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell. snadendla 2016-02-12T13:58:32Z birnlex:2278 current clamp voltage recording evidence eco ECO:0005571 current clamp recording evidence A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell. ECO:SN url:http://www.nature.com/nprot/journal/v4/n8/full/nprot.2009.91.html birnlex:2278 current clamp voltage recording protocol A type of voltage clamp recording evidence that involves direct measurement of ionic current across a membrane while controlling the membrane potential by maintaining the voltage. snadendla 2016-02-12T14:06:40Z birnlex:2281 eco ECO:0005572 whole-cell voltage clamp recording evidence A type of voltage clamp recording evidence that involves direct measurement of ionic current across a membrane while controlling the membrane potential by maintaining the voltage. ECO:SN url:http://circres.ahajournals.org/content/72/1/91.full.pdf birnlex:2281 whole-cell voltage clamp recording protocol A type of patch-clamp recording evidence that involves isolation of a patch of membrane electrically from the external solution and to record current flowing into the patch and this is achieved by pressing a fire-polished glass pipette, which has been filled with a suitable electrolyte solution, against the surface of a cell and applying light suction. snadendla 2016-02-12T14:07:39Z birnlex:2283 cell-attached patch-clamp recording evidence eco ECO:0005573 cell-attached single-channel recording evidence A type of patch-clamp recording evidence that involves isolation of a patch of membrane electrically from the external solution and to record current flowing into the patch and this is achieved by pressing a fire-polished glass pipette, which has been filled with a suitable electrolyte solution, against the surface of a cell and applying light suction. ECO:SN url:http://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch04.pdf birnlex:2283 cell-attached single-channel recording protocol A type of patch-clamp recording evidence that involves study of individual ion channels by gently pulling the patch of membrane away from the cell, and the patch remains attached to the pipette with its cytoplasmic surface exposed to the bathing solution. snadendla 2016-02-12T14:16:53Z birnlex:2286 cell-detached inside-out patch-clamp recording evidence eco ECO:0005574 cell-detached inside-out single-channel recording evidence A type of patch-clamp recording evidence that involves study of individual ion channels by gently pulling the patch of membrane away from the cell, and the patch remains attached to the pipette with its cytoplasmic surface exposed to the bathing solution. ECO:SN url:http://www.acnp.org/g4/GN401000005/CH005.html birnlex:2286 cell-detached inside-out single-channel recording protocol A type of patch-clamp reocrding evidence that involves ion channel analysis by incorporating the ion channels into liposomes suitable for patch-clamping which allows isolation and study of a specific population of channels into that bilayer membrane. snadendla 2016-02-12T14:17:46Z birnlex:2287 eco ECO:0005575 reconstituted bilayer single-channel patch recording evidence A type of patch-clamp reocrding evidence that involves ion channel analysis by incorporating the ion channels into liposomes suitable for patch-clamping which allows isolation and study of a specific population of channels into that bilayer membrane. ECO:SN url:http://nanion.de/images/stories/papers/Bilayers_lab-on-a-chip08.pdf birnlex:2287 reconstituted bilayer single-channel patch recording protocol A type of electrophysiology assay evidence that involves recording membrane potential by controlling the membrane voltage and measuring the transmembrane current required to maintain that voltage. snadendla 2016-02-12T14:18:36Z birnlex:2279 voltage clamp current recording evidence eco ECO:0005576 voltage clamp recording evidence A type of electrophysiology assay evidence that involves recording membrane potential by controlling the membrane voltage and measuring the transmembrane current required to maintain that voltage. ECO:SN url:http://neurobio.drexelmed.edu/GaoWeb/Resources/Recording%20_Techniques.pdf url:http://www.acnp.org/g4/GN401000005/CH005.html birnlex:2279 voltage clamp current recording protocol A type of electrophysiology assay evidence that involves recording the electrical activity of the brain by means of electrodes placed on the surface of the head. snadendla 2016-02-12T14:19:21Z birnlex:2293 eco ECO:0005577 electroencephalography recording evidence A type of electrophysiology assay evidence that involves recording the electrical activity of the brain by means of electrodes placed on the surface of the head. ECO:SN url:http://www.jove.com/science-education/5420/electro-encephalography-eeg birnlex:2293 electroencephalography recording protocol A type of microscopy evidence where the images are taken with a higher resolution than the diffraction limit that help in studying nanoscopic sub-cellular structures. snadendla 2016-02-12T15:20:47Z eco ECO:0005578 super-resolution microscopy evidence A type of microscopy evidence where the images are taken with a higher resolution than the diffraction limit that help in studying nanoscopic sub-cellular structures. ECO:SN url:http://journal.frontiersin.org/article/10.3389/fncel.2015.00007/full A type of immunogold labelling evidence that is used in a manual assertion. snadendla 2016-02-12T15:38:03Z IDA: immunogold labelling eco ECO:0005579 immunogold labelling evidence used in manual assertion true true A type of immunogold labelling evidence that is used in a manual assertion. ECO:SN A type of flow cytometry evidence that is used in a manual assertion. snadendla 2016-02-12T16:04:23Z FCM eco ECO:0005580 flow cytometry evidence used in manual assertion true true A type of flow cytometry evidence that is used in a manual assertion. ECO:SN A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion. snadendla 2016-02-12T16:23:38Z ELISA evidence|enzyme-linked immunosorbent assay evidence eco ECO:0005581 enzyme-linked immunoabsorbent assay evidence used in manual assertion true true A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion. ECO:SN A type of patch-clamp recording evidence where a part of cellular membrane is detached from the cell and whose external face is exposed to the extracellular medium which allows isolating and studying a single or at least a small number of channels into that fragment (patch). snadendla 2016-03-02T10:47:25Z cell-detached outside-out patch-clamp evidence eco ECO:0005582 cell-detached outside-out single-channel recording evidence A type of patch-clamp recording evidence where a part of cellular membrane is detached from the cell and whose external face is exposed to the extracellular medium which allows isolating and studying a single or at least a small number of channels into that fragment (patch). ECO:SN url:http://www.nature.com/nprot/journal/v2/n11/full/nprot.2007.403.html A type of voltage clamp recording evidence that involves inserting the oocyte in a chamber that separates the surface into 3 regions where the top portion of the oocyte membrane is the region that is clamped from which currents are actually recorded while the bottom portion is the region of the oocyte that is cut-open, making it possible to inject current intracellularly through a low resistance pathway. snadendla 2016-03-02T11:29:32Z eco ECO:0005583 cut-open oocyte voltage clamp recording evidence A type of voltage clamp recording evidence that involves inserting the oocyte in a chamber that separates the surface into 3 regions where the top portion of the oocyte membrane is the region that is clamped from which currents are actually recorded while the bottom portion is the region of the oocyte that is cut-open, making it possible to inject current intracellularly through a low resistance pathway. ECO:SN PMID:9711615 A type of voltage clamp recording evidence where recording is done on a fragment of the cell membrane (attached to or detached from the cell) using a large tip diameter pipette that allows isolating and studying a small number of channels into that fragment (patch). snadendla 2016-03-02T11:33:48Z eco ECO:0005584 macropatch voltage clamp recording evidence A type of voltage clamp recording evidence where recording is done on a fragment of the cell membrane (attached to or detached from the cell) using a large tip diameter pipette that allows isolating and studying a small number of channels into that fragment (patch). ECO:SN url:http://jxb.oxfordjournals.org/content/50/Special_Issue/1037.full.pdf A type of mass spectrometry evidence where mass-to-charge ratio (m/z) of gas-phase ions is measured which is used to identify and quantify molecules in complex solutions within the framework of high throughput studies. snadendla 2016-03-02T12:33:07Z eco ECO:0005585 There are significant differences in data analysis and data evaluation if to compare a HTP mass-spec and a regular mass-spec. The regular mass spec method is quite a reliable technique for identifying a protein molecular weight and analysing its post-modifications, other mass-spec applications might require the additional quality controls and more stringent data evaluation. More complex sample mixture is processed, more quality questions should be addressed, such as a sample contamination and sensitivity of the mass spectrometer while using HTP mass-spec. For HTP mass-spec, the analysis of the small data sets allows to manually assign the spectra to proteins or peptides, but for large data sets only the statistical tools can be used instead. high throughput mass spectrometry evidence A type of mass spectrometry evidence where mass-to-charge ratio (m/z) of gas-phase ions is measured which is used to identify and quantify molecules in complex solutions within the framework of high throughput studies. ECO:SN PMID:20805795 A type of high throughput mass spectrometry evidence that is used in a manual assertion. snadendla 2016-03-02T12:50:02Z eco ECO:0005586 high throughput mass spectrometry evidence used in manual assertion true A type of high throughput mass spectrometry evidence that is used in a manual assertion. ECO:SN A type of microscopy evidence where sharp images are taken by excluding most of the light from the specimen that is not from the microscope's focal plane, thus allowing better contrast and less haze, which makes it possible to build three-dimensional reconstructions of a volume of the specimen by assembling a series of thin slices taken along the vertical axis. snadendla 2016-03-17T12:29:45Z eco ECO:0005587 confocal microscopy evidence A type of microscopy evidence where sharp images are taken by excluding most of the light from the specimen that is not from the microscope's focal plane, thus allowing better contrast and less haze, which makes it possible to build three-dimensional reconstructions of a volume of the specimen by assembling a series of thin slices taken along the vertical axis. ECO:SN url:http://www.physics.emory.edu/faculty/weeks//lab/papers/ebbe05.pdf A type of microscopy evidence where imaging of a thin cell or a tissue specimen is performed by full aperture emission of light gathered by the microscope's objective, which maximizes the recorded signal and simultaneously minimizes the required exposure times. snadendla 2016-03-17T12:30:27Z eco ECO:0005588 wide-field microscopy evidence A type of microscopy evidence where imaging of a thin cell or a tissue specimen is performed by full aperture emission of light gathered by the microscope's objective, which maximizes the recorded signal and simultaneously minimizes the required exposure times. ECO:SN url:http://jcb.rupress.org/content/172/1/9.full url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048960/ url:http://zeiss-campus.magnet.fsu.edu/articles/livecellimaging/techniques.html A type confocal microscopy evidence that is used in a manual assertion. snadendla 2016-03-17T12:32:24Z eco ECO:0005589 confocal microscopy evidence used in manual assertion true true A type confocal microscopy evidence that is used in a manual assertion. ECO:SN A type of wide-field microscopy evidence that is used in a manual assertion. snadendla 2016-03-17T12:34:42Z eco ECO:0005590 wide-field microscopy evidence used in manual assertion true true A type of wide-field microscopy evidence that is used in a manual assertion. ECO:SN A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles. snadendla 2016-03-17T15:43:00Z eco ECO:0005591 immunogold labelling electron microscopy assay evidence A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles. ECO:SN PMID:4110101 A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion. snadendla 2016-03-17T16:39:37Z eco ECO:0005592 immunogold labelling electron microscopy assay evidence used in manual assertion true true true A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion. ECO:SN A type of direct assay evidence that involves the use of antibodies to detect biomolecules. snadendla 2016-03-17T17:07:33Z eco ECO:0005593 immunodetection assay evidence A type of direct assay evidence that involves the use of antibodies to detect biomolecules. ECO:SN A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody. snadendla 2016-03-17T17:11:34Z eco ECO:0005594 immunoperoxidase immunolocalization evidence A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody. ECO:SN A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion. snadendla 2016-03-17T17:14:05Z eco ECO:0005595 immunoperoxidase immunolocalization evidence used in manual assertion true true A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion. ECO:SN A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody. snadendla 2016-03-17T17:16:38Z Immunoperoxidase labelling electron microscopy eco ECO:0005596 immunoperoxidase immunolocalization electron microscopy evidence A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody. ECO:SN A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion. snadendla 2016-03-17T17:23:56Z immunoperoxidase labelling electron microscopy evidence eco ECO:0005597 immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion true true true A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion. ECO:SN A type of wide-field microscopy evidence where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter. snadendla 2016-03-18T11:53:56Z eco ECO:0005598 The optical filter is used to select the wavelength of excitation light. The detection camera is typically a CCD camera. Both topographical and dynamic information of a sample are obtained. wide-field fluorescence microscopy evidence A type of wide-field microscopy evidence where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter. ECO:SN url:http://www.bristol.ac.uk/synaptic/research/techniques/widefield.html A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens. snadendla 2016-03-18T11:55:40Z wide-field epifluorescence microscopy eco ECO:0005599 immunofluorescence wide-field microscopy evidence A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens. ECO:SN url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057135 A type of confocal microscopy evidence where light passes through immunofluorescent-stained tissue sections or cells and then the emitted light passes through the dichroic mirror and is focused onto the pinhole for subsequent detection. snadendla 2016-03-18T12:48:42Z eco ECO:0005600 This allows visualization of sub cellular distribution of biomolecules of interest. immunofluorescence confocal microscopy evidence A type of confocal microscopy evidence where light passes through immunofluorescent-stained tissue sections or cells and then the emitted light passes through the dichroic mirror and is focused onto the pinhole for subsequent detection. ECO:SN url:http://www.physics.emory.edu/faculty/weeks/confocal/ url:https://www.hycultbiotech.com/media/wysiwyg/protocol_Immunofluorescence.pdf A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion. snadendla 2016-03-18T12:52:04Z eco ECO:0005601 immunofluorescence confocal microscopy evidence used in manual assertion true true true A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion. ECO:SN A type of protein expression level evidence where the level of expression of a protein is determined in a cell or tissue extract by western blot technique. snadendla 2016-03-18T13:02:29Z eco ECO:0005602 protein expression level evidence based on western blot A type of protein expression level evidence where the level of expression of a protein is determined in a cell or tissue extract by western blot technique. ECO:SN A type of mass spectrometry evidence where one or more protein analyses are performed. snadendla 2016-03-18T13:11:37Z eco ECO:0005603 protein mass spectrometry evidence A type of mass spectrometry evidence where one or more protein analyses are performed. ECO:SN A type of cell proliferation assay evidence where the investigated organism or a potential antagonist is inoculated so as to grow along the diameter line of the agar medium in a Petri dish, then, potentially susceptible microbes (usually bacteria) are streaked perpendicularly to the growth line and inhibition of growth of a test microbe in the vicinity of that line suggests that the antagonist secretes one or more diffusible antibiotics. snadendla 2016-03-29T15:40:54Z eco ECO:0005604 cross-streak test evidence A type of cell proliferation assay evidence where the investigated organism or a potential antagonist is inoculated so as to grow along the diameter line of the agar medium in a Petri dish, then, potentially susceptible microbes (usually bacteria) are streaked perpendicularly to the growth line and inhibition of growth of a test microbe in the vicinity of that line suggests that the antagonist secretes one or more diffusible antibiotics. ECO:SN url:www.jstor.org/stable/3792785 A type of zone of inhibition evidence where sensitivity/resistance to an antimicrobial agent is tested by impregnating small filter disks with a known concentration of antimicrobial agent which is then placed on a Mueller-Hinton agar plate inoculated with the test organism. snadendla 2016-03-29T16:02:22Z eco ECO:0005605 disk diffusion test evidence A type of zone of inhibition evidence where sensitivity/resistance to an antimicrobial agent is tested by impregnating small filter disks with a known concentration of antimicrobial agent which is then placed on a Mueller-Hinton agar plate inoculated with the test organism. ECO:SN url:http://www.cdc.gov/nczved/resources/cholera/ch9.pdf A type of experimental evidence where a foreign genetic material is introduced into the cell for study of gene function and regulation and protein function. snadendla 2016-03-29T16:59:17Z eco ECO:0005606 cell transfection experiment evidence true A type of experimental evidence where a foreign genetic material is introduced into the cell for study of gene function and regulation and protein function. ECO:SN url:http://ch.promega.com/resources/product-guides-and-selectors/protocols-and-applications-guide/transfection/ url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911531/ A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by observing the rotational behavior of the cells tethered to a coverslip by their flagella. snadendla 2016-03-31T15:51:10Z eco ECO:0005607 tethered cell assay evidence A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by observing the rotational behavior of the cells tethered to a coverslip by their flagella. ECO:SN PMID:1103143 A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by measuring chemotaxis in response to sudden concentration changes from one uniform spatial environment to another. snadendla 2016-03-31T16:42:35Z Temporal assay eco ECO:0005608 tumble frequency assay evidence A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by measuring chemotaxis in response to sudden concentration changes from one uniform spatial environment to another. ECO:SN PMID:4576832 A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the rate of accumulation of the cells into a capillary. snadendla 2016-03-31T16:45:29Z eco ECO:0005609 To determine the presence of negative chemotaxis, a repellent is added to the organismal suspension (but not in the capillary) and the organisms that fled into the capillary are measured. To determine the presence of positive chemotaxis, an attractant is placed in the capillary and the presence of positive chemotaxis is determined based on the amount of organism that accumulated in the capillary. capillary assay evidence A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the rate of accumulation of the cells into a capillary. ECO:SN PMID:4632978 A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion. snadendla 2016-03-31T17:00:03Z eco ECO:0005610 Inference may be based on paralogy and/or orthology of the genome-encoded components and is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments in the same or another species. biological system reconstruction evidence based on homology evidence used in manual assertion true true A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion. ECO:SN A type of direct assay evidence used in manual assertion where phenotype or disease association is made with the gene because of involvement in the molecular mechanism of disease or involvement in a pathway known to contribute to a disease. snadendla 2016-04-12T16:55:16Z IED inferred from experimental data eco ECO:0005611 inference from experimental data evidence A type of direct assay evidence used in manual assertion where phenotype or disease association is made with the gene because of involvement in the molecular mechanism of disease or involvement in a pathway known to contribute to a disease. ECO:SN A type of mutant phenotype evidence used in manual assertion where variations or changes, such as mutations or abnormal levels of the product(s) of a single gene of interest, including non-mutational changes such as inhibition with antibodies or other inhibitors are determined. snadendla 2016-04-12T17:09:43Z IPM inferred from phenotype manipulation eco ECO:0005612 Changes can include any gene mutation/knockout, over-expression or ectopic expression of wild-type or mutant genes, anti-sense experiments, RNAi experiments, specific protein inhibitors. inference from phenotype manipulation evidence A type of mutant phenotype evidence used in manual assertion where variations or changes, such as mutations or abnormal levels of the product(s) of a single gene of interest, including non-mutational changes such as inhibition with antibodies or other inhibitors are determined. ECO:SN A type of natural variation mutant evidence used in manual assertion where alleles are directly linked to phenotype and Mendelian diseases as a result of various experiments. snadendla 2016-04-12T17:24:00Z IAGP inferred by association of genotype from phenotype eco ECO:0005613 Used for 1) polymorphism or segregation of genetic markers (SNPs, mutations, RFLPs, microsatellites); 2) polymorphism or segregation of physical markers (FISH, centromeric or heterochromatic regions, chromosomal banding patterns); 3) detection of polymorphisms in inbred stock. inference by association of genotype from phenotype A type of natural variation mutant evidence used in manual assertion where alleles are directly linked to phenotype and Mendelian diseases as a result of various experiments. ECO:SN A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion. snadendla 2016-05-06T11:03:08Z 2D-PAGE evidence eco ECO:0005614 two-dimensional polyacrylamide gel electrophoresis evidence used in manual assertion true true A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion. ECO:SN A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-06T11:05:59Z eco SEAP reporter assay secreted embryonic alkaline phosphatase reporter assay ECO:0005615 alkaline phosphatase reporter gene assay evidence used in manual assertion true true A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-06T11:08:57Z beta-gal reporter gene assay evidence LacZ transcript localization evidence used in manual assertion eco lacZ reporter gene assay ECO:0005616 beta-galactosidase reporter gene assay evidence used in manual assertion true true A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-06T11:11:07Z CAT reporter gene assay evidence eco ECO:0005617 chloramphenicol acetyltransferase reporter gene assay evidence used in manual assertion true true A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion. snadendla 2016-05-06T11:17:04Z ChIP-chip evidence ChIP-on-chip evidence eco ECO:0005618 chromatin immunoprecipitation-chip evidence used in automatic assertion true true A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion. ECO:SN A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion. snadendla 2016-05-06T11:22:25Z ChIP-exo evidence eco ECO:0005619 chromatin immunoprecipitation- exonuclease evidence used in automatic assertion true true A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion. ECO:SN A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion. snadendla 2016-05-06T11:25:01Z ChIP-PCR evidence eco ECO:0005620 chromatin immunoprecipitation-PCR evidence used in manual assertion true true A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion. ECO:SN A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion. snadendla 2016-05-06T11:29:13Z ChIP-SEQ evidence ChIP-seq evidence eco ECO:0005621 chromatin immunoprecipitation-seq evidence used in automatic assertion true true A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion. ECO:SN A type of comparative genomics motif search evidence that is used in a manual assertion. snadendla 2016-05-06T14:49:36Z eco ECO:0005622 comparative genomics motif search evidence used in manual assertion true true A type of comparative genomics motif search evidence that is used in a manual assertion. ECO:SN A type of comparative genomics motif search evidence that is used in an automatic assertion. snadendla 2016-05-06T14:52:21Z eco ECO:0005623 comparative genomics motif search evidence used in automatic assertion true true A type of comparative genomics motif search evidence that is used in an automatic assertion. ECO:SN A type of consensus search evidence that is used in a manual assertion. snadendla 2016-05-06T14:54:53Z eco ECO:0005624 consensus search evidence used in manual assertion true true A type of consensus search evidence that is used in a manual assertion. ECO:SN A type of consensus search evidence that is used in an automatic assertion. snadendla 2016-05-06T14:58:22Z eco ECO:0005625 consensus search evidence used in automatic assertion true true A type of consensus search evidence that is used in an automatic assertion. ECO:SN A type of copper-phenanthroline footprinting evidence that is used in a manual assertion. snadendla 2016-05-06T15:01:25Z 1,10-phenanthroline-copper footprinting evidence eco OP-Cu Complex ECO:0005626 copper-phenanthroline footprinting evidence used in manual assertion true true A type of copper-phenanthroline footprinting evidence that is used in a manual assertion. ECO:SN A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion. snadendla 2016-05-06T15:05:14Z DamID evidence eco ECO:0005627 DNA adenine methyltransferase identification evidence used in manual assertion true true A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion. ECO:SN A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion. snadendla 2016-05-06T15:06:46Z DamID evidence eco ECO:0005628 DNA adenine methyltransferase identification evidence used in automatic assertion true true A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion. ECO:SN A type of DNA affinity chromatography evidence that is used in a manual assertion. snadendla 2016-05-06T15:08:40Z DNA affinity purification evidence eco ECO:0005629 DNA affinity chromatography evidence used in manual assertion true true A type of DNA affinity chromatography evidence that is used in a manual assertion. ECO:SN A type of cDNA to DNA expression microarray evidence that is used in an automatic assertion. snadendla 2016-05-06T15:31:51Z DNA microarray evidence RNA microarray evidence eco ECO:0005630 cDNA to DNA expression microarray evidence used in automatic assertion true true A type of cDNA to DNA expression microarray evidence that is used in an automatic assertion. ECO:SN A type of DNAse footprinting evidence that is used in a manual assertion. snadendla 2016-05-06T15:35:41Z DNase protection evidence eco ECO:0005631 DNAse footprinting evidence used in manual assertion true true A type of DNAse footprinting evidence that is used in a manual assertion. ECO:SN A type of fluorescence anisotropy evidence that is used in a manual assertion. snadendla 2016-05-06T15:45:40Z FA evidence eco FP fluorescence polarization ECO:0005632 fluorescence anisotropy evidence used in manual assertion true true A type of fluorescence anisotropy evidence that is used in a manual assertion. ECO:SN A type of ferric uptake regulator titration assay evidence that is used in a manual assertion. snadendla 2016-05-06T15:49:18Z FURTA evidence eco ECO:0005633 ferric uptake regulator titration assay evidence used in manual assertion true true A type of ferric uptake regulator titration assay evidence that is used in a manual assertion. ECO:SN A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion. snadendla 2016-05-06T16:41:30Z genomic SELEX evidence eco ECO:0005634 genomic systematic evolution of ligands by exponential amplification evidence used in manual assertion true true A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion. ECO:SN A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion. snadendla 2016-05-06T16:43:03Z genomic SELEX evidence eco ECO:0005635 genomic systematic evolution of ligands by exponential amplification evidence used in automatic assertion true true A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion. ECO:SN A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-06T16:46:32Z GFP reporter gene assay evidence green fluorescent protein transcript localization evidence used in manual assertion eco GFP promoter fusion green fluorescent protein promoter fusion ECO:0005636 green fluorescent protein reporter gene assay evidence used in manual assertion true true A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion. snadendla 2016-05-06T16:48:29Z GFP reporter gene assay evidence green fluorescent protein transcript localization evidence used in automatic assertion eco GFP promoter fusion green fluorescent protein promoter fusion ECO:0005637 green fluorescent protein reporter gene assay evidence used in automatic assertion true true A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion. ECO:SN A type of cell growth regulation assay evidence that is used in a manual assertion. snadendla 2016-05-06T16:52:15Z eco growth curve analysis ECO:0005638 cell growth regulation assay evidence used in manual assertion true true A type of cell growth regulation assay evidence that is used in a manual assertion. ECO:SN A type of cell growth regulation assay evidence that is used in an automatic assertion. snadendla 2016-05-06T16:53:28Z eco growth curve analysis ECO:0005639 cell growth regulation assay evidence used in automatic assertion true true A type of cell growth regulation assay evidence that is used in an automatic assertion. ECO:SN A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion. snadendla 2016-05-06T16:56:39Z GST pull-down assay evidence eco ECO:0005640 glutathione S-transferase pull-down assay evidence used in manual assertion true true A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion. ECO:SN A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-06T16:58:29Z GUS reporter gene assay evidence eco ECO:0005641 beta-glucuronidase reporter gene assay evidence used in manual assertion true true A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion. snadendla 2016-05-06T23:10:13Z HSQC evidence eco ECO:0005642 heteronuclear single quantum coherence spectroscopy evidence used in manual assertion true true A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion. ECO:SN A type of hydroxyl-radical footprinting evidence that is used in a manual assertion. snadendla 2016-05-06T23:14:48Z eco ECO:0005643 hydroxyl-radical footprinting evidence used in manual assertion true true A type of hydroxyl-radical footprinting evidence that is used in a manual assertion. ECO:SN A type of immunoprecipitation evidence that is used in a manual assertion. snadendla 2016-05-06T23:20:49Z IDA: immunoprecipitation eco ECO:0005644 immunoprecipitation evidence used in manual assertion true true A type of immunoprecipitation evidence that is used in a manual assertion. ECO:SN A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion. snadendla 2016-05-06T23:27:58Z IRIS evidence SRIB evidence spectral reflectance imaging biosensor evidence eco ECO:0005645 interferometric reflectance imaging sensor evidence used in manual assertion true true A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion. ECO:SN A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion. snadendla 2016-05-06T23:29:23Z IRIS evidence SRIB evidence spectral reflectance imaging biosensor evidence eco ECO:0005646 interferometric reflectance imaging sensor evidence used in automatic assertion true true A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion. ECO:SN A type of isothermal titration calorimetry evidence that is used in a manual assertion. snadendla 2016-05-06T23:36:26Z ITC evidence eco ECO:0005647 isothermal titration calorimetry evidence used in manual assertion true true A type of isothermal titration calorimetry evidence that is used in a manual assertion. ECO:SN A type of luciferase reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-06T23:44:52Z eco ECO:0005648 luciferase reporter gene assay evidence used in manual assertion true true A type of luciferase reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of machine learning prediction of motif instance evidence that is used in a manual assertion. snadendla 2016-05-06T23:51:30Z eco ECO:0005649 machine learning prediction of motif instance evidence used in manual assertion true true A type of machine learning prediction of motif instance evidence that is used in a manual assertion. ECO:SN A type of machine learning prediction of motif instance evidence that is used in an automatic assertion. snadendla 2016-05-06T23:54:00Z eco ECO:0005650 machine learning prediction of motif instance evidence used in automatic assertion true true A type of machine learning prediction of motif instance evidence that is used in an automatic assertion. ECO:SN A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion. snadendla 2016-05-06T23:57:30Z MALDI-TOF mass spectrometry evidence MALDI-TOF-MS evidence eco ECO:0005651 matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in automatic assertion true true A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion. ECO:SN A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion. snadendla 2016-05-09T14:42:28Z MPE-EDTA Fe(II) footprinting evidence Methidiumpropyl-EDTA Fe(II) footprinting evidence eco MPE Fe(II) footprinting ECO:0005652 methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in manual assertion true true A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion. ECO:SN A type of northern assay evidence that is used in a manual assertion. snadendla 2016-05-09T14:48:03Z RNA blot evidence northern assay evidence eco IEP: transcript levels (e.g. Northerns) ECO:0005653 northern assay evidence used in manual assertion true true A type of northern assay evidence that is used in a manual assertion. ECO:SN A type of phylogenetic footprinting evidence that is used in a manual assertion. snadendla 2016-05-09T14:50:52Z eco ECO:0005654 phylogenetic footprinting evidence used in manual assertion true true A type of phylogenetic footprinting evidence that is used in a manual assertion. ECO:SN A type of phylogenetic footprinting evidence that is used in an automatic assertion. snadendla 2016-05-09T14:51:55Z eco ECO:0005655 phylogenetic footprinting evidence used in automatic assertion true true A type of phylogenetic footprinting evidence that is used in an automatic assertion. ECO:SN A type of methylation interference footprinting evidence that is used in a manual assertion. snadendla 2016-05-09T14:55:25Z premethylation interference footprinting evidence used in manual assertion eco ECO:0005656 methylation interference footprinting evidence used in manual assertion true true A type of methylation interference footprinting evidence that is used in a manual assertion. ECO:SN A type of primer extension assay evidence that is used in a manual assertion. snadendla 2016-05-09T14:58:38Z eco ECO:0005657 primer extension assay evidence used in manual assertion true true A type of primer extension assay evidence that is used in a manual assertion. ECO:SN A type of position-specific scoring matrix motif search evidence that is used in a manual assertion. snadendla 2016-05-09T15:01:31Z PSSM motif search evidence eco ECO:0005658 position-specific scoring matrix motif search evidence used in manual assertion true true A type of position-specific scoring matrix motif search evidence that is used in a manual assertion. ECO:SN A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion. snadendla 2016-05-09T15:02:31Z PSSM motif search evidence eco ECO:0005659 position-specific scoring matrix motif search evidence used in automatic assertion true true A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion. ECO:SN A type of quantitative polymerase chain reaction evidence that is used in a manual assertion. snadendla 2016-05-09T15:09:01Z eco ECO:0005660 quantitative polymerase chain reaction evidence used in manual assertion true true A type of quantitative polymerase chain reaction evidence that is used in a manual assertion. ECO:SN A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion. snadendla 2016-05-09T15:19:20Z RACE PCR evidence eco ECO:0005661 rapid amplification of cDNA ends polymerase chain reaction evidence used in manual assertion true true A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion. ECO:SN A type of regular expression motif search evidence that is used in a manual assertion. snadendla 2016-05-09T16:13:55Z eco ECO:0005662 regular expression motif search evidence used in manual assertion true true A type of regular expression motif search evidence that is used in a manual assertion. ECO:SN A type of regular expression motif search evidence that is used in an automatic assertion. snadendla 2016-05-09T16:15:03Z eco ECO:0005663 regular expression motif search evidence used in automatic assertion true true A type of regular expression motif search evidence that is used in an automatic assertion. ECO:SN snadendla 2016-05-09T16:18:35Z eco ECO:0005664 Use ECO:0006068 (RNA-seq evidence used in manual assertion) in place of this term. RNA sequencing assay evidence used in manual assertion true snadendla 2016-05-09T16:19:38Z eco ECO:0005665 Use ECO:0006069 (RNA-seq evidence used in automatic assertion) in place of this term. RNA sequencing assay evidence used in automatic assertion true A type of S1 nuclease protection assay evidence that is used in a manual assertion. snadendla 2016-05-09T16:22:58Z eco ECO:0005666 S1 nuclease protection assay evidence used in manual assertion true true A type of S1 nuclease protection assay evidence that is used in a manual assertion. ECO:SN A type of site-directed mutagenesis evidence that is used in a manual assertion. snadendla 2016-05-09T16:29:13Z site directed mutagenesis evidence eco ECO:0005667 site-directed mutagenesis evidence used in manual assertion true true A type of site-directed mutagenesis evidence that is used in a manual assertion. ECO:SN A type of survival rate analysis evidence that is used in a manual assertion. snadendla 2016-05-09T16:31:08Z eco ECO:0005668 survival rate analysis evidence used in manual assertion true true A type of survival rate analysis evidence that is used in a manual assertion. ECO:SN A type of ultraviolet light footprinting evidence that is used in a manual assertion. snadendla 2016-05-09T16:33:44Z eco UV footprinting ECO:0005669 ultraviolet light footprinting evidence used in manual assertion true true A type of ultraviolet light footprinting evidence that is used in a manual assertion. ECO:SN A type of x-ray crystallography evidence that is used in a manual assertion. snadendla 2016-05-10T11:53:00Z eco ECO:0005670 x-ray crystallography evidence used in manual assertion true true A type of x-ray crystallography evidence that is used in a manual assertion. ECO:SN A type of x-ray crystallography evidence that is used in an automatic assertion. snadendla 2016-05-10T11:54:03Z eco ECO:0005671 x-ray crystallography evidence used in automatic assertion true true A type of x-ray crystallography evidence that is used in an automatic assertion. ECO:SN A type of xylE reporter gene assay evidence that is used in a manual assertion. snadendla 2016-05-10T11:57:15Z eco ECO:0005672 xylE reporter gene assay evidence used in manual assertion true true A type of xylE reporter gene assay evidence that is used in a manual assertion. ECO:SN A type of experimental phenotypic evidence where a non-standard trait (e.g. natural competence) is assessed qualitatively (e.g. presence/absence) and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor. CollecTF snadendla 2016-05-10T12:57:41Z eco ECO:0005673 ad-hoc qualitative phenotype observation evidence A type of experimental phenotypic evidence where a non-standard trait (e.g. natural competence) is assessed qualitatively (e.g. presence/absence) and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor. ECO:SN PMID:15150239 A type of ad-hoc qualitative phenotype observation that is used in a manual assertion. snadendla 2016-05-10T14:28:47Z eco ECO:0005674 ad-hoc qualitative phenotype observation evidence used in manual assertion true true A type of ad-hoc qualitative phenotype observation that is used in a manual assertion. ECO:SN A type of experimental phenotypic evidence where a quantifiable phenotypic trait (e.g. glucose intake) is assessed in a quantitative manner after induction of the regulatory mechanism and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor. CollecTF snadendla 2016-05-10T14:30:50Z eco ECO:0005675 ad-hoc quantitative phenotype observation evidence A type of experimental phenotypic evidence where a quantifiable phenotypic trait (e.g. glucose intake) is assessed in a quantitative manner after induction of the regulatory mechanism and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor. ECO:SN PMID:15150239 A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion. snadendla 2016-05-10T14:34:50Z eco ECO:0005676 ad-hoc quantitative phenotype observation evidence used in manual assertion true true A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion. ECO:SN A direct assay evidence where the activity of a solution is determined by exposing an indicator culture or organism to a series of dilutions and determining the lowest concentration that elicits a biological response. critical dilution assay spot assay For chemicals, bacteriocins, or phage, the indicator culture is typically present in a soft-agar layer on top of nutrient agar and a small quantity of each dilution is spotted onto the soft agar overlay. dilution assay evidence A direct assay evidence where the activity of a solution is determined by exposing an indicator culture or organism to a series of dilutions and determining the lowest concentration that elicits a biological response. http://www.sciencedirect.com/science/article/pii/016770129400068I A type of enzyme assay evidence that is used in a manual assertion. IDA: enzyme assays eco ECO:0005801 enzyme assay evidence used in manual assertion true A type of enzyme assay evidence that is used in a manual assertion. ECO:SN A type of cell transfection experiment evidence that is used in a manual assertion. eco ECO:0005802 cell transfection experiment evidence used in manual assertion true A type of cell transfection experiment evidence that is used in a manual assertion. ECO:SN A type of direct assay evidence where the motility of a cell or cells is determined. eco ECO:0005803 motility assay evidence A type of direct assay evidence where the motility of a cell or cells is determined. ECO:SN A type of immunofluorescence evidence that is used in a manual assertion. IDA: immunofluorescence eco ECO:0005804 immunofluorescence evidence used in manual assertion true A type of immunofluorescence evidence that is used in a manual assertion. ECO:SN A type of yeast 2-hybrid evidence that is used in a manual assertion. IPI: yeast two-hybrid assay eco ECO:0005805 yeast 2-hybrid evidence used in manual assertion true A type of yeast 2-hybrid evidence that is used in a manual assertion. ECO:SN A type of evidence derived from exploiting the CyaA (calmodulin-activated adenylate cyclase toxin) secreted by Bordatella pertussis to synthesize cAMP and alter cellular physiology in a host cell for various biological applications. rctauber 2016-06-15T08:42:16Z eco ECO:0006001 Cya fusion reporter assay evidence A type of evidence derived from exploiting the CyaA (calmodulin-activated adenylate cyclase toxin) secreted by Bordatella pertussis to synthesize cAMP and alter cellular physiology in a host cell for various biological applications. PMID:10217833 PMID:14702323 A type of Cya fusion reporter assay evidence that is used in a manual assertion. CollecTF rctauber 2010-06-15T08:44:10Z eco ECO:0006002 Cya fusion reporter assay evidence used in manual assertion true A type of Cya fusion reporter assay evidence that is used in a manual assertion. ECO:RCT A type of electron microscopy evidence that is used in a manual assertion. rctauber 2016-10-12T12:32:29Z eco ECO:0006003 electron microscopy evidence used in manual assertion true A type of electron microscopy evidence that is used in a manual assertion. ECO:RCT A type of super-resolution microscopy evidence that is used in a manual assertion. rctauber 2016-10-12T12:32:29Z eco ECO:0006004 super-resolution microscopy evidence used in manual assertion true A type of super-resolution microscopy evidence that is used in a manual assertion. ECO:RCT A type of fractionation evidence that is used in a manual assertion. rctauber 2016-10-12T12:32:29Z eco ECO:0006005 fractionation evidence used in manual assertion true A type of fractionation evidence that is used in a manual assertion. ECO:RCT A type of electrophysiology assay evidence that is used in a manual assertion. rctauber 2016-10-12T12:32:29Z eco ECO:0006006 electrophysiology assay evidence used in manual assertion true A type of electrophysiology assay evidence that is used in a manual assertion. ECO:RCT A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion. rctauber 2016-10-21T11:55:53Z ChIP-chip evidence ChIP-on-chip evidence eco ECO:0006007 chromatin immunoprecipitation-chip evidence used in manual assertion true A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion. ECO:RCT A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion. rctauber 2016-10-21T11:55:53Z ChIP-exo eco ECO:0006008 chromatin immunoprecipitation- exonuclease evidence used in manual assertion true A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion. ECO:RCT A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion. rctauber 2016-10-21T11:55:53Z ChIP-SEQ evidence ChIP-seq evidence eco ECO:0006009 chromatin immunoprecipitation-seq evidence used in manual assertion true A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion. ECO:RCT A type of nucleic acid binding evidence in which RNA-binding proteins are identified through cross-linking RNA and proteins by UV light, capturing RNA-protein complexes on oligo(dT) beads, and finally identifying by mass spectrometry. rctauber 2016-10-21T12:28:17Z ultraviolet light cross-linking RNA binding evidence eco ECO:0006010 mRNA interactome capture evidence A type of nucleic acid binding evidence in which RNA-binding proteins are identified through cross-linking RNA and proteins by UV light, capturing RNA-protein complexes on oligo(dT) beads, and finally identifying by mass spectrometry. PMID:27729395 A type of mRNA interactome capture evidence that is used in a manual assertion. rctauber 2016-10-21T12:28:17Z ultraviolet light cross-linking RNA binding evidence eco ECO:0006011 mRNA interactome capture evidence used in manual assertion true A type of mRNA interactome capture evidence that is used in a manual assertion. ECO:RCT A type of electrophysiology assay evidence in which a glass micropipette is sealed to the surface of a cell membrane (patch) to study ion channels. rctauber 2016-11-28T11:44:05Z eco ECO:0006012 patch-clamp recording evidence A type of electrophysiology assay evidence in which a glass micropipette is sealed to the surface of a cell membrane (patch) to study ion channels. ECO:RCT A type of patch-clamp recording evidence that is used in a manual assertion. rctauber 2016-11-28T11:44:05Z eco ECO:0006013 patch-clamp recording evidence used in manual assertion A type of patch-clamp recording evidence that is used in a manual assertion. ECO:RCT A type of patch-clamp recording evidence in which a glass micropipette filled with a prepared solution is used to form a seal with the cell membrane followed by rupture of membrane to provide accurate and high resolution electrical property measurements of the whole cell. rctauber 2016-11-28T11:44:05Z eco ECO:0006014 whole-cell patch-clamp recording evidence A type of patch-clamp recording evidence in which a glass micropipette filled with a prepared solution is used to form a seal with the cell membrane followed by rupture of membrane to provide accurate and high resolution electrical property measurements of the whole cell. PMID:27341060 A type of whole-cell patch-clamp recording evidence that is used in a manual assertion. rctauber 2016-11-28T11:44:05Z eco ECO:0006015 whole-cell patch-clamp recording evidence used in manual assertion A type of whole-cell patch-clamp recording evidence that is used in a manual assertion. ECO:RCT A type of traceable author statement that is based on a publication about a clinical study. rctauber 2016-11-30T09:44:47Z published clinical study evidence eco traceable author statement from published clinical study ECO:0006016 author statement from published clinical study A type of author statement from published clinical study that is used in a manual assertion. rctauber 2016-11-30T09:44:47Z published clinical study evidence PCS eco ECO:0006017 Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used when evidence for an HPO annotation is information extracted from articles in the medical literature. author statement from published clinical study used in manual assertion http://human-phenotype-ontology.github.io/documentation.html#annot true PCS HPO:PCS A type of curator inference that is based on the individual clinical experience of a clinician rctauber 2016-11-30T09:44:47Z individual clinical experience evidence eco ECO:0006018 inference based on individual clinical experience A type of inference based on individual clinical experience that is used in a manual assertion. rctauber 2016-11-30T09:44:47Z individual clinical experience evidence ICE eco ECO:0006019 Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used for annotating disorders with a limited amount of published data, and is accompanied by a reference to the individual or center performing the annotation. inference based on individual clinical experience used in manual assertion http://human-phenotype-ontology.github.io/documentation.html#annot true ICE HPO:ICE A type of cell proliferation assay evidence in which biofilm growth is monitored and detected from attachment to development. rctauber 2016-12-05T09:33:18Z biofilm assay evidence eco ECO:0006020 biofilm formation assay evidence A type of cell proliferation assay evidence in which biofilm growth is monitored and detected from attachment to development. PMID:10547784 A type of biofilm formation assay evidence that is used in a manual assertion. rctauber 2016-12-05T09:33:18Z eco ECO:0006021 biofilm formation assay evidence used in manual assertion true A type of biofilm formation assay evidence that is used in a manual assertion. ECO:RCT A type of biofilm formation assay evidence in which microtiter dishes or tubes are inoculated and incubated to promote biofilm formation, and then biofilms are detected by staining with crystal violet or safranin to observe phenotypes. rctauber 2016-12-05T09:33:18Z 96-well biofilm assay evidence eco ECO:0006022 microtiter plate biofilm assay evidence A type of biofilm formation assay evidence in which microtiter dishes or tubes are inoculated and incubated to promote biofilm formation, and then biofilms are detected by staining with crystal violet or safranin to observe phenotypes. PMID:10547784 A type of microtiter plate biofilm assay evidence that is used in a manual assertion. rctauber 2016-12-05T09:33:18Z eco ECO:0006023 microtiter plate biofilm assay evidence used in manual assertion true A type of microtiter plate biofilm assay evidence that is used in a manual assertion. ECO:RCT A type of biofilm formation assay evidence in which biofilm formation is analyzed, without staining, over 4 to 48 hours by growth on a tilted multiwell plate. rctauber 2016-12-05T09:33:18Z ALI biofilm assay evidence eco ECO:0006024 Tilting of the plate positions the air-liquid interface on a clear portion to improve visability. air-liquid interface assay evidence A type of biofilm formation assay evidence in which biofilm formation is analyzed, without staining, over 4 to 48 hours by growth on a tilted multiwell plate. PMID:18770545 A type of air-liquid interface assay evidence that is used in a manual assertion. rctauber 2016-12-05T09:33:18Z ALI biofilm assay evidence eco ECO:0006025 air-liquid interface assay evidence used in manual assertion true A type of air-liquid interface assay evidence that is used in a manual assertion. ECO:RCT A type of biofilm formation assay evidence in which a colony is grown on a semipermeable membrane on an agar plate. The plate serves to supply nutrients and the semipermeable membrane can be relocated to fresh plates. rctauber 2016-12-05T09:33:18Z eco ECO:0006026 The plates commonly contain different carbon sources or antibiotic treatments to observe properties of the cells. colony biofilm assay evidence A type of biofilm formation assay evidence in which a colony is grown on a semipermeable membrane on an agar plate. The plate serves to supply nutrients and the semipermeable membrane can be relocated to fresh plates. PMID:18770545 A type of colony biofilm assay evidence that is used in a manual assertion. rctauber 2016-12-05T09:33:18Z eco ECO:0006027 colony biofilm assay evidence used in manual assertion true A type of colony biofilm assay evidence that is used in a manual assertion. ECO:RCT A type of biofilm formation assay evidence in which mature bacterial biofilms are grown in a multiwell plate that has a growth medium continually pumped through the wells while waste is continually pumped out. rctauber 2016-12-05T09:33:18Z eco ECO:0006028 Kadouri drip-fed biofilm assay evidence A type of biofilm formation assay evidence in which mature bacterial biofilms are grown in a multiwell plate that has a growth medium continually pumped through the wells while waste is continually pumped out. PMID:18770545 A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion. rctauber 2016-12-05T09:33:18Z eco ECO:0006029 Kadouri drip-fed biofilm assay evidence used in manual assertion true A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion. ECO:RCT A type of co-immunoprecipitation evidence that is used in a manual assertion. rctauber 2016-01-13T11:32:26Z IPI: co-immunoprecipitation eco ECO:0006030 co-immunoprecipitation evidence used in manual assertion true true A type of co-immunoprecipitation evidence that is used in a manual assertion. ECO:RCT A type of immunolocalization evidence that is used in a manual assertion. rctauber 2017-01-23T07:54:37Z IDA: immunolocalization eco ECO:0006031 immunolocalization evidence used in manual assertion true A type of immunolocalization evidence that is used in a manual assertion. ECO:RCT A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators. rctauber 2017-01-23T11:58:48Z optogenetic actuator evidence eco ECO:0006032 optogenetic evidence A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators. GOC:DOS PMID:17035522 A type of optogenetic evidence that is used in a manual assertion. rctauber 2017-01-23T11:58:48Z optogenetic actuator evidence eco ECO:0006033 optogenetic evidence used in manual assertion true A type of optogenetic evidence that is used in a manual assertion. ECO:RCT A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor. rctauber 2017-01-23T11:58:48Z eco ECO:0006034 Examples include sensors for ion concentration and potential difference across a membrane. fluorescent sensor evidence A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor. GOC:DOS A type of fluorescent sensor evidence that is used in a manual assertion. rctauber 2017-01-23T11:58:48Z eco ECO:0006035 fluorescent sensor evidence used in manual assertion true A type of fluorescent sensor evidence that is used in a manual assertion. ECO:RCT A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor. rctauber 2017-01-23T11:58:48Z optogenetic sensor evidence eco ECO:0006036 genetically encoded fluorescent sensor evidence A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor. GOC:DOS A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion. rctauber 2017-01-23T11:58:48Z optogenetic sensor evidence eco ECO:0006037 genetically encoded fluorescent sensor evidence used in manual assertion true A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion. ECO:RCT A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors. rctauber 2017-01-23T11:58:48Z electrophysiology - optical assay evidence eco ECO:0006038 Examples include genetically encoded sensors that detect potential difference across plasma membrane. genetically encoded fluorescent electrophysiology assay evidence A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors. GOC:DOS A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion. rctauber 2017-01-23T11:58:48Z electrophysiology - optical assay evidence eco ECO:0006039 genetically encoded fluorescent electrophysiology assay evidence used in manual assertion true true A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion. ECO:RCT A type of genetically encoded fluorescent electrophysiology assay evidence that is based on direct, quantitative measurement of ion concentration using a genetically encoded fluorescent sensor. rctauber 2017-01-23T11:58:48Z eco ECO:0006040 Examples include the genetically encoded calcium indicator GCaMP. genetically encoded fluorescent ion concentration sensor assay evidence A type of genetically encoded fluorescent electrophysiology assay evidence that is based on direct, quantitative measurement of ion concentration using a genetically encoded fluorescent sensor. GOC:DOS A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion. rctauber 2017-01-23T11:58:48Z eco ECO:0006041 genetically encoded fluorescent ion concentration sensor assay evidence used in manual assertion true A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion. ECO:RCT A type of cell fractionation evidence that is used in a manual assertion. rctauber 2017-02-21T07:26:28Z IDA: cell fractionation eco ECO:0006042 cell fractionation evidence used in manual assertion true A type of cell fractionation evidence that is used in a manual assertion. ECO:RCT A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons. rctauber 2017-02-21T07:26:28Z eco ECO:0006043 extracellular recording evidence A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons. url:http://www.nature.com/subjects/extracellular-recording A type of extracellular recording evidence that is used in a manual assertion. rctauber 2017-02-21T07:26:28Z eco ECO:0006044 extracellular recording evidence used in manual assertion true A type of extracellular recording evidence that is used in a manual assertion. ECO:RCT A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron. rctauber 2017-02-21T07:26:28Z eco ECO:0006045 single-unit extracellular recording evidence A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron. doi:10.1385/0-89603-185-3:1 A type of single-unit extracellular recording evidence that is used in a manual assertion. rctauber 2017-02-21T07:26:28Z eco ECO:0006046 single-unit extracellular recording evidence used in manual assertion true A type of single-unit extracellular recording evidence that is used in a manual assertion. ECO:RCT A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes. rctauber 2017-02-21T07:26:28Z local field potential recording evidence eco ECO:0006047 field potential recording evidence A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes. ECO:RCT A type of field potential recording evidence that is used in a manual assertion. rctauber 2017-02-21T07:26:28Z eco local field potential recording evidence ECO:0006048 field potential recording evidence used in manual assertion true A type of field potential recording evidence that is used in a manual assertion. ECO:RCT A type of genetic transformation evidence that is used in a manual assertion rctauber 02-21-2017T18:98:58Z eco ECO:0006049 genetic transformation evidence used in manual assertion true A type of genetic transformation evidence that is used in a manual assertion ECO:RCT A type of anti-sense experiment evidence that is used in a manual assertion. rctauber 02-21-2017T18:98:58Z IMP: anti-sense experiments eco ECO:0006050 anti-sense experiment evidence used in manual assertion true A type of anti-sense experiment evidence that is used in a manual assertion. ECO:RCT A type of morpholino experiment evidence that is used in a manual assertion. rctauber 02-21-2017T18:98:58Z anti-sense evidence eco ECO:0006051 morpholino experiment evidence used in manual assertion true A type of morpholino experiment evidence that is used in a manual assertion. ECO:RCT A type of RNAi evidence that is used in a manual assertion. rctauber 02-21-2017T18:98:58Z IMP: RNAi experiment eco ECO:0006052 RNAi evidence used in manual assertion true A type of RNAi evidence that is used in a manual assertion. ECO:RCT A type of experimental phenotypic evidence that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist. dosumis 2017-03-07T08:51:02Z eco ECO:0006053 pharmacological assay evidence A type of experimental phenotypic evidence that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist. GOC:DOS A type of experimental phenotypic evidence used in a manual assertion that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist. rctauber 2017-03-07T08:51:02Z eco ECO:0006054 pharmacological assay evidence used in manual assertion true A type of experimental phenotypic evidence used in a manual assertion that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist. GOC:DOS A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel. mchibucos 2017-03-28T14:48:39Z HT evidence high-throughput evidence high throughput cell biology evidence high throughput screening evidence eco ECO:0006055 Some relevant articles include: PMID: 23340846, doi:10.1038/nmeth0607-523 high throughput evidence A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel. ECO:MCC A type of evidence that is used in a manual assertion where data generation is automated with equipment to allow for assaying large numbers of samples or molecules in parallel. rctauber 2017-03-28T14:48:39Z HT evidence high-throughput evidence GOECO:HTP HTP inferred from high throughput experiment eco high throughput cell biology evidence high throughput screening evidence ECO:0006056 high throughput evidence used in manual assertion true A type of evidence that is used in a manual assertion where data generation is automated with equipment to allow for assaying large numbers of samples or molecules in parallel. ECO:RCT GOECO:HTP inferred from high throughput experiment HTP GOECO:HTP inferred from high throughput experiment GOECO:HTP A type of evidence that is used in an automatic assertion where data generation is automated with equipment to allow for assaying samples or molecules in parallel. rctauber 2017-03-28T14:48:39Z HT evidence high-throughput evidence eco high throughput cell biology evidence high throughput screening evidence ECO:0006057 high throughput evidence used in automatic assertion true A type of evidence that is used in an automatic assertion where data generation is automated with equipment to allow for assaying samples or molecules in parallel. ECO:RCT A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel. mchibucos 2017-03-28T14:48:39Z eco omics experiment ECO:0006058 HT methodologies may incorporate techniques from optics, chemistry, biology or image analysis (https://en.wikipedia.org/wiki/High_throughput_biology) high throughput cell biology evidence A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel. ECO:MCC A type of high throughput evidence used in a manual assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel. rctauber 2017-03-28T14:48:39Z eco omics experiment ECO:0006059 high throughput cell biology evidence used in manual assertion true A type of high throughput evidence used in a manual assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel. ECO:RCT A type of high throughput evidence used in an automatic assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel. rctauber 2017-03-28T14:48:39Z eco omics experiment ECO:0006060 high throughput cell biology evidence used in automatic assertion true A type of high throughput evidence used in an automatic assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel. ECO:RCT A type of wide-field fluorescence microscopy evidence used in a manual assertion where fluorescently tagged antibodies are imaged that are used to bind to their antigens. rctauber 2017-05-15T08:57:07Z wide-field epifluorescence microscopy evidence eco ECO:0006061 immunofluorescence wide-field microscopy evidence used in manual assertion true true A type of wide-field fluorescence microscopy evidence used in a manual assertion where fluorescently tagged antibodies are imaged that are used to bind to their antigens. ECO:SN url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057135 A type of wide-field microscopy evidence that is used in a manual assertion where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter. rctauber 2017-05-15T09:01:19Z eco ECO:0006062 wide-field fluorescence microscopy evidence used in manual assertion true A type of wide-field microscopy evidence that is used in a manual assertion where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter. ECO:SN url:http://www.bristol.ac.uk/synaptic/research/techniques/widefield.html A type of experimental phenotypic evidence that is used in a manual assertion where a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product. rctauber 2017-05-15T09:03:49Z eco IMP: analysis of overexpression/ectopic expression phenotype ECO:0006063 over expression analysis evidence used in manual assertion true A type of experimental phenotypic evidence that is used in a manual assertion where a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product. PMID:22419077 A type of cell-free assay evidence that is used in a manual assertion. rctauber 2017-05-15T09:08:17Z in vitro assay evidence eco ECO:0006064 cell-free assay evidence used in manual assertion true A type of cell-free assay evidence that is used in a manual assertion. PMID:18453125 rctauber 2017-05-15T09:11:13Z eco ECO:0006065 Use children of ECO:0001565 (cell-based assay evidence) in place of this term. in vitro cell based assay evidence used in manual assertion true A type of fluorescence evidence where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse. dosumis rctauber 2017-05-16T10:55:40Z FRAP evidence eco ECO:0006066 FRAP is a fluorescence microscopy-based technique. fluorescence recovery after photobleaching evidence A type of fluorescence evidence where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse. PMID:26314367 FRAP is a fluorescence microscopy-based technique. PMID:26314367 A type of fluorescence evidence that is used in a manual assertion where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse. rctauber 2017-05-16T10:55:40Z FRAP evidence eco ECO:0006067 fluorescence recovery after photobleaching evidence used in manual assertion true A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules. rctauber 2017-06-28T10:37:02Z WTSS evidence whole transcriptome shotgun sequencing eco RNA sequencing|differential gene expression evidence from RNA-seq experiment ECO:0006068 RNA-seq evidence used in manual assertion true A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules. ECO:MCC A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules. rctauber 2017-06-28T10:37:02Z WTSS evidence whole transcriptome shotgun sequencing eco RNA sequencing|differential gene expression evidence from RNA-seq experiment ECO:0006069 RNA-seq evidence used in automatic assertion true A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules. ECO:MCC A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues. dosumis rctauber 2017-07-05T09:59:10Z immunolabelling electron microscopy evidence eco ECO:0006070 immuno-labelling electron microscopy evidence A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues. PMID:25151300 A type of electron microscopy evidence used in a manual assertion resulting from the use of antibodies to identify the localization of antigens in cells and tissues. PMID:25151300 dosumis rctauber 2017-07-05T09:59:10Z immunolabelling electron microscopy evidence eco ECO:0006071 immuno-labelling electron microscopy evidence used in manual assertion true A type of electron microscopy evidence used in a manual assertion resulting from the use of antibodies to identify the localization of antigens in cells and tissues. PMID:25151300 A type of super-resolution microscopy evidence resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue. dosumis rctauber 2017-07-05T09:59:10Z eco ECO:0006072 immunofluorescence super resolution microscopy evidence A type of super-resolution microscopy evidence resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue. PMID:19245833 A type of super-resolution microscopy evidence used in a manual assertion resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue. dosumis rctauber 2017-07-05T09:59:10Z eco ECO:0006073 immunofluorescence super resolution microscopy evidence used in manual assertion true A type of super-resolution microscopy evidence used in a manual assertion resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue. PMID:19245833 A type of physical interaction evidence that is used in manual assertion where a cellular component subunit is isolated as part of purification of its larger complex. rctauber 2017-09-14T09:19:19 IPI: co-purification eco ECO:0006074 co-purification evidence used in manual assertion true A type of physical interaction evidence that is used in manual assertion where a cellular component subunit is isolated as part of purification of its larger complex. TAIR:TED A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities. rctauber 2017-09-14T09:19:20 eco ligand binding evidence ECO:0006075 affinity evidence used in manual assertion true A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities. ECO:MCC A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex. rctauber 2017-09-14T09:19:21 eco ECO:0006076 protein binding evidence used in manual assertion true true A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex. GO:0005515 A type of affinity evidence that is used in manual assertion where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein. rctauber 2017-09-14T09:19:22 eco ECO:0006077 hybrid interaction evidence used in manual assertion true A type of affinity evidence that is used in manual assertion where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein. ECO:MCC A type of affinity evidence that is used in manual assertion resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody. rctauber 2017-09-14T09:19:23 eco ECO:0006078 immunological assay evidence used in manual assertion true A type of affinity evidence that is used in manual assertion resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody. ERO:0001362 A type of hybrid interaction evidence that is used in manual assertion that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors. rctauber 2017-09-14T09:19:24 IPI: yeast one-hybrid assay eco ECO:0006079 yeast one-hybrid evidence used in manual assertion true A type of hybrid interaction evidence that is used in manual assertion that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors. ECO:MCC A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein. rctauber 2017-09-14T09:19:25 IPI: split-ubiquitin assay eco ECO:0006080 split-ubiquitin assay evidence used in manual assertion true A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein. PMID:15064465 A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes. rctauber 2017-09-14T09:19:26 IPI: far-Western analysis eco ECO:0006081 far-Western blotting evidence used in manual assertion true A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes. PMID:18079728 A type of affinity evidence that is used in a manual assertion that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound. rctauber 2017-09-14T09:19:27 IDA: affinity chromatography eco ECO:0006082 affinity chromatography evidence used in manual assertion true A type of affinity evidence that is used in a manual assertion that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound. ECO:MCC A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid. rctauber 2017-09-14T09:19:28 eco ECO:0006083 nucleic acid binding evidence used in manual assertion true A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid. GO:0003676 A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer. rctauber 2017-09-14T09:19:29 IDA: ribohomopolymer binding assay eco ECO:0006084 ribohomopolymer binding assay evidence used in manual assertion true A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer. PMC:102612 A type of protein binding evidence that is used in a manual assertion resulting from a metal ion binding to a protein at a specific binding site. rctauber 2017-09-14T09:19:30 eco ECO:0006085 protein:ion binding evidence used in manual assertion true A type of protein binding evidence that is used in a manual assertion resulting from a metal ion binding to a protein at a specific binding site. PMID:2377604 A type of nucleic acid binding evidence that is used in a manual assertion in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins. rctauber 2017-09-14T09:19:31 IDA: Southwestern analysis eco ECO:0006086 Southwestern blot evidence used in manual assertion true A type of nucleic acid binding evidence that is used in a manual assertion in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins. ECO:RCT A type of nucleic acid binding evidence that is used in a manual assertion in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins. rctauber 2017-09-14T09:19:32 IDA: Northwestern analysis eco ECO:0006087 Northwestern blot evidence used in manual assertion true A type of nucleic acid binding evidence that is used in a manual assertion in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins. ECO:RCT A type of evidence that is used in a manual assertion arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand. rctauber 2017-09-14T09:19:33 SELEX evidence in vitro selection evidence eco in vitro evolution evidence ECO:0006088 systematic evolution of ligands by exponential amplification evidence used in manual assertion true A type of evidence that is used in a manual assertion arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand. ECO:MCC A type of hybrid interaction evidence that is used in a manual assertion that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey). rctauber 2017-09-14T09:19:34 B1H evidence eco ECO:0006089 bacterial one-hybrid evidence used in manual assertion true A type of hybrid interaction evidence that is used in a manual assertion that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey). ECO:MCC A type of oligonucleotide microarray evidence that is used in a manual assertion that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites. rctauber 2017-09-14T09:19:35 PBM evidence eco ECO:0006090 protein-binding microarray evidence used in manual assertion true true A type of oligonucleotide microarray evidence that is used in a manual assertion that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites. PMID:22146299 A type of genetic interaction evidence that is used in a manual assertion where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background. rctauber 2017-09-14T09:19:36 IGI: functional complementation eco ECO:0006091 functional complementation evidence used in manual assertion true A type of genetic interaction evidence that is used in a manual assertion where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background. PMID:27403640 A type of functional complementation evidence that is used in a manual assertion that is used in manual assertion resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition. rctauber 2017-09-14T09:19:37 eco ECO:0006092 transgenic rescue experiment evidence used in manual assertion true A type of functional complementation evidence that is used in a manual assertion that is used in manual assertion resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition. url:http://www.nature.com/gt/journal/v11/n15/full/3302282a.html A type of transient rescue experiment evidence that is used in a manual assertion. rctauber 2017-09-14T09:19:38 eco ECO:0006093 transient rescue experiment evidence used in manual assertion true A type of transient rescue experiment evidence that is used in a manual assertion. ECO:RCT A type of genetic interaction evidence that is used in a manual assertion resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation. rctauber 2017-09-14T09:19:39 IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals) eco ECO:0006094 suppressor/enhancer interaction evidence used in manual assertion true A type of genetic interaction evidence that is used in a manual assertion resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation. url:http://www.wormbook.org/chapters/www:geneticsuppression/geneticsuppression.html A type of genetic interaction evidence that is used in a manual assertion that is based on the phenotypic outcome of two mutations in unrelated genetic loci. rctauber 2017-09-14T09:19:40 IGI: double mutant analysis eco ECO:0006095 double mutant phenotype evidence used in manual assertion true A type of genetic interaction evidence that is used in a manual assertion that is based on the phenotypic outcome of two mutations in unrelated genetic loci. ECO:RCT A type of genetic interaction evidence that is used in a manual assertion that is based on the suppression of one allelic effect by an allele at another genetic locus. rctauber 2017-09-14T09:19:41 IGI: epistatic interactions eco ECO:0006096 epistatic interaction evidence used in manual assertion true A type of genetic interaction evidence that is used in a manual assertion that is based on the suppression of one allelic effect by an allele at another genetic locus. PMID:18852697 A type of functional complementation evidence that is used in a manual assertion that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene. rctauber 2017-09-14T09:19:42 IGI: functional complementation in heterologous system eco ECO:0006097 functional complementation in heterologous system evidence used in manual assertion true A type of functional complementation evidence that is used in a manual assertion that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene. TAIR:TED A type of mutant phenotype evidence based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures. pgaudet rctauber 2017-09-18T07:58:28 Ts mutation evidence eco ECO:0006098 temperature-sensitive mutant phenotype evidence A type of mutant phenotype evidence based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures. GOC:PG PMID:19596904 A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures. pgaudet rctauber 2017-09-18T07:58:28 Ts mutation evidence eco ECO:0006099 temperature-sensitive mutant phenotype evidence used in manual assertion true A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures. GOC:PG PMID:19596904 A type of mutant phenotype evidence based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself. pgaudet rctauber 2017-09-18T07:58:28 eco ECO:0006100 recessive mutant phenotype evidence A type of mutant phenotype evidence based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself. GOC:PG NBK:21578 A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself. pgaudet rctauber 2017-09-18T07:58:28 eco ECO:0006101 recessive mutant phenotype evidence used in manual assertion true A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself. GOC:PG NBK:21578 A type of high throughput evidence derived from high throughput analysis of differences in alleles of a corresponding gene. GOC rctauber 2017-10–05T07:39:47Z eco ECO:0007000 high throughput mutant phenotype evidence A type of high throughput evidence derived from high throughput analysis of differences in alleles of a corresponding gene. GO:IMP A type of high throughput evidence that is used in a manual assertion derived from high throughput analysis of differences in alleles of a corresponding gene. GOC rctauber 2017-10–05T07:39:47Z GOECO:HMP HMP inferred from high throughput mutant phenotype eco ECO:0007001 When using the HMP evidence code, the guidelines for IMP should be adhered to (http://geneontology.org/page/imp-inferred-mutant-phenotype) high throughput mutant phenotype evidence used in manual assertion true true A type of high throughput evidence that is used in a manual assertion derived from high throughput analysis of differences in alleles of a corresponding gene. GO:IMP GOECO:HMP inferred from high throughput mutant phenotype HMP GOECO:HMP inferred from high throughput mutant phenotype GOECO:HMP A type of high throughput evidence derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products. GOC rctauber 2017-10–05T07:39:47Z eco ECO:0007002 high throughput genetic interaction evidence A type of high throughput evidence derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products. PMID:11822023 A type of high throughput evidence that is used in a manual assertion derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products. GOC rctauber 2017-10–05T07:39:47Z GOECO:HGI HGI inferred from high throughput genetic interaction eco ECO:0007003 When using the HGI evidence code, the guidelines for IGI should be adhered to (http://geneontology.org/page/igi-inferred-genetic-interaction) high throughput genetic interaction evidence used in manual assertion true true A type of high throughput evidence that is used in a manual assertion derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products. PMID:11822023 GOECO:HGI inferred from high throughput genetic interaction HGI GOECO:HGI inferred from high throughput genetic interaction GOECO:HGI A type of high throughput evidence derived from the high throughput direct measurement of some aspect of a biological feature. GOC rctauber 2017-10–05T07:39:47Z eco ECO:0007004 high throughput direct assay evidence A type of high throughput evidence derived from the high throughput direct measurement of some aspect of a biological feature. ECO:MCC A type of high throughput evidence that is used in a manual assertion derived from the high throughput direct measurement of some aspect of a biological feature. GOC rctauber 2017-10–05T07:39:47Z GOECO:HDA HDA inferred from high throughput direct assay eco ECO:0007005 When using the HDA evidence code, the guidelines for IDA should be adhered to (http://geneontology.org/page/ida-inferred-direct-assay) high throughput direct assay evidence used in manual assertion true true A type of high throughput evidence that is used in a manual assertion derived from the high throughput direct measurement of some aspect of a biological feature. ECO:MCC GOECO:HDA inferred from high throughput direct assay HDA GOECO:HDA inferred from high throughput direct assay GOECO:HDA A type of high throughput evidence derived from the high throughput characterization of gene expression. GOC rctauber 2017-10–05T07:39:47Z eco ECO:0007006 high throughput expression pattern evidence A type of high throughput evidence derived from the high throughput characterization of gene expression. GO:IEP A type of high throughput evidence that is used in a manual assertion derived from the high throughput characterization of gene expression. GOC rctauber 2017-10–05T07:39:47Z GOECO:HEP HEP inferred from high throughput expression pattern eco ECO:0007007 When using the HEP evidence code, the guidelines for EXP should be adhered to (http://geneontology.org/page/iep-inferred-expression-pattern) high throughput expression pattern evidence used in manual assertion true true A type of high throughput evidence that is used in a manual assertion derived from the high throughput characterization of gene expression. GO:IEP GOECO:HEP inferred from high throughput expression pattern HEP GOECO:HEP inferred from high throughput expression pattern GOECO:HEP A type of protein binding evidence in which radioactive ligands are used to measure receptor-ligand interactions, such as in determining selectivity for a particular ligand. fjungo rctauber 2017-12-15T10:46:19Z radioactive ligand binding assay evidence radiometric ligand-binding assay evidence competitive binding assay evidence eco ECO:0007008 radioligand binding assay evidence A type of protein binding evidence in which radioactive ligands are used to measure receptor-ligand interactions, such as in determining selectivity for a particular ligand. PMID:27471749 A type of radioligand binding assay evidence that is used in a manual assertion. rctauber 2017-12-15T10:48:44Z radioactive ligand binding assay evidence eco competitive binding assay evidence ECO:0007009 radioligand binding assay evidence used in manual assertion true A type of radioligand binding assay evidence that is used in a manual assertion. ECO:RCT A type of inferential evidence resulting from a conclusion drawn by the author of the publication. rctauber 2018-02-08T09:11:07Z eco ECO:0007010 author inference A type of inferential evidence resulting from a conclusion drawn by the author of the publication. ECO:RCT A type of combinatorial evidence in which the author draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments. sbello rctauber 2018-02-15T11:17:11Z eco ECO:0007011 combinatorial evidence from author knowledge and experimental evidence true true A type of combinatorial evidence in which the author draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments. ECO:RCT A type of combinatorial evidence in which the curator draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments. ZFIN rctauber 2018-02-15T11:17:11Z eco ECO:0007012 combinatorial evidence from curator knowledge and experimental evidence true true A type of combinatorial evidence in which the curator draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments. ECO:RCT A type of combinatorial evidence from author knowledge and experimental evidence that is used in a manual assertion. rctauber 2018-02-15T11:22:10Z eco ECO:0007013 combinatorial evidence from author knowledge and experimental evidence used in manual assertion true true A type of combinatorial evidence from author knowledge and experimental evidence that is used in a manual assertion. ECO:RCT A type of combinatorial evidence from curator knowledge and experimental evidence that is used in a manual assertion. rctauber 2018-02-15T11:22:10Z eco ECO:0007014 combinatorial evidence from curator knowledge and experimental evidence used in manual assertion true true true A type of combinatorial evidence from curator knowledge and experimental evidence that is used in a manual assertion. ECO:RCT A type of substance quantification evidence where an electrical gradient potential is applied to analyze an analyte of interest, resulting in a measurement amount of electrical current across the potential range applied. SynGO rctauber 2018-02-28T12:11:00Z eco ECO:0007015 voltammetry evidence A type of substance quantification evidence where an electrical gradient potential is applied to analyze an analyte of interest, resulting in a measurement amount of electrical current across the potential range applied. ECO:JBM PMID:28127962 A type of voltammetry evidence that is used in a manual assertion. rctauber 2018-02-28T12:12:34Z eco ECO:0007016 voltammetry evidence used in manual assertion true A type of voltammetry evidence that is used in a manual assertion. ECO:RCT A type of fluorescence evidence where a molecule tagged with a fluorescent protein is exposed to ultraviolet or blue light to shift the spectral emission properties for visualization. SynGO rctauber 2018-03-02T09:01:00Z eco ECO:0007017 photoconversion evidence A type of fluorescence evidence where a molecule tagged with a fluorescent protein is exposed to ultraviolet or blue light to shift the spectral emission properties for visualization. ECO:RCT PMID:28574633 A type of photoconversion evidence that is used in a manual assertion. rctauber 2018-03-02T09:05:04Z eco ECO:0007018 photoconversion evidence used in manual assertion true A type of photoconversion evidence that is used in a manual assertion. ECO:RCT A type of immunological assay evidence that involves observation of visible clumping of antibody and antigen into a complex. OMP snadendla 2018-03-14T12:44:11Z agglutination assay evidence ECO:0007019 agglutination test evidence A type of immunological assay evidence that involves observation of visible clumping of antibody and antigen into a complex. URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC380037/ A type of agglutination test evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z agglutination assay evidence ECO:0007020 agglutination test evidence used in manual assertion true A type of agglutination test evidence that is used in a manual assertion. ECO:RCT A type of agglutination test evidence that involves observaiton of visible clumping of antibody and antigen into a complex on a slide. OMP snadendla 2018-03-14T12:44:11Z ECO:0007021 slide agglutination test evidence A type of agglutination test evidence that involves observaiton of visible clumping of antibody and antigen into a complex on a slide. URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC380037/ A type of slide agglutination test evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007022 slide agglutination test evidence used in manual assertion true A type of slide agglutination test evidence that is used in a manual assertion. ECO:RCT A type of agglutination test evidence that results in detection of nonagglutinating antibodies or complement proteins on red blood cells in vivo. OMP snadendla 2018-03-14T12:44:11Z direct antihuman globulin test (DAT) ECO:0007023 direct Coombs test evidence A type of agglutination test evidence that results in detection of nonagglutinating antibodies or complement proteins on red blood cells in vivo. URL:https://courses.lumenlearning.com/microbiology/chapter/agglutination-assays/ A type of direct Coombs test evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z direct antihuman globulin test (DAT) ECO:0007024 direct Coombs test evidence used in manual assertion true A type of direct Coombs test evidence that is used in a manual assertion. ECO:RCT A type of agglutination test evidence that results in screening of antibodies against red blood cell antigens (other than the A and B antigens) that are unbound in a patient's serum in vitro. OMP snadendla 2018-03-14T12:44:11Z indirect antiglobulin test (IAT) ECO:0007025 indirect Coombs test evidence A type of agglutination test evidence that results in screening of antibodies against red blood cell antigens (other than the A and B antigens) that are unbound in a patient's serum in vitro. URL:https://courses.lumenlearning.com/microbiology/chapter/agglutination-assays/ A type of indirect Coombs test evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z indirect antiglobulin test (IAT) ECO:0007026 indirect Coombs test evidence used in manual assertion true A type of indirect Coombs test evidence that is used in a manual assertion. ECO:RCT A type of agglutination test evidence where some bacteria and viruses cross-link red blood cells and clump together. OMP snadendla 2018-03-14T12:44:11Z ECO:0007027 direct hemagglutination assay evidence A type of agglutination test evidence where some bacteria and viruses cross-link red blood cells and clump together. URL:https://courses.lumenlearning.com/microbiology/chapter/agglutination-assays/ A type of direct hemagglutination assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007028 direct hemagglutination assay evidence used in manual assertion true A type of direct hemagglutination assay evidence that is used in a manual assertion. ECO:RCT A type of agglutination test evidence where antiviral antibodies in a patient's serum or in a lab-produced antiserum neutralize the virus and block it from agglutinating the red blood cells. OMP snadendla 2018-03-14T12:44:11Z ECO:0007029 viral hemagglutination inhibition assay evidence A type of agglutination test evidence where antiviral antibodies in a patient's serum or in a lab-produced antiserum neutralize the virus and block it from agglutinating the red blood cells. URL:https://courses.lumenlearning.com/microbiology/chapter/agglutination-assays/ A type of viral hemagglutination inhibition assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007030 viral hemagglutination inhibition assay evidence used in manual assertion true A type of viral hemagglutination inhibition assay evidence that is used in a manual assertion. ECO:RCT A type of immunological assay evidence that results in the detection of presence of specific antibodies in the patient's serum based on the use of complement, a biologically labile serum factor. OMP snadendla 2018-03-14T12:44:11Z ECO:0007031 compement fixation assay evidence A type of immunological assay evidence that results in the detection of presence of specific antibodies in the patient's serum based on the use of complement, a biologically labile serum factor. URL:http://laboratoryinfo.com/complement-fixation-test/ A type of compement fixation assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007032 compement fixation assay evidence used in manual assertion true A type of compement fixation assay evidence that is used in a manual assertion. ECO:RCT A type of immunogical assay evidence that results in detection of specific neutralizing antibodies in a sample. OMP snadendla 2018-03-14T12:44:11Z ECO:0007033 neutralization test assay evidence A type of immunogical assay evidence that results in detection of specific neutralizing antibodies in a sample. PMID:24899440 url:http://www.creative-biolabs.com/drug-discovery/therapeutics/neutralization-assay.htm?gclid=Cj0KEQjwqvvLBRDIt-D7q7iqiOcBEiQAxi68ERRz00a0x9sWSKSLDu7d5-kMi4AdiLNdUq1mXzePdywaArli8P8HAQ) A type of neutralization test assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007034 neutralization test assay evidence used in manual assertion true A type of neutralization test assay evidence that is used in a manual assertion. ECO:RCT A type of transport assay evidence where the rate of copper transport is estimated. OMP snadendla 2018-03-14T12:44:11Z ECO:0007035 copper transport assay evidence A type of transport assay evidence where the rate of copper transport is estimated. URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689948/ A type of copper transport assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007036 copper transport assay evidence used in manual assertion true A type of copper transport assay evidence that is used in a manual assertion. ECO:RCT A type of staining evidence that involves the use of the redox dye 5-cyano-2,3-ditolyl tetrazolium chloride to evaluate the respiratory activity of cells. OMP snadendla 2018-03-14T12:44:11Z CTC staining ECO:0007037 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence A type of staining evidence that involves the use of the redox dye 5-cyano-2,3-ditolyl tetrazolium chloride to evaluate the respiratory activity of cells. PMID:1622256 A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z CTC staining ECO:0007038 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence used in manual assertion true A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in a manual assertion. ECO:RCT A type of cell growth assay evidence resulting in direct quantification of infectious virons and antiviral substances through the counting of discrete plaques (infectious units and cellular dead zones) in cell culture. OMP snadendla 2018-03-14T12:44:11Z ECO:0007039 plaque assay evidence A type of cell growth assay evidence resulting in direct quantification of infectious virons and antiviral substances through the counting of discrete plaques (infectious units and cellular dead zones) in cell culture. PMID:25407402 A type of plaque assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007040 plaque assay evidence used in manual assertion true A type of plaque assay evidence that is used in a manual assertion. ECO:RCT A type of microscopy evidence where the light source is mounted above the specimen and the excitation light passes through the microscope objective lens on its way toward the specimen. OMP snadendla 2018-03-14T12:44:11Z ECO:0007041 epifluorescence microscopy evidence A type of microscopy evidence where the light source is mounted above the specimen and the excitation light passes through the microscope objective lens on its way toward the specimen. URL:http://www.rsc.org/publishing/journals/prospect/ontology.asp?id=CMO:0001096|URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4713126/ A type of epifluorescence microscopy evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007042 epifluorescence microscopy evidence used in manual assertion true A type of epifluorescence microscopy evidence that is used in a manual assertion. ECO:RCT A type of electron microscopy evidence where a beam of electrons are transmitted through an ultra thin specimen forming an image which is magnified and focused onto an imaging device, such as a fluorescent screen, on a layer of photographic film, or to be detected by a sensor such as a CCD camera. OMP snadendla 2018-03-14T12:44:11Z TEM conventional transmission electron microscopy(CTEM) ECO:0007043 transmission electron microscopy evidence A type of electron microscopy evidence where a beam of electrons are transmitted through an ultra thin specimen forming an image which is magnified and focused onto an imaging device, such as a fluorescent screen, on a layer of photographic film, or to be detected by a sensor such as a CCD camera. ERO:0000329|URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907272/ A type of transmission electron microscopy evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z TEM conventional transmission electron microscopy(CTEM) ECO:0007044 transmission electron microscopy evidence used in manual assertion true A type of transmission electron microscopy evidence that is used in a manual assertion. ECO:RCT A type of electron microscopy evidence where a focused beam of high-energy electrons is used to generate a variety of signals at the surface of solid specimens. OMP snadendla 2018-03-14T12:44:11Z ECO:0007045 scanning electron microscopy evidence A type of electron microscopy evidence where a focused beam of high-energy electrons is used to generate a variety of signals at the surface of solid specimens. URL:https://serc.carleton.edu/research_education/geochemsheets/techniques/SEM.html A type of scanning electron microscopy evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007046 scanning electron microscopy evidence used in manual assertion true A type of scanning electron microscopy evidence that is used in a manual assertion. ECO:RCT A type of microscopy evidence where a serial images are taken at regular time points to capture the dynamics of what is being observed. OMP snadendla 2018-03-14T12:44:11Z ECO:0007047 time-lapsed microscopy evidence A type of microscopy evidence where a serial images are taken at regular time points to capture the dynamics of what is being observed. URL:https://www.nature.com/subjects/time-lapse-imaging A type of time-lapsed microscopy evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007048 time-lapsed microscopy evidence used in manual assertion true A type of time-lapsed microscopy evidence that is used in a manual assertion. ECO:RCT A type of microscopy evidence where a transparent specimen is illuminated with visible light and small phase shifts in the light passing through the specimen are used to produce an image. OMP snadendla 2018-03-14T12:44:11Z ECO:0007049 phase contrast microscopy evidence A type of microscopy evidence where a transparent specimen is illuminated with visible light and small phase shifts in the light passing through the specimen are used to produce an image. CHMO:0000110 A type of phase contrast microscopy evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007050 phase contrast microscopy evidence used in manual assertion true A type of phase contrast microscopy evidence that is used in a manual assertion. ECO:RCT A type of microscopy evidence where a sample is illuminated with transmitted white light from below and observed from above. OMP snadendla 2018-03-14T12:44:11Z ECO:0007051 transmitted light brightfied mircoscopy evidence A type of microscopy evidence where a sample is illuminated with transmitted white light from below and observed from above. BAO:0000457 A type of transmitted light brightfied mircoscopy evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007052 transmitted light brightfied mircoscopy evidence used in manual assertion true A type of transmitted light brightfied mircoscopy evidence that is used in a manual assertion. ECO:RCT A type of microscopy evidence that results in a bright image without glare and minimum heating of the specimen by employing both field and an aperture iris diaphragm for illumination. OMP snadendla 2018-03-14T12:44:11Z ECO:0007053 koehler illumination microscopy evidence A type of microscopy evidence that results in a bright image without glare and minimum heating of the specimen by employing both field and an aperture iris diaphragm for illumination. URL:http://www.gonda.ucla.edu/bri_core/kohler.htm A type of koehler illumination microscopy evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007054 koehler illumination microscopy evidence used in manual assertion true A type of koehler illumination microscopy evidence that is used in a manual assertion. ECO:RCT A type of microscopy evidence that results in visualization of living cells and transparent specimens by taking advantage of differences in the light refraction of different parts of the specimen. OMP snadendla 2018-03-14T12:44:11Z DIC microscopy NIC microscopy Nomarski interference contrast microscopy Nomarski microscopy ECO:0007055 differential interference contrast microscopy evidence A type of microscopy evidence that results in visualization of living cells and transparent specimens by taking advantage of differences in the light refraction of different parts of the specimen. URL:http://www.microscopemaster.com/differential-interference-contrast.html A type of differential interference contrast microscopy evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z DIC microscopy NIC microscopy Nomarski interference contrast microscopy Nomarski microscopy ECO:0007056 differential interference contrast microscopy evidence used in manual assertion true A type of differential interference contrast microscopy evidence that is used in a manual assertion. ECO:RCT A type of confocal microscopy evidence that results in creation of a continuous confocal multi-colour mosaic from thousands of individually captured images. OMP snadendla 2018-03-14T12:44:11Z EFLCM ECO:0007057 extended field laser confocal microscopy evidence A type of confocal microscopy evidence that results in creation of a continuous confocal multi-colour mosaic from thousands of individually captured images. PMID:18627634 A type of extended field laser confocal microscopy evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z EFLCM ECO:0007058 extended field laser confocal microscopy evidence used in manual assertion true A type of extended field laser confocal microscopy evidence that is used in a manual assertion. ECO:RCT A type of confocal microscopy evidence that results in an image that is built up pixel-by-pixel by collecting the emitted photons from the fluorophores in the sample by passing a laser beam through a light source aperture which is then focused by an objective lens into a small area on the surface of the sample. OMP snadendla 2018-03-14T12:44:11Z CLSM LSCM confocal laser scanning fluorescence microscopy confocal-laser scanning microscopy fluorescence confocal scanning laser microscopy scanning confocal fluorescence microscopy ECO:0007059 confocal laser scanning microscopy evidence A type of confocal microscopy evidence that results in an image that is built up pixel-by-pixel by collecting the emitted photons from the fluorophores in the sample by passing a laser beam through a light source aperture which is then focused by an objective lens into a small area on the surface of the sample. URL:http://bitesizebio.com/19958/what-is-confocal-laser-scanning-microscopy/ A type of confocal laser scanning microscopy evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z CLSM LSCM confocal laser scanning fluorescence microscopy confocal-laser scanning microscopy fluorescence confocal scanning laser microscopy scanning confocal fluorescence microscopy ECO:0007060 confocal laser scanning microscopy evidence used in manual assertion true A type of confocal laser scanning microscopy evidence that is used in a manual assertion. ECO:RCT A type of direct assay evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight, diffusion and interaction strength by illuminating the sample with a laser beam and the scattered intensity is probed at a certain angle by a detector. OMP snadendla 2018-03-14T12:44:11Z ECO:0007061 light scattering assay evidence A type of direct assay evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight, diffusion and interaction strength by illuminating the sample with a laser beam and the scattered intensity is probed at a certain angle by a detector. PMID:9013660 url:http://www.lsinstruments.ch/technology/dynamic_light_scattering_dls/ url:http://www.soft-matter.uni-tuebingen.de/index.html?dls.html A type of light scattering assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007062 light scattering assay evidence used in manual assertion true A type of light scattering assay evidence that is used in a manual assertion. ECO:RCT A type of light scattering assay evidence derived by analyzing the fluctuations in the internsity of the scattered light by the particles in motion. OMP snadendla 2018-03-14T12:44:11Z Photon Correlation Spectroscopy Quasi-Elastic Light Scattering ECO:0007063 dynamic light scattering assay evidence A type of light scattering assay evidence derived by analyzing the fluctuations in the internsity of the scattered light by the particles in motion. PMID:9013660 url:http://www.soft-matter.uni-tuebingen.de/index.html?dls.html A type of dynamic light scattering assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z Photon Correlation Spectroscopy Quasi-Elastic Light Scattering ECO:0007064 dynamic light scattering assay evidence used in manual assertion true A type of dynamic light scattering assay evidence that is used in a manual assertion. ECO:RCT A type of light scattering assay evidence derived by measuring the average intensity of scattered light by the particles at multiple angles. OMP snadendla 2018-03-14T12:44:11Z Rayleigh scattering ECO:0007065 static light scattering assay evidence A type of light scattering assay evidence derived by measuring the average intensity of scattered light by the particles at multiple angles. PMID:9013660 A type of static light scattering assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z Rayleigh scattering ECO:0007066 static light scattering assay evidence used in manual assertion true A type of static light scattering assay evidence that is used in a manual assertion. ECO:RCT A type of mutant phenotype evidence derived from formation of papillae that protrude outwards from the main colony by mutant cells. OMP snadendla 2018-03-14T12:44:11Z ECO:0007067 colony papillation assay evidence A type of mutant phenotype evidence derived from formation of papillae that protrude outwards from the main colony by mutant cells. PMID:27447898 A type of colony papillation assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007068 colony papillation assay evidence used in manual assertion true A type of colony papillation assay evidence that is used in a manual assertion. ECO:RCT A type of staining evidence that is derived from the use of gentian violet as a general biological stain and an acid-base indicator. OMP snadendla 2018-03-14T12:44:11Z gentian violet hexamethyl pararosaniline chloride methyl violet 10B ECO:0007069 crystal violet staining evidence A type of staining evidence that is derived from the use of gentian violet as a general biological stain and an acid-base indicator. BAO:0002468 A type of crystal violet staining evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z gentian violet hexamethyl pararosaniline chloride methyl violet 10B ECO:0007070 crystal violet staining evidence used in manual assertion true A type of crystal violet staining evidence that is used in a manual assertion. ECO:RCT A type of biofilm formation assay evidence derived from in vitro cultivation and evaluation of bacterial biofilms under hydrodynamic conditions of flow. OMP snadendla 2018-03-14T12:44:11Z ECO:0007071 flow cell biofilm assay evidence A type of biofilm formation assay evidence derived from in vitro cultivation and evaluation of bacterial biofilms under hydrodynamic conditions of flow. URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438488/ A type of flow cell biofilm assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007072 flow cell biofilm assay evidence used in manual assertion true A type of flow cell biofilm assay evidence that is used in a manual assertion. ECO:RCT A type of hybrid interaction evidence that involves the detection of protein-protein interaction by fusing the protein target (the "bait") to RNA polymerase and fusing protein or peptide library to be analyzed (the "prey") to DNA-binding domain. OMP snadendla 2018-03-14T12:44:11Z ECO:0007073 bacterial 2-hybrid assay evidence A type of hybrid interaction evidence that involves the detection of protein-protein interaction by fusing the protein target (the "bait") to RNA polymerase and fusing protein or peptide library to be analyzed (the "prey") to DNA-binding domain. URL:http://www.pnas.org/content/97/13/7382.full.pdf A type of bacterial 2-hybrid assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007074 bacterial 2-hybrid assay evidence used in manual assertion true A type of bacterial 2-hybrid assay evidence that is used in a manual assertion. ECO:RCT A type of experimental phenotypic evidence that results from the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. OMP snadendla 2018-03-14T12:44:11Z ECO:0007075 phenomic profiling assay evidence A type of experimental phenotypic evidence that results from the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. EDAM:topic:3298 A type of phenomic profiling assay evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007076 phenomic profiling assay evidence used in manual assertion true A type of phenomic profiling assay evidence that is used in a manual assertion. ECO:RCT A type of experimental phenotypic evidence that results from studying the physical characteristics of an assemblage of microorganisms growing on a solid surface such as the surface of an agar culture medium. OMP snadendla 2018-03-14T12:44:11Z ECO:0007077 colony morphology evidence A type of experimental phenotypic evidence that results from studying the physical characteristics of an assemblage of microorganisms growing on a solid surface such as the surface of an agar culture medium. OMP:0000100 A type of colony morphology evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007078 colony morphology evidence used in manual assertion true A type of colony morphology evidence that is used in a manual assertion. ECO:RCT A type of colony morphology evidence that results from studying the colony pigmentation. OMP snadendla 2018-03-14T12:44:11Z colony pigmentation ECO:0007079 colony color evidence A type of colony morphology evidence that results from studying the colony pigmentation. URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671912/ A type of colony color evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z colony pigmentation ECO:0007080 colony color evidence used in manual assertion true A type of colony color evidence that is used in a manual assertion. ECO:RCT A type of colony morphology evidence that results from studying the size of the colony. OMP snadendla 2018-03-14T12:44:11Z ECO:0007081 colony size evidence A type of colony morphology evidence that results from studying the size of the colony. URL:http://www.nature.com/nrmicro/journal/v4/n4/full/nrmicro1384.html A type of colony size evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007082 colony size evidence used in manual assertion true A type of colony size evidence that is used in a manual assertion. ECO:RCT A type of cell growth assay evidence resulting from assessing the sensitivity or resistance of bacteria or fungi to an antimicrobial agent or chemical by measuring the size of the zone of inhibition that results when the test organism is grown on a solid surface in the presence of the antimicrobial agent or chemical. OMP snadendla 2018-03-14T12:44:11Z ECO:0007083 zone of inhibition evidence A type of cell growth assay evidence resulting from assessing the sensitivity or resistance of bacteria or fungi to an antimicrobial agent or chemical by measuring the size of the zone of inhibition that results when the test organism is grown on a solid surface in the presence of the antimicrobial agent or chemical. URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC153338/ A type of zone of inhibition evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z ECO:0007084 zone of inhibition evidence used in manual assertion true A type of zone of inhibition evidence that is used in a manual assertion. ECO:RCT A type of zone of inhibition evidence resulting from testing the antimicrobial susceptibility by using predefined, continuous, and exponential gradient of antibiotic concentrations immobilized along a rectangular plastic test strip. OMP snadendla 2018-03-14T12:44:11Z epsilometer test ECO:0007085 Etest evidence A type of zone of inhibition evidence resulting from testing the antimicrobial susceptibility by using predefined, continuous, and exponential gradient of antibiotic concentrations immobilized along a rectangular plastic test strip. URL:http://www.joponline.org/doi/pdf/10.1902/jop.1992.63.7.576 A type of Etest evidence that is used in a manual assertion. OMP rctauber 2018-03-14T12:44:11Z epsilometer test ECO:0007086 Etest evidence used in manual assertion true A type of Etest evidence that is used in a manual assertion. ECO:RCT A type of expression pattern evidence in which translation is measured by the positions of ribosomes active in a cell, identified through deep sequencing of ribosome-protected mRNA fragments. GOC:VW rctauber 2018-03-28T10:27:09Z ribo-seq evidence ribosome footprinting evidence eco ECO:0007087 ribosome profiling evidence A type of expression pattern evidence in which translation is measured by the positions of ribosomes active in a cell, identified through deep sequencing of ribosome-protected mRNA fragments. PMID:27015305 A type of ribosome profiling evidence that is used in a manual assertion. rctauber 2018-03-28T10:33:26Z ribo-seq evidence ribosome footprinting evidence eco ECO:0007087 ribosome profiling evidence used in manual assertion true A type of ribosome profiling evidence that is used in a manual assertion. ECO:RCT A type of loss-of-function mutant phenotype evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007089 loss-of-function mutant phenotype evidence used in manual assertion true true A type of loss-of-function mutant phenotype evidence that is used in a manual assertion. ECO:RCT A type of structural similarity evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007090 structural similarity evidence used in manual assertion true true A type of structural similarity evidence that is used in a manual assertion. ECO:RCT A type of gain-of-function mutant phenotype evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007092 gain-of-function mutant phenotype evidence used in manual assertion true true A type of gain-of-function mutant phenotype evidence that is used in a manual assertion. ECO:RCT A type of voucher specimen analysis evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007093 voucher specimen analysis evidence used in manual assertion true true A type of voucher specimen analysis evidence that is used in a manual assertion. ECO:RCT A type of positional similarity evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007094 positional similarity evidence used in manual assertion true true A type of positional similarity evidence that is used in a manual assertion. ECO:RCT A type of quantitative trait analysis evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007095 quantitative trait analysis evidence used in manual assertion true true A type of quantitative trait analysis evidence that is used in a manual assertion. ECO:RCT A type of compositional similarity evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007096 compositional similarity evidence used in manual assertion true true A type of compositional similarity evidence that is used in a manual assertion. ECO:RCT A type of developmental similarity evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007097 developmental similarity evidence used in manual assertion true true A type of developmental similarity evidence that is used in a manual assertion. ECO:RCT A type of morphological similarity evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007098 morphological similarity evidence used in manual assertion true true A type of morphological similarity evidence that is used in a manual assertion. ECO:RCT A type of gene expression similarity evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007099 gene expression similarity evidence used in manual assertion true true A type of gene expression similarity evidence that is used in a manual assertion. ECO:RCT A type of methylation-specific polymerase chain reaction evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007100 methylation-specific polymerase chain reaction evidence used in manual assertion true true A type of methylation-specific polymerase chain reaction evidence that is used in a manual assertion. ECO:RCT A type of southern hybridization evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007101 southern hybridization evidence used in manual assertion true true A type of southern hybridization evidence that is used in a manual assertion. ECO:RCT A type of intermethylated site amplification evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007102 intermethylated site amplification evidence used in manual assertion true true A type of intermethylated site amplification evidence that is used in a manual assertion. ECO:RCT A type of epitope-tagged protein immunolocalization evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007103 epitope-tagged protein immunolocalization evidence used in manual assertion true true A type of epitope-tagged protein immunolocalization evidence that is used in a manual assertion. ECO:RCT A type of co-fractionation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007104 co-fractionation evidence used in manual assertion true true A type of co-fractionation evidence that is used in a manual assertion. ECO:RCT A type of green fluorescent protein fusion protein localization evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007106 green fluorescent protein fusion protein localization evidence used in manual assertion true true A type of green fluorescent protein fusion protein localization evidence that is used in a manual assertion. ECO:RCT A type of yellow fluorescent protein fusion protein localization evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007107 yellow fluorescent protein fusion protein localization evidence used in manual assertion true true A type of yellow fluorescent protein fusion protein localization evidence that is used in a manual assertion. ECO:RCT A type of beta-glucuronidase fusion protein localization evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007108 beta-glucuronidase fusion protein localization evidence used in manual assertion true true A type of beta-glucuronidase fusion protein localization evidence that is used in a manual assertion. ECO:RCT A type of beta-galactosidase fusion protein localization evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007109 beta-galactosidase fusion protein localization evidence used in manual assertion true true A type of beta-galactosidase fusion protein localization evidence that is used in a manual assertion. ECO:RCT A type of thin layer chromatography evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007110 thin layer chromatography evidence used in manual assertion true true A type of thin layer chromatography evidence that is used in a manual assertion. ECO:RCT A type of in vitro recombinant protein transcription reconstitution assay evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007111 in vitro recombinant protein transcription reconstitution assay evidence used in manual assertion true true A type of in vitro recombinant protein transcription reconstitution assay evidence that is used in a manual assertion. ECO:RCT A type of protein separation followed by direct sequencing evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007112 protein separation followed by direct sequencing evidence used in manual assertion true true A type of protein separation followed by direct sequencing evidence that is used in a manual assertion. ECO:RCT A type of protein separation followed by fragment identification evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007113 protein separation followed by fragment identification evidence used in manual assertion true true A type of protein separation followed by fragment identification evidence that is used in a manual assertion. ECO:RCT A type of heterologous system uptake evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007114 heterologous system uptake evidence used in manual assertion true true A type of heterologous system uptake evidence that is used in a manual assertion. ECO:RCT A type of two-electrode voltage clamp recording evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007115 two-electrode voltage clamp recording evidence used in manual assertion true true A type of two-electrode voltage clamp recording evidence that is used in a manual assertion. ECO:RCT A type of biochemical trait analysis evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007116 biochemical trait analysis evidence used in manual assertion true true A type of biochemical trait analysis evidence that is used in a manual assertion. ECO:RCT A type of mutant physiological response evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007117 mutant physiological response evidence used in manual assertion true true A type of mutant physiological response evidence that is used in a manual assertion. ECO:RCT A type of mutant visible phenotype evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007118 mutant visible phenotype evidence used in manual assertion true true A type of mutant visible phenotype evidence that is used in a manual assertion. ECO:RCT A type of in vivo assay evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007119 in vivo assay evidence used in manual assertion true true A type of in vivo assay evidence that is used in a manual assertion. ECO:RCT A type of animal model system study evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007120 animal model system study evidence used in manual assertion true true A type of animal model system study evidence that is used in a manual assertion. ECO:RCT A type of clinical study evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007121 clinical study evidence used in manual assertion true true A type of clinical study evidence that is used in a manual assertion. ECO:RCT A type of in vitro assay evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007122 in vitro assay evidence used in manual assertion true true A type of in vitro assay evidence that is used in a manual assertion. ECO:RCT A type of enzyme inhibition evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007123 enzyme inhibition evidence used in manual assertion true true A type of enzyme inhibition evidence that is used in a manual assertion. ECO:RCT A type of Illumina sequencing evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007125 Illumina sequencing evidence used in manual assertion true true A type of Illumina sequencing evidence that is used in a manual assertion. ECO:RCT A type of 454 pyrosequencing evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007126 454 pyrosequencing evidence used in manual assertion true true A type of 454 pyrosequencing evidence that is used in a manual assertion. ECO:RCT A type of SOLiD sequencing evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007127 SOLiD sequencing evidence used in manual assertion true true A type of SOLiD sequencing evidence that is used in a manual assertion. ECO:RCT A type of chain termination sequencing evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007128 chain termination sequencing evidence used in manual assertion true true A type of chain termination sequencing evidence that is used in a manual assertion. ECO:RCT A type of chromatin immunoprecipitation-qPCR evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007129 chromatin immunoprecipitation-qPCR evidence used in manual assertion true true A type of chromatin immunoprecipitation-qPCR evidence that is used in a manual assertion. ECO:RCT A type of 4C evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z circularized chromosome conformation capture evidence used in manual assertion eco ECO:0007130 4C evidence used in manual assertion true true A type of 4C evidence that is used in a manual assertion. ECO:RCT A type of 5C evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z carbon-copy chromosome conformation capture evidence used in manual assertion eco ECO:0007131 5C evidence used in manual assertion true true A type of 5C evidence that is used in a manual assertion. ECO:RCT A type of 3C-qPCR evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z chromosome conformation capture-qPCR evidence used in manual assertion eco ECO:0007133 3C-qPCR evidence used in manual assertion true true A type of 3C-qPCR evidence that is used in a manual assertion. ECO:RCT A type of Hi-C evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007134 Hi-C evidence used in manual assertion true true A type of Hi-C evidence that is used in a manual assertion. ECO:RCT A type of 3C-seq evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z chromosome conformation capture sequencing evidence used in manual assertion eco ECO:0007135 3C-seq evidence used in manual assertion true true A type of 3C-seq evidence that is used in a manual assertion. ECO:RCT A type of environmental perturbation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007136 environmental perturbation evidence used in manual assertion true true A type of environmental perturbation evidence that is used in a manual assertion. ECO:RCT A type of tissue ablation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007137 tissue ablation evidence used in manual assertion true true A type of tissue ablation evidence that is used in a manual assertion. ECO:RCT A type of tissue grafting evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007138 tissue grafting evidence used in manual assertion true true A type of tissue grafting evidence that is used in a manual assertion. ECO:RCT A type of cytochalasin experiment evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007141 cytochalasin experiment evidence used in manual assertion true true A type of cytochalasin experiment evidence that is used in a manual assertion. ECO:RCT A type of green fluorescent protein immunolocalization evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007142 green fluorescent protein immunolocalization evidence used in manual assertion true true A type of green fluorescent protein immunolocalization evidence that is used in a manual assertion. ECO:RCT A type of beta-galactosidase protein immunolocalization evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007143 beta-galactosidase protein immunolocalization evidence used in manual assertion true true A type of beta-galactosidase protein immunolocalization evidence that is used in a manual assertion. ECO:RCT A type of cap analysis of gene expression evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007144 cap analysis of gene expression evidence used in manual assertion true true A type of cap analysis of gene expression evidence that is used in a manual assertion. ECO:RCT A type of nano-cap analysis of gene expression evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007145 nano-cap analysis of gene expression evidence used in manual assertion true true A type of nano-cap analysis of gene expression evidence that is used in a manual assertion. ECO:RCT A type of particle size and count assay evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007146 particle size and count assay evidence used in manual assertion true true A type of particle size and count assay evidence that is used in a manual assertion. ECO:RCT A type of competitive growth assay evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007147 competitive growth assay evidence used in manual assertion true true A type of competitive growth assay evidence that is used in a manual assertion. ECO:RCT A type of pulsed-field gel electrophoresis evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007148 pulsed-field gel electrophoresis evidence used in manual assertion true true A type of pulsed-field gel electrophoresis evidence that is used in a manual assertion. ECO:RCT A type of two-dimensional agarose gel electrophoresis evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007149 two-dimensional agarose gel electrophoresis evidence used in manual assertion true true A type of two-dimensional agarose gel electrophoresis evidence that is used in a manual assertion. ECO:RCT A type of plasmid maintenance assay evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007150 plasmid maintenance assay evidence used in manual assertion true true A type of plasmid maintenance assay evidence that is used in a manual assertion. ECO:RCT A type of specific protein inhibition by antibody evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007151 specific protein inhibition by antibody evidence used in manual assertion true true A type of specific protein inhibition by antibody evidence that is used in a manual assertion. ECO:RCT A type of single exon transcript confirmation via alignment evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007152 single exon transcript confirmation via alignment evidence used in manual assertion true true A type of single exon transcript confirmation via alignment evidence that is used in a manual assertion. ECO:RCT A type of phylogenetic distribution evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007153 phylogenetic distribution evidence used in manual assertion true true A type of phylogenetic distribution evidence that is used in a manual assertion. ECO:RCT A type of differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007154 differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) used in manual assertion true true A type of differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) that is used in a manual assertion. ECO:RCT A type of differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007155 differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) used in manual assertion true true A type of differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) that is used in a manual assertion. ECO:RCT A type of biological target-disease association via drug that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007156 biological target-disease association via drug used in manual assertion true true A type of biological target-disease association via drug that is used in a manual assertion. ECO:RCT A type of cell staining evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007157 cell staining evidence used in manual assertion true true A type of cell staining evidence that is used in a manual assertion. ECO:RCT A type of visual sequence inspection evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007158 visual sequence inspection evidence used in manual assertion true A type of visual sequence inspection evidence that is used in a manual assertion. ECO:RCT A type of ATP bioluminescence assay evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007159 ATP bioluminescence assay evidence used in manual assertion true true A type of ATP bioluminescence assay evidence that is used in a manual assertion. ECO:RCT A type of missense mutation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007160 missense mutation evidence used in manual assertion true true A type of missense mutation evidence that is used in a manual assertion. ECO:RCT A type of nonsense mutation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007161 nonsense mutation evidence used in manual assertion true true A type of nonsense mutation evidence that is used in a manual assertion. ECO:RCT A type of silent mutation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007162 silent mutation evidence used in manual assertion true true A type of silent mutation evidence that is used in a manual assertion. ECO:RCT A type of insertion mutation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007163 insertion mutation evidence used in manual assertion true true A type of insertion mutation evidence that is used in a manual assertion. ECO:RCT A type of duplication mutation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007164 duplication mutation evidence used in manual assertion true true A type of duplication mutation evidence that is used in a manual assertion. ECO:RCT A type of frameshift mutation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007165 frameshift mutation evidence used in manual assertion true true A type of frameshift mutation evidence that is used in a manual assertion. ECO:RCT A type of repeat expansion mutation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007166 repeat expansion mutation evidence used in manual assertion true true A type of repeat expansion mutation evidence that is used in a manual assertion. ECO:RCT A type of splice site mutation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007167 splice site mutation evidence used in manual assertion true true A type of splice site mutation evidence that is used in a manual assertion. ECO:RCT A type of translocation mutation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007168 translocation mutation evidence used in manual assertion true true A type of translocation mutation evidence that is used in a manual assertion. ECO:RCT A type of in-gel protein kinase assay evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007169 in-gel protein kinase assay evidence used in manual assertion true true A type of in-gel protein kinase assay evidence that is used in a manual assertion. ECO:RCT A type of macroscopic current trace evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007170 macroscopic current trace evidence used in manual assertion true true A type of macroscopic current trace evidence that is used in a manual assertion. ECO:RCT A type of current density evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007171 current density evidence used in manual assertion true true A type of current density evidence that is used in a manual assertion. ECO:RCT A type of sustained current evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007172 sustained current evidence used in manual assertion true true A type of sustained current evidence that is used in a manual assertion. ECO:RCT A type of use dependence of inactivation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007173 use dependence of inactivation evidence used in manual assertion true true A type of use dependence of inactivation evidence that is used in a manual assertion. ECO:RCT A type of current clamp recording evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007174 current clamp recording evidence used in manual assertion true true A type of current clamp recording evidence that is used in a manual assertion. ECO:RCT A type of whole-cell voltage clamp recording evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007175 whole-cell voltage clamp recording evidence used in manual assertion true true A type of whole-cell voltage clamp recording evidence that is used in a manual assertion. ECO:RCT A type of cell-attached single-channel recording evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007176 cell-attached single-channel recording evidence used in manual assertion true true A type of cell-attached single-channel recording evidence that is used in a manual assertion. ECO:RCT A type of cell-detached inside-out single-channel recording evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007177 cell-detached inside-out single-channel recording evidence used in manual assertion true true A type of cell-detached inside-out single-channel recording evidence that is used in a manual assertion. ECO:RCT A type of reconstituted bilayer single-channel patch recording evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007178 reconstituted bilayer single-channel patch recording evidence used in manual assertion true true A type of reconstituted bilayer single-channel patch recording evidence that is used in a manual assertion. ECO:RCT A type of electroencephalography recording evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007179 electroencephalography recording evidence used in manual assertion true true A type of electroencephalography recording evidence that is used in a manual assertion. ECO:RCT A type of cell-detached outside-out single-channel recording evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007180 cell-detached outside-out single-channel recording evidence used in manual assertion true true A type of cell-detached outside-out single-channel recording evidence that is used in a manual assertion. ECO:RCT A type of cut-open oocyte voltage clamp recording evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007181 cut-open oocyte voltage clamp recording evidence used in manual assertion true true A type of cut-open oocyte voltage clamp recording evidence that is used in a manual assertion. ECO:RCT A type of macropatch voltage clamp recording evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007182 macropatch voltage clamp recording evidence used in manual assertion true true A type of macropatch voltage clamp recording evidence that is used in a manual assertion. ECO:RCT A type of protein expression level evidence based on western blot that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007183 protein expression level evidence based on western blot used in manual assertion true true true A type of protein expression level evidence based on western blot that is used in a manual assertion. ECO:RCT A type of protein mass spectrometry evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007184 protein mass spectrometry evidence used in manual assertion true true true A type of protein mass spectrometry evidence that is used in a manual assertion. ECO:RCT A type of cross-streak test evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007185 cross-streak test evidence used in manual assertion true true A type of cross-streak test evidence that is used in a manual assertion. ECO:RCT A type of tethered cell assay evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007186 tethered cell assay evidence used in manual assertion true true A type of tethered cell assay evidence that is used in a manual assertion. ECO:RCT A type of tumble frequency assay evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007187 tumble frequency assay evidence used in manual assertion true true A type of tumble frequency assay evidence that is used in a manual assertion. ECO:RCT A type of capillary assay evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007188 capillary assay evidence used in manual assertion true true A type of capillary assay evidence that is used in a manual assertion. ECO:RCT A type of inference from experimental data evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007189 inference from experimental data evidence used in manual assertion true A type of inference from experimental data evidence that is used in a manual assertion. ECO:RCT A type of inference from phenotype manipulation evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007190 inference from phenotype manipulation evidence used in manual assertion true A type of inference from phenotype manipulation evidence that is used in a manual assertion. ECO:RCT A type of inference by association of genotype from phenotype that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007191 inference by association of genotype from phenotype used in manual assertion true A type of inference by association of genotype from phenotype that is used in a manual assertion. ECO:RCT A type of motility assay evidence that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007192 motility assay evidence used in manual assertion true true A type of motility assay evidence that is used in a manual assertion. ECO:RCT A type of loss-of-function mutant phenotype evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007193 loss-of-function mutant phenotype evidence used in automatic assertion true true A type of loss-of-function mutant phenotype evidence that is used in an automatic assertion. ECO:RCT A type of structural similarity evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007194 structural similarity evidence used in automatic assertion true true A type of structural similarity evidence that is used in an automatic assertion. ECO:RCT A type of gain-of-function mutant phenotype evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007196 gain-of-function mutant phenotype evidence used in automatic assertion true true A type of gain-of-function mutant phenotype evidence that is used in an automatic assertion. ECO:RCT A type of voucher specimen analysis evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007197 voucher specimen analysis evidence used in automatic assertion true true A type of voucher specimen analysis evidence that is used in an automatic assertion. ECO:RCT A type of positional similarity evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007198 positional similarity evidence used in automatic assertion true true A type of positional similarity evidence that is used in an automatic assertion. ECO:RCT A type of quantitative trait analysis evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007199 quantitative trait analysis evidence used in automatic assertion true true A type of quantitative trait analysis evidence that is used in an automatic assertion. ECO:RCT A type of compositional similarity evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007200 compositional similarity evidence used in automatic assertion true true A type of compositional similarity evidence that is used in an automatic assertion. ECO:RCT A type of developmental similarity evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007201 developmental similarity evidence used in automatic assertion true true A type of developmental similarity evidence that is used in an automatic assertion. ECO:RCT A type of morphological similarity evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007202 morphological similarity evidence used in automatic assertion true true A type of morphological similarity evidence that is used in an automatic assertion. ECO:RCT A type of gene expression similarity evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007203 gene expression similarity evidence used in automatic assertion true true A type of gene expression similarity evidence that is used in an automatic assertion. ECO:RCT A type of methylation-specific polymerase chain reaction evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007204 methylation-specific polymerase chain reaction evidence used in automatic assertion true true A type of methylation-specific polymerase chain reaction evidence that is used in an automatic assertion. ECO:RCT A type of southern hybridization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007205 southern hybridization evidence used in automatic assertion true true A type of southern hybridization evidence that is used in an automatic assertion. ECO:RCT A type of intermethylated site amplification evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007206 intermethylated site amplification evidence used in automatic assertion true true A type of intermethylated site amplification evidence that is used in an automatic assertion. ECO:RCT A type of epitope-tagged protein immunolocalization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007207 epitope-tagged protein immunolocalization evidence used in automatic assertion true true A type of epitope-tagged protein immunolocalization evidence that is used in an automatic assertion. ECO:RCT A type of co-fractionation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007208 co-fractionation evidence used in automatic assertion true true A type of co-fractionation evidence that is used in an automatic assertion. ECO:RCT A type of green fluorescent protein fusion protein localization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007210 green fluorescent protein fusion protein localization evidence used in automatic assertion true true A type of green fluorescent protein fusion protein localization evidence that is used in an automatic assertion. ECO:RCT A type of yellow fluorescent protein fusion protein localization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007211 yellow fluorescent protein fusion protein localization evidence used in automatic assertion true true A type of yellow fluorescent protein fusion protein localization evidence that is used in an automatic assertion. ECO:RCT A type of beta-glucuronidase fusion protein localization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007212 beta-glucuronidase fusion protein localization evidence used in automatic assertion true true A type of beta-glucuronidase fusion protein localization evidence that is used in an automatic assertion. ECO:RCT A type of beta-galactosidase fusion protein localization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007213 beta-galactosidase fusion protein localization evidence used in automatic assertion true true A type of beta-galactosidase fusion protein localization evidence that is used in an automatic assertion. ECO:RCT A type of thin layer chromatography evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007214 thin layer chromatography evidence used in automatic assertion true true A type of thin layer chromatography evidence that is used in an automatic assertion. ECO:RCT A type of in vitro recombinant protein transcription reconstitution assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007215 in vitro recombinant protein transcription reconstitution assay evidence used in automatic assertion true true A type of in vitro recombinant protein transcription reconstitution assay evidence that is used in an automatic assertion. ECO:RCT A type of protein separation followed by direct sequencing evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007216 protein separation followed by direct sequencing evidence used in automatic assertion true true A type of protein separation followed by direct sequencing evidence that is used in an automatic assertion. ECO:RCT A type of protein separation followed by fragment identification evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007217 protein separation followed by fragment identification evidence used in automatic assertion true true A type of protein separation followed by fragment identification evidence that is used in an automatic assertion. ECO:RCT A type of heterologous system uptake evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007218 heterologous system uptake evidence used in automatic assertion true true A type of heterologous system uptake evidence that is used in an automatic assertion. ECO:RCT A type of two-electrode voltage clamp recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007219 two-electrode voltage clamp recording evidence used in automatic assertion true true A type of two-electrode voltage clamp recording evidence that is used in an automatic assertion. ECO:RCT A type of biochemical trait analysis evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007220 biochemical trait analysis evidence used in automatic assertion true true A type of biochemical trait analysis evidence that is used in an automatic assertion. ECO:RCT A type of mutant physiological response evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007221 mutant physiological response evidence used in automatic assertion true true A type of mutant physiological response evidence that is used in an automatic assertion. ECO:RCT A type of mutant visible phenotype evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007222 mutant visible phenotype evidence used in automatic assertion true true A type of mutant visible phenotype evidence that is used in an automatic assertion. ECO:RCT A type of in vivo assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007223 in vivo assay evidence used in automatic assertion true true A type of in vivo assay evidence that is used in an automatic assertion. ECO:RCT A type of animal model system study evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007224 animal model system study evidence used in automatic assertion true true A type of animal model system study evidence that is used in an automatic assertion. ECO:RCT A type of clinical study evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007225 clinical study evidence used in automatic assertion true true A type of clinical study evidence that is used in an automatic assertion. ECO:RCT A type of in vitro assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007226 in vitro assay evidence used in automatic assertion true true A type of in vitro assay evidence that is used in an automatic assertion. ECO:RCT A type of enzyme inhibition evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007227 enzyme inhibition evidence used in automatic assertion true true A type of enzyme inhibition evidence that is used in an automatic assertion. ECO:RCT A type of Illumina sequencing evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007229 Illumina sequencing evidence used in automatic assertion true true A type of Illumina sequencing evidence that is used in an automatic assertion. ECO:RCT A type of 454 pyrosequencing evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007230 454 pyrosequencing evidence used in automatic assertion true true A type of 454 pyrosequencing evidence that is used in an automatic assertion. ECO:RCT A type of SOLiD sequencing evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007231 SOLiD sequencing evidence used in automatic assertion true true A type of SOLiD sequencing evidence that is used in an automatic assertion. ECO:RCT A type of chain termination sequencing evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007232 chain termination sequencing evidence used in automatic assertion true true A type of chain termination sequencing evidence that is used in an automatic assertion. ECO:RCT A type of chromatin immunoprecipitation-qPCR evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007233 chromatin immunoprecipitation-qPCR evidence used in automatic assertion true true A type of chromatin immunoprecipitation-qPCR evidence that is used in an automatic assertion. ECO:RCT A type of 4C evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z circularized chromosome conformation capture evidence used in automatic assertion eco ECO:0007234 4C evidence used in automatic assertion true true A type of 4C evidence that is used in an automatic assertion. ECO:RCT A type of 5C evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z carbon-copy chromosome conformation capture evidence used in automatic assertion eco ECO:0007235 5C evidence used in automatic assertion true true A type of 5C evidence that is used in an automatic assertion. ECO:RCT A type of 3C-qPCR evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z chromosome conformation capture-qPCR evidence used in automatic assertion eco ECO:0007237 3C-qPCR evidence used in automatic assertion true true A type of 3C-qPCR evidence that is used in an automatic assertion. ECO:RCT A type of Hi-C evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007238 Hi-C evidence used in automatic assertion true true A type of Hi-C evidence that is used in an automatic assertion. ECO:RCT A type of 3C-seq evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z chromosome conformation capture sequencing evidence used in automatic assertion eco ECO:0007239 3C-seq evidence used in automatic assertion true true A type of 3C-seq evidence that is used in an automatic assertion. ECO:RCT A type of environmental perturbation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007240 environmental perturbation evidence used in automatic assertion true true A type of environmental perturbation evidence that is used in an automatic assertion. ECO:RCT A type of tissue ablation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007241 tissue ablation evidence used in automatic assertion true true A type of tissue ablation evidence that is used in an automatic assertion. ECO:RCT A type of tissue grafting evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007242 tissue grafting evidence used in automatic assertion true true A type of tissue grafting evidence that is used in an automatic assertion. ECO:RCT A type of cytochalasin experiment evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007245 cytochalasin experiment evidence used in automatic assertion true true A type of cytochalasin experiment evidence that is used in an automatic assertion. ECO:RCT A type of green fluorescent protein immunolocalization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007246 green fluorescent protein immunolocalization evidence used in automatic assertion true true A type of green fluorescent protein immunolocalization evidence that is used in an automatic assertion. ECO:RCT A type of beta-galactosidase protein immunolocalization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007247 beta-galactosidase protein immunolocalization evidence used in automatic assertion true true A type of beta-galactosidase protein immunolocalization evidence that is used in an automatic assertion. ECO:RCT A type of cap analysis of gene expression evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007248 cap analysis of gene expression evidence used in automatic assertion true true A type of cap analysis of gene expression evidence that is used in an automatic assertion. ECO:RCT A type of nano-cap analysis of gene expression evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007249 nano-cap analysis of gene expression evidence used in automatic assertion true true A type of nano-cap analysis of gene expression evidence that is used in an automatic assertion. ECO:RCT A type of particle size and count assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007250 particle size and count assay evidence used in automatic assertion true true A type of particle size and count assay evidence that is used in an automatic assertion. ECO:RCT A type of competitive growth assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007251 competitive growth assay evidence used in automatic assertion true true A type of competitive growth assay evidence that is used in an automatic assertion. ECO:RCT A type of pulsed-field gel electrophoresis evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007252 pulsed-field gel electrophoresis evidence used in automatic assertion true true A type of pulsed-field gel electrophoresis evidence that is used in an automatic assertion. ECO:RCT A type of two-dimensional agarose gel electrophoresis evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007253 two-dimensional agarose gel electrophoresis evidence used in automatic assertion true true A type of two-dimensional agarose gel electrophoresis evidence that is used in an automatic assertion. ECO:RCT A type of plasmid maintenance assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007254 plasmid maintenance assay evidence used in automatic assertion true true A type of plasmid maintenance assay evidence that is used in an automatic assertion. ECO:RCT A type of specific protein inhibition by antibody evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007255 specific protein inhibition by antibody evidence used in automatic assertion true true A type of specific protein inhibition by antibody evidence that is used in an automatic assertion. ECO:RCT A type of single exon transcript confirmation via alignment evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007256 single exon transcript confirmation via alignment evidence used in automatic assertion true true A type of single exon transcript confirmation via alignment evidence that is used in an automatic assertion. ECO:RCT A type of phylogenetic distribution evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007257 phylogenetic distribution evidence used in automatic assertion true true A type of phylogenetic distribution evidence that is used in an automatic assertion. ECO:RCT A type of differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007258 differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) used in automatic assertion true true A type of differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) that is used in an automatic assertion. ECO:RCT A type of differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007259 differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) used in automatic assertion true true A type of differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) that is used in an automatic assertion. ECO:RCT A type of biological target-disease association via drug that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007260 biological target-disease association via drug used in automatic assertion true true A type of biological target-disease association via drug that is used in an automatic assertion. ECO:RCT A type of cell staining evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007261 cell staining evidence used in automatic assertion true true A type of cell staining evidence that is used in an automatic assertion. ECO:RCT A type of visual sequence inspection evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007262 visual sequence inspection evidence used in automatic assertion true A type of visual sequence inspection evidence that is used in an automatic assertion. ECO:RCT A type of ATP bioluminescence assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007263 ATP bioluminescence assay evidence used in automatic assertion true true A type of ATP bioluminescence assay evidence that is used in an automatic assertion. ECO:RCT A type of missense mutation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007264 missense mutation evidence used in automatic assertion true true A type of missense mutation evidence that is used in an automatic assertion. ECO:RCT A type of nonsense mutation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007265 nonsense mutation evidence used in automatic assertion true true A type of nonsense mutation evidence that is used in an automatic assertion. ECO:RCT A type of silent mutation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007266 silent mutation evidence used in automatic assertion true true A type of silent mutation evidence that is used in an automatic assertion. ECO:RCT A type of insertion mutation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007267 insertion mutation evidence used in automatic assertion true true A type of insertion mutation evidence that is used in an automatic assertion. ECO:RCT A type of duplication mutation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007268 duplication mutation evidence used in automatic assertion true true A type of duplication mutation evidence that is used in an automatic assertion. ECO:RCT A type of frameshift mutation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007269 frameshift mutation evidence used in automatic assertion true true A type of frameshift mutation evidence that is used in an automatic assertion. ECO:RCT A type of repeat expansion mutation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007270 repeat expansion mutation evidence used in automatic assertion true true A type of repeat expansion mutation evidence that is used in an automatic assertion. ECO:RCT A type of splice site mutation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007271 splice site mutation evidence used in automatic assertion true true A type of splice site mutation evidence that is used in an automatic assertion. ECO:RCT A type of translocation mutation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007272 translocation mutation evidence used in automatic assertion true true A type of translocation mutation evidence that is used in an automatic assertion. ECO:RCT A type of in-gel protein kinase assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007273 in-gel protein kinase assay evidence used in automatic assertion true true A type of in-gel protein kinase assay evidence that is used in an automatic assertion. ECO:RCT A type of macroscopic current trace evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007274 macroscopic current trace evidence used in automatic assertion true true A type of macroscopic current trace evidence that is used in an automatic assertion. ECO:RCT A type of current density evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007275 current density evidence used in automatic assertion true true A type of current density evidence that is used in an automatic assertion. ECO:RCT A type of sustained current evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007276 sustained current evidence used in automatic assertion true true A type of sustained current evidence that is used in an automatic assertion. ECO:RCT A type of use dependence of inactivation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007277 use dependence of inactivation evidence used in automatic assertion true true A type of use dependence of inactivation evidence that is used in an automatic assertion. ECO:RCT A type of current clamp recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007278 current clamp recording evidence used in automatic assertion true true A type of current clamp recording evidence that is used in an automatic assertion. ECO:RCT A type of whole-cell voltage clamp recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007279 whole-cell voltage clamp recording evidence used in automatic assertion true true A type of whole-cell voltage clamp recording evidence that is used in an automatic assertion. ECO:RCT A type of cell-attached single-channel recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007280 cell-attached single-channel recording evidence used in automatic assertion true true A type of cell-attached single-channel recording evidence that is used in an automatic assertion. ECO:RCT A type of cell-detached inside-out single-channel recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007281 cell-detached inside-out single-channel recording evidence used in automatic assertion true true A type of cell-detached inside-out single-channel recording evidence that is used in an automatic assertion. ECO:RCT A type of reconstituted bilayer single-channel patch recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007282 reconstituted bilayer single-channel patch recording evidence used in automatic assertion true true A type of reconstituted bilayer single-channel patch recording evidence that is used in an automatic assertion. ECO:RCT A type of electroencephalography recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007283 electroencephalography recording evidence used in automatic assertion true true A type of electroencephalography recording evidence that is used in an automatic assertion. ECO:RCT A type of cell-detached outside-out single-channel recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007284 cell-detached outside-out single-channel recording evidence used in automatic assertion true true A type of cell-detached outside-out single-channel recording evidence that is used in an automatic assertion. ECO:RCT A type of cut-open oocyte voltage clamp recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007285 cut-open oocyte voltage clamp recording evidence used in automatic assertion true true A type of cut-open oocyte voltage clamp recording evidence that is used in an automatic assertion. ECO:RCT A type of macropatch voltage clamp recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007286 macropatch voltage clamp recording evidence used in automatic assertion true true A type of macropatch voltage clamp recording evidence that is used in an automatic assertion. ECO:RCT A type of protein expression level evidence based on western blot that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007287 protein expression level evidence based on western blot used in automatic assertion true true true A type of protein expression level evidence based on western blot that is used in an automatic assertion. ECO:RCT A type of protein mass spectrometry evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007288 protein mass spectrometry evidence used in automatic assertion true true true A type of protein mass spectrometry evidence that is used in an automatic assertion. ECO:RCT A type of cross-streak test evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007289 cross-streak test evidence used in automatic assertion true true A type of cross-streak test evidence that is used in an automatic assertion. ECO:RCT A type of tethered cell assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007290 tethered cell assay evidence used in automatic assertion true true A type of tethered cell assay evidence that is used in an automatic assertion. ECO:RCT A type of tumble frequency assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007291 tumble frequency assay evidence used in automatic assertion true true A type of tumble frequency assay evidence that is used in an automatic assertion. ECO:RCT A type of capillary assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007292 capillary assay evidence used in automatic assertion true true A type of capillary assay evidence that is used in an automatic assertion. ECO:RCT A type of inference from experimental data evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007293 inference from experimental data evidence used in automatic assertion true true true A type of inference from experimental data evidence that is used in an automatic assertion. ECO:RCT A type of inference from phenotype manipulation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007294 inference from phenotype manipulation evidence used in automatic assertion true true true A type of inference from phenotype manipulation evidence that is used in an automatic assertion. ECO:RCT A type of inference by association of genotype from phenotype that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007295 inference by association of genotype from phenotype used in automatic assertion true true true A type of inference by association of genotype from phenotype that is used in an automatic assertion. ECO:RCT A type of motility assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007296 motility assay evidence used in automatic assertion true true A type of motility assay evidence that is used in an automatic assertion. ECO:RCT A type of experimental evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007297 experimental evidence used in automatic assertion true true A type of experimental evidence that is used in an automatic assertion. ECO:RCT A type of expression pattern evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007298 expression pattern evidence used in automatic assertion true true A type of expression pattern evidence that is used in an automatic assertion. ECO:RCT A type of Affymetrix GeneChip evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007299 Affymetrix GeneChip evidence used in automatic assertion true true A type of Affymetrix GeneChip evidence that is used in an automatic assertion. ECO:RCT A type of cRNA to DNA expression microarray evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007300 cRNA to DNA expression microarray evidence used in automatic assertion true true A type of cRNA to DNA expression microarray evidence that is used in an automatic assertion. ECO:RCT A type of expression microarray evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007301 expression microarray evidence used in automatic assertion true true A type of expression microarray evidence that is used in an automatic assertion. ECO:RCT A type of differential methylation hybridization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007302 differential methylation hybridization evidence used in automatic assertion true true A type of differential methylation hybridization evidence that is used in an automatic assertion. ECO:RCT A type of transcript expression evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007303 transcript expression evidence used in automatic assertion true true A type of transcript expression evidence that is used in an automatic assertion. ECO:RCT A type of Nimblegen array evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007304 Nimblegen array evidence used in automatic assertion true true A type of Nimblegen array evidence that is used in an automatic assertion. ECO:RCT A type of array-based sequence capture evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007305 array-based sequence capture evidence used in automatic assertion true true A type of array-based sequence capture evidence that is used in an automatic assertion. ECO:RCT A type of western blot evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007306 western blot evidence used in automatic assertion true true A type of western blot evidence that is used in an automatic assertion. ECO:RCT A type of direct assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007307 direct assay evidence used in automatic assertion true true A type of direct assay evidence that is used in an automatic assertion. ECO:RCT A type of protein expression level evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007308 protein expression level evidence used in automatic assertion true true A type of protein expression level evidence that is used in an automatic assertion. ECO:RCT A type of protein expression evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007309 protein expression evidence used in automatic assertion true true true A type of protein expression evidence that is used in an automatic assertion. ECO:RCT A type of expression library screen evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007310 expression library screen evidence used in automatic assertion true true A type of expression library screen evidence that is used in an automatic assertion. ECO:RCT A type of heterologous protein expression evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007311 heterologous protein expression evidence used in automatic assertion true true A type of heterologous protein expression evidence that is used in an automatic assertion. ECO:RCT A type of spatial pattern of protein expression evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007312 spatial pattern of protein expression evidence used in automatic assertion true true A type of spatial pattern of protein expression evidence that is used in an automatic assertion. ECO:RCT A type of DNA to cDNA expression microarray evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007313 DNA to cDNA expression microarray evidence used in automatic assertion true true A type of DNA to cDNA expression microarray evidence that is used in an automatic assertion. ECO:RCT A type of differential hybridization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007314 differential hybridization evidence used in automatic assertion true true A type of differential hybridization evidence that is used in an automatic assertion. ECO:RCT A type of RNA protection assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007315 RNA protection assay evidence used in automatic assertion true true A type of RNA protection assay evidence that is used in an automatic assertion. ECO:RCT A type of nuclease protection assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007316 nuclease protection assay evidence used in automatic assertion true true A type of nuclease protection assay evidence that is used in an automatic assertion. ECO:RCT A type of spatial pattern of transcript expression evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007317 spatial pattern of transcript expression evidence used in automatic assertion true true A type of spatial pattern of transcript expression evidence that is used in an automatic assertion. ECO:RCT A type of subtractive hybridization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007318 subtractive hybridization evidence used in automatic assertion true true A type of subtractive hybridization evidence that is used in an automatic assertion. ECO:RCT A type of author statement that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007319 author statement used in automatic assertion true true A type of author statement that is used in an automatic assertion. ECO:RCT A type of author statement without traceable support that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco non-traceable author statement used in automatic assertion ECO:0007320 author statement without traceable support used in automatic assertion true true A type of author statement without traceable support that is used in an automatic assertion. ECO:RCT A type of author statement supported by traceable reference that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco traceable author statement used in automatic assertion ECO:0007321 author statement supported by traceable reference used in automatic assertion true true A type of author statement supported by traceable reference that is used in an automatic assertion. ECO:RCT A type of curator inference that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007322 curator inference used in automatic assertion true true A type of curator inference that is used in an automatic assertion. ECO:RCT A type of inference from background scientific knowledge that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007323 inference from background scientific knowledge used in automatic assertion true true A type of inference from background scientific knowledge that is used in an automatic assertion. ECO:RCT A type of no biological data found that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007324 no biological data found used in automatic assertion true true A type of no biological data found that is used in an automatic assertion. ECO:RCT A type of mutant phenotype evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007325 mutant phenotype evidence used in automatic assertion true true A type of mutant phenotype evidence that is used in an automatic assertion. ECO:RCT A type of genetic interaction evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007326 genetic interaction evidence used in automatic assertion true true A type of genetic interaction evidence that is used in an automatic assertion. ECO:RCT A type of genomic context evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007327 genomic context evidence used in automatic assertion true true A type of genomic context evidence that is used in an automatic assertion. ECO:RCT A type of biological aspect of ancestor evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007328 biological aspect of ancestor evidence used in automatic assertion true true A type of biological aspect of ancestor evidence that is used in an automatic assertion. ECO:RCT A type of biological aspect of descendant evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007329 biological aspect of descendant evidence used in automatic assertion true true A type of biological aspect of descendant evidence that is used in an automatic assertion. ECO:RCT A type of phylogenetic determination of loss of key residues evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007330 phylogenetic determination of loss of key residues evidence used in automatic assertion true true A type of phylogenetic determination of loss of key residues evidence that is used in an automatic assertion. ECO:RCT A type of rapid divergence from ancestral sequence evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007331 rapid divergence from ancestral sequence evidence used in automatic assertion true true A type of rapid divergence from ancestral sequence evidence that is used in an automatic assertion. ECO:RCT A type of physical interaction evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007332 physical interaction evidence used in automatic assertion true true A type of physical interaction evidence that is used in an automatic assertion. ECO:RCT A type of gene neighbors evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007333 gene neighbors evidence used in automatic assertion true true A type of gene neighbors evidence that is used in an automatic assertion. ECO:RCT A type of Edman degradation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007334 Edman degradation evidence used in automatic assertion true true A type of Edman degradation evidence that is used in an automatic assertion. ECO:RCT A type of 3D cell culture evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007335 3D cell culture evidence used in automatic assertion true true A type of 3D cell culture evidence that is used in an automatic assertion. ECO:RCT A type of 51Cr release assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007336 51Cr release assay evidence used in automatic assertion true true A type of 51Cr release assay evidence that is used in an automatic assertion. ECO:RCT A type of 7-aminoactinomycin staining evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007337 7-aminoactinomycin staining evidence used in automatic assertion true true A type of 7-aminoactinomycin staining evidence that is used in an automatic assertion. ECO:RCT A type of [3H]-thymidine incorporation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007338 [3H]-thymidine incorporation assay evidence used in automatic assertion true true A type of [3H]-thymidine incorporation assay evidence that is used in an automatic assertion. ECO:RCT A type of [3H]arachidonic acid release assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007339 [3H]arachidonic acid release assay evidence used in automatic assertion true true A type of [3H]arachidonic acid release assay evidence that is used in an automatic assertion. ECO:RCT A type of adhesion assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007340 adhesion assay evidence used in automatic assertion true true A type of adhesion assay evidence that is used in an automatic assertion. ECO:RCT A type of adoptive cell transfer evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007341 adoptive cell transfer evidence used in automatic assertion true true A type of adoptive cell transfer evidence that is used in an automatic assertion. ECO:RCT A type of alamarBlue assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007342 alamarBlue assay evidence used in automatic assertion true true A type of alamarBlue assay evidence that is used in an automatic assertion. ECO:RCT A type of allograft transplantation experiment evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007343 allograft transplantation experiment evidence used in automatic assertion true true A type of allograft transplantation experiment evidence that is used in an automatic assertion. ECO:RCT A type of anion-exchange chromatography evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007344 anion-exchange chromatography evidence used in automatic assertion true true A type of anion-exchange chromatography evidence that is used in an automatic assertion. ECO:RCT A type of annexin-V staining evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007345 annexin-V staining evidence used in automatic assertion true true A type of annexin-V staining evidence that is used in an automatic assertion. ECO:RCT A type of behavioral assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007346 behavioral assay evidence used in automatic assertion true true A type of behavioral assay evidence that is used in an automatic assertion. ECO:RCT A type of blocking monoclonal antibody evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007347 blocking monoclonal antibody evidence used in automatic assertion true true A type of blocking monoclonal antibody evidence that is used in an automatic assertion. ECO:RCT A type of immunological assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007348 immunological assay evidence used in automatic assertion true true A type of immunological assay evidence that is used in an automatic assertion. ECO:RCT A type of blocking peptide evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007349 blocking peptide evidence used in automatic assertion true true A type of blocking peptide evidence that is used in an automatic assertion. ECO:RCT A type of blocking polyclonal antibody evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007350 blocking polyclonal antibody evidence used in automatic assertion true true A type of blocking polyclonal antibody evidence that is used in an automatic assertion. ECO:RCT A type of blood test evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007351 blood test evidence used in automatic assertion true true A type of blood test evidence that is used in an automatic assertion. ECO:RCT A type of Boyden chamber assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007352 Boyden chamber assay evidence used in automatic assertion true true A type of Boyden chamber assay evidence that is used in an automatic assertion. ECO:RCT A type of bromodeoxyuridine incorporation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007353 bromodeoxyuridine incorporation assay evidence used in automatic assertion true true A type of bromodeoxyuridine incorporation assay evidence that is used in an automatic assertion. ECO:RCT A type of nucleotide analog incorporation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007354 nucleotide analog incorporation assay evidence used in automatic assertion true true A type of nucleotide analog incorporation assay evidence that is used in an automatic assertion. ECO:RCT A type of caspase assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007355 caspase assay evidence used in automatic assertion true true A type of caspase assay evidence that is used in an automatic assertion. ECO:RCT A type of cell counting evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007356 cell counting evidence used in automatic assertion true true A type of cell counting evidence that is used in an automatic assertion. ECO:RCT A type of cell permeability assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007357 cell permeability assay evidence used in automatic assertion true true A type of cell permeability assay evidence that is used in an automatic assertion. ECO:RCT A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007358 carboxyfluorescein diacetate succinimidyl ester staining evidence used in automatic assertion true true A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in an automatic assertion. ECO:RCT A type of chemiluminescence-linked immunoassay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007359 chemiluminescence-linked immunoassay evidence used in automatic assertion true true A type of chemiluminescence-linked immunoassay evidence that is used in an automatic assertion. ECO:RCT A type of chimeric protein evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007360 chimeric protein evidence used in automatic assertion true true A type of chimeric protein evidence that is used in an automatic assertion. ECO:RCT A type of co-electrophoresis evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007361 co-electrophoresis evidence used in automatic assertion true true A type of co-electrophoresis evidence that is used in an automatic assertion. ECO:RCT A type of co-localization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007362 co-localization evidence used in automatic assertion true true A type of co-localization evidence that is used in an automatic assertion. ECO:RCT A type of imaging assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007363 imaging assay evidence used in automatic assertion true true A type of imaging assay evidence that is used in an automatic assertion. ECO:RCT A type of co-sedimentation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007364 co-sedimentation assay evidence used in automatic assertion true true A type of co-sedimentation assay evidence that is used in an automatic assertion. ECO:RCT A type of colony counting evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007365 colony counting evidence used in automatic assertion true true A type of colony counting evidence that is used in an automatic assertion. ECO:RCT A type of comet assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007366 comet assay evidence used in automatic assertion true true A type of comet assay evidence that is used in an automatic assertion. ECO:RCT A type of conditional knockin evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007367 conditional knockin evidence used in automatic assertion true true A type of conditional knockin evidence that is used in an automatic assertion. ECO:RCT A type of knockin evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007368 knockin evidence used in automatic assertion true true A type of knockin evidence that is used in an automatic assertion. ECO:RCT A type of conditional knockout evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007369 conditional knockout evidence used in automatic assertion true true A type of conditional knockout evidence that is used in an automatic assertion. ECO:RCT A type of knockout evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007370 knockout evidence used in automatic assertion true true A type of knockout evidence that is used in an automatic assertion. ECO:RCT A type of constitutively active mutant evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007371 constitutively active mutant evidence used in automatic assertion true true A type of constitutively active mutant evidence that is used in an automatic assertion. ECO:RCT A type of cross-linking evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007372 cross-linking evidence used in automatic assertion true true A type of cross-linking evidence that is used in an automatic assertion. ECO:RCT A type of protein binding evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007373 protein binding evidence used in automatic assertion true true true A type of protein binding evidence that is used in an automatic assertion. ECO:RCT A type of crystallography evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007374 crystallography evidence used in automatic assertion true true A type of crystallography evidence that is used in an automatic assertion. ECO:RCT A type of cytochemistry evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007375 cytochemistry evidence used in automatic assertion true true A type of cytochemistry evidence that is used in an automatic assertion. ECO:RCT A type of histochemistry evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007376 histochemistry evidence used in automatic assertion true true A type of histochemistry evidence that is used in an automatic assertion. ECO:RCT A type of cytochrome C release assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007377 cytochrome C release assay evidence used in automatic assertion true true A type of cytochrome C release assay evidence that is used in an automatic assertion. ECO:RCT A type of 4',6-diamidino-2-phenylindole staining evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007378 4',6-diamidino-2-phenylindole staining evidence used in automatic assertion true true A type of 4',6-diamidino-2-phenylindole staining evidence that is used in an automatic assertion. ECO:RCT A type of deletion mutation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007379 deletion mutation evidence used in automatic assertion true true A type of deletion mutation evidence that is used in an automatic assertion. ECO:RCT A type of DNA laddering assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007380 DNA laddering assay evidence used in automatic assertion true true A type of DNA laddering assay evidence that is used in an automatic assertion. ECO:RCT A type of RNA dot blot assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007381 RNA dot blot assay evidence used in automatic assertion true true A type of RNA dot blot assay evidence that is used in an automatic assertion. ECO:RCT A type of dominant-negative mutant evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007382 dominant-negative mutant evidence used in automatic assertion true true A type of dominant-negative mutant evidence that is used in an automatic assertion. ECO:RCT A type of eTag assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007383 eTag assay evidence used in automatic assertion true true A type of eTag assay evidence that is used in an automatic assertion. ECO:RCT A type of affinity evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007384 affinity evidence used in automatic assertion true true A type of affinity evidence that is used in an automatic assertion. ECO:RCT A type of filter binding assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007385 filter binding assay evidence used in automatic assertion true true A type of filter binding assay evidence that is used in an automatic assertion. ECO:RCT A type of fluorescence in situ hybridization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007386 fluorescence in situ hybridization evidence used in automatic assertion true true true A type of fluorescence in situ hybridization evidence that is used in an automatic assertion. ECO:RCT A type of fluorescence resonance energy transfer evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007387 fluorescence resonance energy transfer evidence used in automatic assertion true true A type of fluorescence resonance energy transfer evidence that is used in an automatic assertion. ECO:RCT A type of gel-filtration evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007388 gel-filtration evidence used in automatic assertion true true A type of gel-filtration evidence that is used in an automatic assertion. ECO:RCT A type of histology evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007389 histology evidence used in automatic assertion true true A type of histology evidence that is used in an automatic assertion. ECO:RCT A type of immunocytochemistry evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007390 immunocytochemistry evidence used in automatic assertion true true A type of immunocytochemistry evidence that is used in an automatic assertion. ECO:RCT A type of immunodepletion evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007391 immunodepletion evidence used in automatic assertion true true A type of immunodepletion evidence that is used in an automatic assertion. ECO:RCT A type of immunohistochemistry evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007392 immunohistochemistry evidence used in automatic assertion true true A type of immunohistochemistry evidence that is used in an automatic assertion. ECO:RCT A type of in vitro acetylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007393 in vitro acetylation assay evidence used in automatic assertion true true A type of in vitro acetylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro cleavage assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007394 in vitro cleavage assay evidence used in automatic assertion true true A type of in vitro cleavage assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro deacetylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007395 in vitro deacetylation assay evidence used in automatic assertion true true A type of in vitro deacetylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro defarnesylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007396 in vitro defarnesylation assay evidence used in automatic assertion true true A type of in vitro defarnesylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro demethylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007397 in vitro demethylation assay evidence used in automatic assertion true true A type of in vitro demethylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro desumoylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007398 in vitro desumoylation assay evidence used in automatic assertion true true A type of in vitro desumoylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro deubiquitination assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007399 in vitro deubiquitination assay evidence used in automatic assertion true true A type of in vitro deubiquitination assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro farnesylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007400 in vitro farnesylation assay evidence used in automatic assertion true true A type of in vitro farnesylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro methylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007401 in vitro methylation assay evidence used in automatic assertion true true A type of in vitro methylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro palmitoylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007402 in vitro palmitoylation assay evidence used in automatic assertion true true A type of in vitro palmitoylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro phosphatase assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007403 in vitro phosphatase assay evidence used in automatic assertion true true A type of in vitro phosphatase assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro polyADP-ribosylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007404 in vitro polyADP-ribosylation assay evidence used in automatic assertion true true A type of in vitro polyADP-ribosylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro protein kinase assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007405 in vitro protein kinase assay evidence used in automatic assertion true true A type of in vitro protein kinase assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro sumoylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007406 in vitro sumoylation assay evidence used in automatic assertion true true A type of in vitro sumoylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro transcription assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007407 in vitro transcription assay evidence used in automatic assertion true true A type of in vitro transcription assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro translation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007408 in vitro translation assay evidence used in automatic assertion true true A type of in vitro translation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vitro ubiquitination assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007409 in vitro ubiquitination assay evidence used in automatic assertion true true A type of in vitro ubiquitination assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo acetylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007410 in vivo acetylation assay evidence used in automatic assertion true true A type of in vivo acetylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo cleavage assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007411 in vivo cleavage assay evidence used in automatic assertion true true A type of in vivo cleavage assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo deacetylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007412 in vivo deacetylation assay evidence used in automatic assertion true true A type of in vivo deacetylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo defarnesylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007413 in vivo defarnesylation assay evidence used in automatic assertion true true A type of in vivo defarnesylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo demethylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007414 in vivo demethylation assay evidence used in automatic assertion true true A type of in vivo demethylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo desumoylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007415 in vivo desumoylation assay evidence used in automatic assertion true true A type of in vivo desumoylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo deubiquitination assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007416 in vivo deubiquitination assay evidence used in automatic assertion true true A type of in vivo deubiquitination assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo farnesylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007417 in vivo farnesylation assay evidence used in automatic assertion true true A type of in vivo farnesylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo methylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007418 in vivo methylation assay evidence used in automatic assertion true true A type of in vivo methylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo palmitoylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007419 in vivo palmitoylation assay evidence used in automatic assertion true true A type of in vivo palmitoylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo phosphatase assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007420 in vivo phosphatase assay evidence used in automatic assertion true true A type of in vivo phosphatase assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo protein kinase assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007421 in vivo protein kinase assay evidence used in automatic assertion true true A type of in vivo protein kinase assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo sumoylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007422 in vivo sumoylation assay evidence used in automatic assertion true true A type of in vivo sumoylation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo transcription assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007423 in vivo transcription assay evidence used in automatic assertion true true A type of in vivo transcription assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo translation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007424 in vivo translation assay evidence used in automatic assertion true true A type of in vivo translation assay evidence that is used in an automatic assertion. ECO:RCT A type of in vivo ubiquitination assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007425 in vivo ubiquitination assay evidence used in automatic assertion true true A type of in vivo ubiquitination assay evidence that is used in an automatic assertion. ECO:RCT A type of induced mutation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007426 induced mutation evidence used in automatic assertion true true A type of induced mutation evidence that is used in an automatic assertion. ECO:RCT A type of genetic transformation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007427 genetic transformation evidence used in automatic assertion true true A type of genetic transformation evidence that is used in an automatic assertion. ECO:RCT A type of lipid binding assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007428 lipid binding assay evidence used in automatic assertion true true A type of lipid binding assay evidence that is used in an automatic assertion. ECO:RCT A type of luminescence-based mammalian interactome mapping assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007429 luminescence-based mammalian interactome mapping assay evidence used in automatic assertion true true A type of luminescence-based mammalian interactome mapping assay evidence that is used in an automatic assertion. ECO:RCT A type of macroscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007430 macroscopy evidence used in automatic assertion true true A type of macroscopy evidence that is used in an automatic assertion. ECO:RCT A type of mammalian 2-hybrid assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007431 mammalian 2-hybrid assay evidence used in automatic assertion true true A type of mammalian 2-hybrid assay evidence that is used in an automatic assertion. ECO:RCT A type of hybrid interaction evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007432 hybrid interaction evidence used in automatic assertion true true A type of hybrid interaction evidence that is used in an automatic assertion. ECO:RCT A type of mass spectrometry evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007433 mass spectrometry evidence used in automatic assertion true true A type of mass spectrometry evidence that is used in an automatic assertion. ECO:RCT A type of medical imaging evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007434 medical imaging evidence used in automatic assertion true true A type of medical imaging evidence that is used in an automatic assertion. ECO:RCT A type of microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007435 microscopy evidence used in automatic assertion true true A type of microscopy evidence that is used in an automatic assertion. ECO:RCT A type of motility wound healing assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007436 motility wound healing assay evidence used in automatic assertion true true A type of motility wound healing assay evidence that is used in an automatic assertion. ECO:RCT A type of MTS assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007437 MTS assay evidence used in automatic assertion true true A type of MTS assay evidence that is used in an automatic assertion. ECO:RCT A type of MTT assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007438 MTT assay evidence used in automatic assertion true true A type of MTT assay evidence that is used in an automatic assertion. ECO:RCT A type of multiplex bead-based immunoassay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007439 multiplex bead-based immunoassay evidence used in automatic assertion true true A type of multiplex bead-based immunoassay evidence that is used in an automatic assertion. ECO:RCT A type of natural variation mutant evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007440 natural variation mutant evidence used in automatic assertion true true A type of natural variation mutant evidence that is used in an automatic assertion. ECO:RCT A type of nuclear magnetic resonance spectroscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007441 nuclear magnetic resonance spectroscopy evidence used in automatic assertion true true A type of nuclear magnetic resonance spectroscopy evidence that is used in an automatic assertion. ECO:RCT A type of nuclear fragmentation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007442 nuclear fragmentation evidence used in automatic assertion true true A type of nuclear fragmentation evidence that is used in an automatic assertion. ECO:RCT A type of phage display evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007443 phage display evidence used in automatic assertion true true A type of phage display evidence that is used in an automatic assertion. ECO:RCT A type of phosphoamino acid analysis evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007444 phosphoamino acid analysis evidence used in automatic assertion true true A type of phosphoamino acid analysis evidence that is used in an automatic assertion. ECO:RCT A type of peptide affinity enrichment evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007445 peptide affinity enrichment evidence used in automatic assertion true true A type of peptide affinity enrichment evidence that is used in an automatic assertion. ECO:RCT A type of peptide array evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007446 peptide array evidence used in automatic assertion true true A type of peptide array evidence that is used in an automatic assertion. ECO:RCT A type of physical examination evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007447 physical examination evidence used in automatic assertion true true A type of physical examination evidence that is used in an automatic assertion. ECO:RCT A type of point mutation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007448 point mutation evidence used in automatic assertion true true A type of point mutation evidence that is used in an automatic assertion. ECO:RCT A type of propidium iodide staining evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007449 propidium iodide staining evidence used in automatic assertion true true A type of propidium iodide staining evidence that is used in an automatic assertion. ECO:RCT A type of fluorescence evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007450 fluorescence evidence used in automatic assertion true true A type of fluorescence evidence that is used in an automatic assertion. ECO:RCT A type of protein dot blot assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007451 protein dot blot assay evidence used in automatic assertion true true A type of protein dot blot assay evidence that is used in an automatic assertion. ECO:RCT A type of protein microarray evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007452 protein microarray evidence used in automatic assertion true true A type of protein microarray evidence that is used in an automatic assertion. ECO:RCT A type of protein sequencing assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007453 protein sequencing assay evidence used in automatic assertion true true A type of protein sequencing assay evidence that is used in an automatic assertion. ECO:RCT A type of quantitative mass spectrometry evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007454 quantitative mass spectrometry evidence used in automatic assertion true true A type of quantitative mass spectrometry evidence that is used in an automatic assertion. ECO:RCT A type of radioisotope assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007455 radioisotope assay evidence used in automatic assertion true true A type of radioisotope assay evidence that is used in an automatic assertion. ECO:RCT A type of radioimmunoassay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007456 radioimmunoassay evidence used in automatic assertion true true A type of radioimmunoassay evidence that is used in an automatic assertion. ECO:RCT A type of restriction fragment detection evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007457 restriction fragment detection evidence used in automatic assertion true true A type of restriction fragment detection evidence that is used in an automatic assertion. ECO:RCT A type of spectrophotometry evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007458 spectrophotometry evidence used in automatic assertion true true A type of spectrophotometry evidence that is used in an automatic assertion. ECO:RCT A type of syngeneic transplantation experiment evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007459 syngeneic transplantation experiment evidence used in automatic assertion true true A type of syngeneic transplantation experiment evidence that is used in an automatic assertion. ECO:RCT A type of xenotransplantation experiment evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007460 xenotransplantation experiment evidence used in automatic assertion true true A type of xenotransplantation experiment evidence that is used in an automatic assertion. ECO:RCT A type of WST-1 assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007461 WST-1 assay evidence used in automatic assertion true true A type of WST-1 assay evidence that is used in an automatic assertion. ECO:RCT A type of urine test evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007462 urine test evidence used in automatic assertion true true A type of urine test evidence that is used in an automatic assertion. ECO:RCT A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007463 terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in automatic assertion true true A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence that is used in an automatic assertion. ECO:RCT A type of tryptic phosphopeptide mapping assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007464 tryptic phosphopeptide mapping assay evidence used in automatic assertion true true A type of tryptic phosphopeptide mapping assay evidence that is used in an automatic assertion. ECO:RCT A type of transgenic organism evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007465 transgenic organism evidence used in automatic assertion true true A type of transgenic organism evidence that is used in an automatic assertion. ECO:RCT A type of tissue microarray evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007466 tissue microarray evidence used in automatic assertion true true A type of tissue microarray evidence that is used in an automatic assertion. ECO:RCT A type of TACE activity assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007467 TACE activity assay evidence used in automatic assertion true true A type of TACE activity assay evidence that is used in an automatic assertion. ECO:RCT A type of enzyme assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007468 enzyme assay evidence used in automatic assertion true true A type of enzyme assay evidence that is used in an automatic assertion. ECO:RCT A type of surface plasmon resonance evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007469 surface plasmon resonance evidence used in automatic assertion true true A type of surface plasmon resonance evidence that is used in an automatic assertion. ECO:RCT A type of restriction landmark genomic scanning evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007470 restriction landmark genomic scanning evidence used in automatic assertion true true A type of restriction landmark genomic scanning evidence that is used in an automatic assertion. ECO:RCT A type of resonant mirror biosensor evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007471 resonant mirror biosensor evidence used in automatic assertion true true A type of resonant mirror biosensor evidence that is used in an automatic assertion. ECO:RCT A type of high-performance liquid chromatography evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007472 high-performance liquid chromatography evidence used in automatic assertion true true A type of high-performance liquid chromatography evidence that is used in an automatic assertion. ECO:RCT A type of ectopic expression evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007473 ectopic expression evidence used in automatic assertion true true A type of ectopic expression evidence that is used in an automatic assertion. ECO:RCT A type of electrophoretic mobility shift assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007474 electrophoretic mobility shift assay evidence used in automatic assertion true true A type of electrophoretic mobility shift assay evidence that is used in an automatic assertion. ECO:RCT A type of reverse transcription polymerase chain reaction evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z ECO:000108 eco ECO:0007475 reverse transcription polymerase chain reaction evidence used in automatic assertion true true A type of reverse transcription polymerase chain reaction evidence that is used in an automatic assertion. ECO:RCT A type of in vivo polyADP-ribosylation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007476 in vivo polyADP-ribosylation assay evidence used in automatic assertion true true A type of in vivo polyADP-ribosylation assay evidence that is used in an automatic assertion. ECO:RCT A type of DNA dot blot assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007477 DNA dot blot assay evidence used in automatic assertion true true A type of DNA dot blot assay evidence that is used in an automatic assertion. ECO:RCT A type of random mutagenesis evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007478 random mutagenesis evidence used in automatic assertion true true A type of random mutagenesis evidence that is used in an automatic assertion. ECO:RCT A type of biological system reconstruction evidence by experimental evidence from single species that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007479 biological system reconstruction evidence by experimental evidence from single species used in automatic assertion true true A type of biological system reconstruction evidence by experimental evidence from single species that is used in an automatic assertion. ECO:RCT A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007480 biological system reconstruction evidence by experimental evidence from mixed species used in automatic assertion true true A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in an automatic assertion. ECO:RCT A type of biological system reconstruction evidence based on orthology evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007481 biological system reconstruction evidence based on orthology evidence used in automatic assertion true true A type of biological system reconstruction evidence based on orthology evidence that is used in an automatic assertion. ECO:RCT A type of biological system reconstruction evidence based on homology evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007482 biological system reconstruction evidence based on homology evidence used in automatic assertion true true A type of biological system reconstruction evidence based on homology evidence that is used in an automatic assertion. ECO:RCT A type of biological system reconstruction evidence based on paralogy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007483 biological system reconstruction evidence based on paralogy evidence used in automatic assertion true true A type of biological system reconstruction evidence based on paralogy evidence that is used in an automatic assertion. ECO:RCT A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007484 biological system reconstruction evidence based on inference from background scientific knowledge used in automatic assertion true true A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in an automatic assertion. ECO:RCT A type of immunogold labelling evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007485 immunogold labelling evidence used in automatic assertion true true A type of immunogold labelling evidence that is used in an automatic assertion. ECO:RCT A type of immunolocalization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007486 immunolocalization evidence used in automatic assertion true true A type of immunolocalization evidence that is used in an automatic assertion. ECO:RCT A type of flow cytometry evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007487 flow cytometry evidence used in automatic assertion true true A type of flow cytometry evidence that is used in an automatic assertion. ECO:RCT A type of enzyme-linked immunoabsorbent assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007488 enzyme-linked immunoabsorbent assay evidence used in automatic assertion true true A type of enzyme-linked immunoabsorbent assay evidence that is used in an automatic assertion. ECO:RCT A type of high throughput mass spectrometry evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007489 high throughput mass spectrometry evidence used in automatic assertion true true A type of high throughput mass spectrometry evidence that is used in an automatic assertion. ECO:RCT A type of confocal microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007490 confocal microscopy evidence used in automatic assertion true true A type of confocal microscopy evidence that is used in an automatic assertion. ECO:RCT A type of wide-field microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007491 wide-field microscopy evidence used in automatic assertion true true A type of wide-field microscopy evidence that is used in an automatic assertion. ECO:RCT A type of immunogold labelling electron microscopy assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007492 immunogold labelling electron microscopy assay evidence used in automatic assertion true true true A type of immunogold labelling electron microscopy assay evidence that is used in an automatic assertion. ECO:RCT A type of electron microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007493 electron microscopy evidence used in automatic assertion true true A type of electron microscopy evidence that is used in an automatic assertion. ECO:RCT A type of immunoperoxidase immunolocalization evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007494 immunoperoxidase immunolocalization evidence used in automatic assertion true true A type of immunoperoxidase immunolocalization evidence that is used in an automatic assertion. ECO:RCT A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007495 immunoperoxidase immunolocalization electron microscopy evidence used in automatic assertion true true true A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in an automatic assertion. ECO:RCT A type of immunofluorescence confocal microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007496 immunofluorescence confocal microscopy evidence used in automatic assertion true true true A type of immunofluorescence confocal microscopy evidence that is used in an automatic assertion. ECO:RCT A type of immunofluorescence evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007497 immunofluorescence evidence used in automatic assertion true true A type of immunofluorescence evidence that is used in an automatic assertion. ECO:RCT A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007498 two-dimensional polyacrylamide gel electrophoresis evidence used in automatic assertion true true A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in an automatic assertion. ECO:RCT A type of alkaline phosphatase reporter gene assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007499 alkaline phosphatase reporter gene assay evidence used in automatic assertion true true A type of alkaline phosphatase reporter gene assay evidence that is used in an automatic assertion. ECO:RCT A type of beta-galactosidase reporter gene assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z LacZ transcript localization evidence used in automatic assertion eco ECO:0007500 beta-galactosidase reporter gene assay evidence used in automatic assertion true true A type of beta-galactosidase reporter gene assay evidence that is used in an automatic assertion. ECO:RCT A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007501 chloramphenicol acetyltransferase reporter gene assay evidence used in automatic assertion true true A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in an automatic assertion. ECO:RCT A type of chromatin immunoprecipitation-PCR evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007502 chromatin immunoprecipitation-PCR evidence used in automatic assertion true true A type of chromatin immunoprecipitation-PCR evidence that is used in an automatic assertion. ECO:RCT A type of immunoprecipitation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007503 immunoprecipitation evidence used in automatic assertion true true A type of immunoprecipitation evidence that is used in an automatic assertion. ECO:RCT A type of copper-phenanthroline footprinting evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007504 copper-phenanthroline footprinting evidence used in automatic assertion true true A type of copper-phenanthroline footprinting evidence that is used in an automatic assertion. ECO:RCT A type of nucleic acid binding evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007505 nucleic acid binding evidence used in automatic assertion true true A type of nucleic acid binding evidence that is used in an automatic assertion. ECO:RCT A type of DNA affinity chromatography evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007506 DNA affinity chromatography evidence used in automatic assertion true true A type of DNA affinity chromatography evidence that is used in an automatic assertion. ECO:RCT A type of DNAse footprinting evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007507 DNAse footprinting evidence used in automatic assertion true true A type of DNAse footprinting evidence that is used in an automatic assertion. ECO:RCT A type of fluorescence anisotropy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007508 fluorescence anisotropy evidence used in automatic assertion true true A type of fluorescence anisotropy evidence that is used in an automatic assertion. ECO:RCT A type of ferric uptake regulator titration assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007509 ferric uptake regulator titration assay evidence used in automatic assertion true true A type of ferric uptake regulator titration assay evidence that is used in an automatic assertion. ECO:RCT A type of systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007510 systematic evolution of ligands by exponential amplification evidence used in automatic assertion true true A type of systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion. ECO:RCT A type of glutathione S-transferase pull-down assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007511 glutathione S-transferase pull-down assay evidence used in automatic assertion true true A type of glutathione S-transferase pull-down assay evidence that is used in an automatic assertion. ECO:RCT A type of beta-glucuronidase reporter gene assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007512 beta-glucuronidase reporter gene assay evidence used in automatic assertion true true A type of beta-glucuronidase reporter gene assay evidence that is used in an automatic assertion. ECO:RCT A type of heteronuclear single quantum coherence spectroscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007513 heteronuclear single quantum coherence spectroscopy evidence used in automatic assertion true true A type of heteronuclear single quantum coherence spectroscopy evidence that is used in an automatic assertion. ECO:RCT A type of hydroxyl-radical footprinting evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007514 hydroxyl-radical footprinting evidence used in automatic assertion true true A type of hydroxyl-radical footprinting evidence that is used in an automatic assertion. ECO:RCT A type of isothermal titration calorimetry evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007515 isothermal titration calorimetry evidence used in automatic assertion true true A type of isothermal titration calorimetry evidence that is used in an automatic assertion. ECO:RCT A type of luciferase reporter gene assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007516 luciferase reporter gene assay evidence used in automatic assertion true true A type of luciferase reporter gene assay evidence that is used in an automatic assertion. ECO:RCT A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007517 methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in automatic assertion true true A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in an automatic assertion. ECO:RCT A type of northern blot evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007518 northern blot evidence used in automatic assertion true true A type of northern blot evidence that is used in an automatic assertion. ECO:RCT A type of methylation interference footprinting evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z premethylation interference footprinting evidence used in automatic assertion eco ECO:0007519 methylation interference footprinting evidence used in automatic assertion true true A type of methylation interference footprinting evidence that is used in an automatic assertion. ECO:RCT A type of primer extension assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007520 primer extension assay evidence used in automatic assertion true true A type of primer extension assay evidence that is used in an automatic assertion. ECO:RCT A type of quantitative polymerase chain reaction evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007521 quantitative polymerase chain reaction evidence used in automatic assertion true true A type of quantitative polymerase chain reaction evidence that is used in an automatic assertion. ECO:RCT A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007522 rapid amplification of cDNA ends polymerase chain reaction evidence used in automatic assertion true true A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in an automatic assertion. ECO:RCT A type of S1 nuclease protection assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007523 S1 nuclease protection assay evidence used in automatic assertion true true A type of S1 nuclease protection assay evidence that is used in an automatic assertion. ECO:RCT A type of site-directed mutagenesis evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007524 site-directed mutagenesis evidence used in automatic assertion true true A type of site-directed mutagenesis evidence that is used in an automatic assertion. ECO:RCT A type of survival rate analysis evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007525 survival rate analysis evidence used in automatic assertion true true A type of survival rate analysis evidence that is used in an automatic assertion. ECO:RCT A type of ultraviolet light footprinting evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007526 ultraviolet light footprinting evidence used in automatic assertion true true A type of ultraviolet light footprinting evidence that is used in an automatic assertion. ECO:RCT A type of xylE reporter gene assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007527 xylE reporter gene assay evidence used in automatic assertion true true A type of xylE reporter gene assay evidence that is used in an automatic assertion. ECO:RCT A type of ad-hoc qualitative phenotype observation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007528 ad-hoc qualitative phenotype observation evidence used in automatic assertion true true A type of ad-hoc qualitative phenotype observation evidence that is used in an automatic assertion. ECO:RCT A type of ad-hoc quantitative phenotype observation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007529 ad-hoc quantitative phenotype observation evidence used in automatic assertion true true A type of ad-hoc quantitative phenotype observation evidence that is used in an automatic assertion. ECO:RCT A type of cell transfection experiment evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007530 cell transfection experiment evidence used in automatic assertion true true A type of cell transfection experiment evidence that is used in an automatic assertion. ECO:RCT A type of yeast 2-hybrid evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007531 yeast 2-hybrid evidence used in automatic assertion true true A type of yeast 2-hybrid evidence that is used in an automatic assertion. ECO:RCT A type of Cya fusion reporter assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007532 Cya fusion reporter assay evidence used in automatic assertion true true A type of Cya fusion reporter assay evidence that is used in an automatic assertion. ECO:RCT A type of super-resolution microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007533 super-resolution microscopy evidence used in automatic assertion true true A type of super-resolution microscopy evidence that is used in an automatic assertion. ECO:RCT A type of fractionation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007534 fractionation evidence used in automatic assertion true true A type of fractionation evidence that is used in an automatic assertion. ECO:RCT A type of electrophysiology assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007535 electrophysiology assay evidence used in automatic assertion true true A type of electrophysiology assay evidence that is used in an automatic assertion. ECO:RCT A type of mRNA interactome capture evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007536 mRNA interactome capture evidence used in automatic assertion true true A type of mRNA interactome capture evidence that is used in an automatic assertion. ECO:RCT A type of patch-clamp recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007537 patch-clamp recording evidence used in automatic assertion true true A type of patch-clamp recording evidence that is used in an automatic assertion. ECO:RCT A type of whole-cell patch-clamp recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007538 whole-cell patch-clamp recording evidence used in automatic assertion true true A type of whole-cell patch-clamp recording evidence that is used in an automatic assertion. ECO:RCT A type of author statement from published clinical study that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco traceable author statement from published clinical study used in automatic assertion ECO:0007539 author statement from published clinical study used in automatic assertion true true A type of author statement from published clinical study that is used in an automatic assertion. ECO:RCT A type of inference based on individual clinical experience that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007540 inference based on individual clinical experience used in automatic assertion true true A type of inference based on individual clinical experience that is used in an automatic assertion. ECO:RCT A type of biofilm formation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007541 biofilm formation assay evidence used in automatic assertion true true A type of biofilm formation assay evidence that is used in an automatic assertion. ECO:RCT A type of microtiter plate biofilm assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007542 microtiter plate biofilm assay evidence used in automatic assertion true true A type of microtiter plate biofilm assay evidence that is used in an automatic assertion. ECO:RCT A type of air-liquid interface assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007543 air-liquid interface assay evidence used in automatic assertion true true A type of air-liquid interface assay evidence that is used in an automatic assertion. ECO:RCT A type of colony biofilm assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007544 colony biofilm assay evidence used in automatic assertion true true A type of colony biofilm assay evidence that is used in an automatic assertion. ECO:RCT A type of Kadouri drip-fed biofilm assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007545 Kadouri drip-fed biofilm assay evidence used in automatic assertion true true A type of Kadouri drip-fed biofilm assay evidence that is used in an automatic assertion. ECO:RCT A type of co-immunoprecipitation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007546 co-immunoprecipitation evidence used in automatic assertion true true true A type of co-immunoprecipitation evidence that is used in an automatic assertion. ECO:RCT A type of optogenetic evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007547 optogenetic evidence used in automatic assertion true true A type of optogenetic evidence that is used in an automatic assertion. ECO:RCT A type of fluorescent sensor evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007548 fluorescent sensor evidence used in automatic assertion true true A type of fluorescent sensor evidence that is used in an automatic assertion. ECO:RCT A type of genetically encoded fluorescent sensor evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007549 genetically encoded fluorescent sensor evidence used in automatic assertion true true A type of genetically encoded fluorescent sensor evidence that is used in an automatic assertion. ECO:RCT A type of genetically encoded fluorescent electrophysiology assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007550 genetically encoded fluorescent electrophysiology assay evidence used in automatic assertion true true true A type of genetically encoded fluorescent electrophysiology assay evidence that is used in an automatic assertion. ECO:RCT A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007551 genetically encoded fluorescent ion concentration sensor assay evidence used in automatic assertion true true A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in an automatic assertion. ECO:RCT A type of cell fractionation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007552 cell fractionation evidence used in automatic assertion true true A type of cell fractionation evidence that is used in an automatic assertion. ECO:RCT A type of extracellular recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007553 extracellular recording evidence used in automatic assertion true true A type of extracellular recording evidence that is used in an automatic assertion. ECO:RCT A type of single-unit extracellular recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007554 single-unit extracellular recording evidence used in automatic assertion true true A type of single-unit extracellular recording evidence that is used in an automatic assertion. ECO:RCT A type of field potential recording evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007555 field potential recording evidence used in automatic assertion true true A type of field potential recording evidence that is used in an automatic assertion. ECO:RCT A type of anti-sense experiment evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007556 anti-sense experiment evidence used in automatic assertion true true A type of anti-sense experiment evidence that is used in an automatic assertion. ECO:RCT A type of morpholino experiment evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007557 morpholino experiment evidence used in automatic assertion true true A type of morpholino experiment evidence that is used in an automatic assertion. ECO:RCT A type of RNAi evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007558 RNAi evidence used in automatic assertion true true A type of RNAi evidence that is used in an automatic assertion. ECO:RCT A type of pharmacological assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007559 pharmacological assay evidence used in automatic assertion true true A type of pharmacological assay evidence that is used in an automatic assertion. ECO:RCT A type of immunofluorescence wide-field microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007560 immunofluorescence wide-field microscopy evidence used in automatic assertion true true true A type of immunofluorescence wide-field microscopy evidence that is used in an automatic assertion. ECO:RCT A type of wide-field fluorescence microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007561 wide-field fluorescence microscopy evidence used in automatic assertion true true A type of wide-field fluorescence microscopy evidence that is used in an automatic assertion. ECO:RCT A type of over expression analysis evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007562 over expression analysis evidence used in automatic assertion true true A type of over expression analysis evidence that is used in an automatic assertion. ECO:RCT A type of cell-free assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007563 cell-free assay evidence used in automatic assertion true true A type of cell-free assay evidence that is used in an automatic assertion. ECO:RCT A type of fluorescence recovery after photobleaching evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007564 fluorescence recovery after photobleaching evidence used in automatic assertion true true A type of fluorescence recovery after photobleaching evidence that is used in an automatic assertion. ECO:RCT A type of immuno-labelling electron microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007565 immuno-labelling electron microscopy evidence used in automatic assertion true true A type of immuno-labelling electron microscopy evidence that is used in an automatic assertion. ECO:RCT A type of immunofluorescence super resolution microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007566 immunofluorescence super resolution microscopy evidence used in automatic assertion true true A type of immunofluorescence super resolution microscopy evidence that is used in an automatic assertion. ECO:RCT A type of co-purification evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007567 co-purification evidence used in automatic assertion true true A type of co-purification evidence that is used in an automatic assertion. ECO:RCT A type of yeast one-hybrid evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007568 yeast one-hybrid evidence used in automatic assertion true true A type of yeast one-hybrid evidence that is used in an automatic assertion. ECO:RCT A type of split-ubiquitin assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007569 split-ubiquitin assay evidence used in automatic assertion true true A type of split-ubiquitin assay evidence that is used in an automatic assertion. ECO:RCT A type of far-Western blotting evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007570 far-Western blotting evidence used in automatic assertion true true A type of far-Western blotting evidence that is used in an automatic assertion. ECO:RCT A type of affinity chromatography evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007571 affinity chromatography evidence used in automatic assertion true true A type of affinity chromatography evidence that is used in an automatic assertion. ECO:RCT A type of ribohomopolymer binding assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007572 ribohomopolymer binding assay evidence used in automatic assertion true true A type of ribohomopolymer binding assay evidence that is used in an automatic assertion. ECO:RCT A type of protein:ion binding evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007573 protein:ion binding evidence used in automatic assertion true true A type of protein:ion binding evidence that is used in an automatic assertion. ECO:RCT A type of Southwestern blot evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007574 Southwestern blot evidence used in automatic assertion true true A type of Southwestern blot evidence that is used in an automatic assertion. ECO:RCT A type of Northwestern blot evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007575 Northwestern blot evidence used in automatic assertion true true A type of Northwestern blot evidence that is used in an automatic assertion. ECO:RCT A type of bacterial one-hybrid evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007576 bacterial one-hybrid evidence used in automatic assertion true true A type of bacterial one-hybrid evidence that is used in an automatic assertion. ECO:RCT A type of protein-binding microarray evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007577 protein-binding microarray evidence used in automatic assertion true true true A type of protein-binding microarray evidence that is used in an automatic assertion. ECO:RCT A type of functional complementation evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007578 functional complementation evidence used in automatic assertion true true A type of functional complementation evidence that is used in an automatic assertion. ECO:RCT A type of transgenic rescue experiment evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007579 transgenic rescue experiment evidence used in automatic assertion true true A type of transgenic rescue experiment evidence that is used in an automatic assertion. ECO:RCT A type of transient rescue experiment evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007580 transient rescue experiment evidence used in automatic assertion true true A type of transient rescue experiment evidence that is used in an automatic assertion. ECO:RCT A type of suppressor/enhancer interaction evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007581 suppressor/enhancer interaction evidence used in automatic assertion true true A type of suppressor/enhancer interaction evidence that is used in an automatic assertion. ECO:RCT A type of double mutant phenotype evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007582 double mutant phenotype evidence used in automatic assertion true true A type of double mutant phenotype evidence that is used in an automatic assertion. ECO:RCT A type of epistatic interaction evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007583 epistatic interaction evidence used in automatic assertion true true A type of epistatic interaction evidence that is used in an automatic assertion. ECO:RCT A type of functional complementation in heterologous system evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007584 functional complementation in heterologous system evidence used in automatic assertion true true A type of functional complementation in heterologous system evidence that is used in an automatic assertion. ECO:RCT A type of temperature-sensitive mutant phenotype evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007585 temperature-sensitive mutant phenotype evidence used in automatic assertion true true A type of temperature-sensitive mutant phenotype evidence that is used in an automatic assertion. ECO:RCT A type of recessive mutant phenotype evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007586 recessive mutant phenotype evidence used in automatic assertion true true A type of recessive mutant phenotype evidence that is used in an automatic assertion. ECO:RCT A type of high throughput mutant phenotype evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007587 high throughput mutant phenotype evidence used in automatic assertion true true true A type of high throughput mutant phenotype evidence that is used in an automatic assertion. ECO:RCT A type of high throughput genetic interaction evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007588 high throughput genetic interaction evidence used in automatic assertion true true true A type of high throughput genetic interaction evidence that is used in an automatic assertion. ECO:RCT A type of high throughput direct assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007589 high throughput direct assay evidence used in automatic assertion true true true A type of high throughput direct assay evidence that is used in an automatic assertion. ECO:RCT A type of high throughput expression pattern evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007590 high throughput expression pattern evidence used in automatic assertion true true true A type of high throughput expression pattern evidence that is used in an automatic assertion. ECO:RCT A type of radioligand binding assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007591 radioligand binding assay evidence used in automatic assertion true true A type of radioligand binding assay evidence that is used in an automatic assertion. ECO:RCT A type of combinatorial evidence from author knowledge and experimental evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007592 combinatorial evidence from author knowledge and experimental evidence used in automatic assertion true true true A type of combinatorial evidence from author knowledge and experimental evidence that is used in an automatic assertion. ECO:RCT A type of combinatorial evidence from curator knowledge and experimental evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007593 combinatorial evidence from curator knowledge and experimental evidence used in automatic assertion true true true true A type of combinatorial evidence from curator knowledge and experimental evidence that is used in an automatic assertion. ECO:RCT A type of voltammetry evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007594 voltammetry evidence used in automatic assertion true true A type of voltammetry evidence that is used in an automatic assertion. ECO:RCT A type of photoconversion evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007595 photoconversion evidence used in automatic assertion true true A type of photoconversion evidence that is used in an automatic assertion. ECO:RCT A type of agglutination test evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007596 agglutination test evidence used in automatic assertion true true A type of agglutination test evidence that is used in an automatic assertion. ECO:RCT A type of slide agglutination test evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007597 slide agglutination test evidence used in automatic assertion true true A type of slide agglutination test evidence that is used in an automatic assertion. ECO:RCT A type of direct Coombs test evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007598 direct Coombs test evidence used in automatic assertion true true A type of direct Coombs test evidence that is used in an automatic assertion. ECO:RCT A type of indirect Coombs test evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007599 indirect Coombs test evidence used in automatic assertion true true A type of indirect Coombs test evidence that is used in an automatic assertion. ECO:RCT A type of direct hemagglutination assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007600 direct hemagglutination assay evidence used in automatic assertion true true A type of direct hemagglutination assay evidence that is used in an automatic assertion. ECO:RCT A type of viral hemagglutination inhibition assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007601 viral hemagglutination inhibition assay evidence used in automatic assertion true true A type of viral hemagglutination inhibition assay evidence that is used in an automatic assertion. ECO:RCT A type of compement fixation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007602 compement fixation assay evidence used in automatic assertion true true A type of compement fixation assay evidence that is used in an automatic assertion. ECO:RCT A type of neutralization test assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007603 neutralization test assay evidence used in automatic assertion true true A type of neutralization test assay evidence that is used in an automatic assertion. ECO:RCT A type of copper transport assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007604 copper transport assay evidence used in automatic assertion true true A type of copper transport assay evidence that is used in an automatic assertion. ECO:RCT A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007605 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence used in automatic assertion true true A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in an automatic assertion. ECO:RCT A type of plaque assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007606 plaque assay evidence used in automatic assertion true true A type of plaque assay evidence that is used in an automatic assertion. ECO:RCT A type of epifluorescence microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007607 epifluorescence microscopy evidence used in automatic assertion true true A type of epifluorescence microscopy evidence that is used in an automatic assertion. ECO:RCT A type of transmission electron microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007608 transmission electron microscopy evidence used in automatic assertion true true A type of transmission electron microscopy evidence that is used in an automatic assertion. ECO:RCT A type of scanning electron microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007609 scanning electron microscopy evidence used in automatic assertion true true A type of scanning electron microscopy evidence that is used in an automatic assertion. ECO:RCT A type of time-lapsed microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007610 time-lapsed microscopy evidence used in automatic assertion true true A type of time-lapsed microscopy evidence that is used in an automatic assertion. ECO:RCT A type of phase contrast microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007611 phase contrast microscopy evidence used in automatic assertion true true A type of phase contrast microscopy evidence that is used in an automatic assertion. ECO:RCT A type of transmitted light brightfied mircoscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007612 transmitted light brightfied mircoscopy evidence used in automatic assertion true true A type of transmitted light brightfied mircoscopy evidence that is used in an automatic assertion. ECO:RCT A type of koehler illumination microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007613 koehler illumination microscopy evidence used in automatic assertion true true A type of koehler illumination microscopy evidence that is used in an automatic assertion. ECO:RCT A type of differential interference contrast microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007614 differential interference contrast microscopy evidence used in automatic assertion true true A type of differential interference contrast microscopy evidence that is used in an automatic assertion. ECO:RCT A type of extended field laser confocal microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007615 extended field laser confocal microscopy evidence used in automatic assertion true true A type of extended field laser confocal microscopy evidence that is used in an automatic assertion. ECO:RCT A type of confocal laser scanning microscopy evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007616 confocal laser scanning microscopy evidence used in automatic assertion true true A type of confocal laser scanning microscopy evidence that is used in an automatic assertion. ECO:RCT A type of light scattering assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007617 light scattering assay evidence used in automatic assertion true true A type of light scattering assay evidence that is used in an automatic assertion. ECO:RCT A type of dynamic light scattering assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007618 dynamic light scattering assay evidence used in automatic assertion true true A type of dynamic light scattering assay evidence that is used in an automatic assertion. ECO:RCT A type of static light scattering assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007619 static light scattering assay evidence used in automatic assertion true true A type of static light scattering assay evidence that is used in an automatic assertion. ECO:RCT A type of colony papillation assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007620 colony papillation assay evidence used in automatic assertion true true A type of colony papillation assay evidence that is used in an automatic assertion. ECO:RCT A type of crystal violet staining evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007621 crystal violet staining evidence used in automatic assertion true true A type of crystal violet staining evidence that is used in an automatic assertion. ECO:RCT A type of flow cell biofilm assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007622 flow cell biofilm assay evidence used in automatic assertion true true A type of flow cell biofilm assay evidence that is used in an automatic assertion. ECO:RCT A type of bacterial 2-hybrid assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007623 bacterial 2-hybrid assay evidence used in automatic assertion true true A type of bacterial 2-hybrid assay evidence that is used in an automatic assertion. ECO:RCT A type of phenomic profiling assay evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007624 phenomic profiling assay evidence used in automatic assertion true true A type of phenomic profiling assay evidence that is used in an automatic assertion. ECO:RCT A type of colony morphology evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007625 colony morphology evidence used in automatic assertion true true A type of colony morphology evidence that is used in an automatic assertion. ECO:RCT A type of colony color evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007626 colony color evidence used in automatic assertion true true A type of colony color evidence that is used in an automatic assertion. ECO:RCT A type of colony size evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007627 colony size evidence used in automatic assertion true true A type of colony size evidence that is used in an automatic assertion. ECO:RCT A type of zone of inhibition evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007628 zone of inhibition evidence used in automatic assertion true true A type of zone of inhibition evidence that is used in an automatic assertion. ECO:RCT A type of Etest evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007629 Etest evidence used in automatic assertion true true A type of Etest evidence that is used in an automatic assertion. ECO:RCT A type of ribosome profiling evidence that is used in an automatic assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007630 ribosome profiling evidence used in automatic assertion true true A type of ribosome profiling evidence that is used in an automatic assertion. ECO:RCT A type of evidence based on computational logical inference that is used in a manual assertion. rctauber 2018-05-14T09:47:55Z eco ECO:0007631 evidence based on computational logical inference used in manual assertion true true A type of evidence based on computational logical inference that is used in a manual assertion. ECO:RCT A type of transcriptional activation assay evidence that is used in a manual assertion. rctauber 2018-05-18T08:34:35Z eco ECO:0007632 transcriptional activation assay evidence used in manual assertion true true A type of transcriptional activation assay evidence that is used in a manual assertion. ECO:RCT A type of transcriptional activation assay evidence that is used in an automatic assertion. rctauber 2018-05-18T08:34:35Z eco ECO:0007633 transcriptional activation assay evidence used in automatic assertion true true A type of transcriptional activation assay evidence that is used in an automatic assertion. ECO:RCT A type of experimental phenotypic evidence that is used in a manual assertion. rctauber 2018-06-20T02:12:00Z eco experimental phenotypic evidence used in manual assertion true true A type of experimental phenotypic evidence that is used in a manual assertion. ECO:RCT A type of experimental phenotypic evidence that is used in an automatic assertion. rctauber 2018-06-20T02:12:00Z eco experimental phenotypic evidence used in automatic assertion true true A type of experimental phenotypic evidence that is used in an automatic assertion. ECO:RCT The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides. DNA breakdown, endonucleolytic DNA degradation, endonucleolytic endonucleolytic DNA catabolism endonucleolytic degradation of DNA biological_process GO:0000737 DNA catabolic process, endonucleolytic The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides. GOC:elh GOC:mah core promoter binding 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. kchris 2010-08-27T03:00:52Z molecular_function GO:0001047 core promoter binding 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. GOC:txnOH 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. kchris 2010-10-21T04:08:56Z molecular_function GO:0001067 regulatory region nucleic acid binding 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. GOC:txnOH action potential 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. biological_process GO:0001508 Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. action potential 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. GOC:dph GOC:go_curators GOC:tb ISBN:978-0-07-139011-8 Any process that modulates the frequency, rate, extent or direction of cell growth. Reactome:REACT_6201 biological_process GO:0001558 regulation of cell growth Any process that modulates the frequency, rate, extent or direction of cell growth. GOC:go_curators Reactome:REACT_6201 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 biological_process GO:0001677 formation of translation initiation ternary complex 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). GOC:hjd The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interferon production interleukin production biological_process GO:0001816 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. cytokine production The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. GOC:add ISBN:0781735149 interferon production GOC:add GOC:mah interleukin production GOC:add GOC:mah http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F Any process that modulates the frequency, rate, or extent of production of a cytokine. biological_process GO:0001817 regulation of cytokine production Any process that modulates the frequency, rate, or extent of production of a cytokine. GOC:add ISBN:0781735149 Any process that stops, prevents, or reduces the rate of production of a cytokine. down regulation of cytokine production down-regulation of cytokine production downregulation of cytokine production inhibition of cytokine production biological_process GO:0001818 negative regulation of cytokine production Any process that stops, prevents, or reduces the rate of production of a cytokine. GOC:add ISBN:0781735149 Any process that activates or increases the frequency, rate or extent of production of a cytokine. up regulation of cytokine production up-regulation of cytokine production upregulation of cytokine production activation of cytokine production stimulation of cytokine production biological_process GO:0001819 positive regulation of cytokine production Any process that activates or increases the frequency, rate or extent of production of a cytokine. GOC:add ISBN:0781735149 cell killing Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. biological_process necrosis GO:0001906 cell killing Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. GOC:add The controlled release of a peptide from a cell or a tissue. biological_process GO:0002790 peptide secretion The controlled release of a peptide from a cell or a tissue. GOC:add Any process that modulates the frequency, rate, or extent of peptide secretion. biological_process GO:0002791 regulation of peptide secretion Any process that modulates the frequency, rate, or extent of peptide secretion. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion. down regulation of peptide secretion down-regulation of peptide secretion downregulation of peptide secretion inhibition of peptide secretion biological_process GO:0002792 negative regulation of peptide secretion Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion. GOC:add Any process that activates or increases the frequency, rate, or extent of peptide secretion. up regulation of peptide secretion up-regulation of peptide secretion upregulation of peptide secretion activation of peptide secretion stimulation of peptide secretion biological_process GO:0002793 positive regulation of peptide secretion Any process that activates or increases the frequency, rate, or extent of peptide secretion. GOC:add Any process that modulates the frequency, rate, or extent of a response to biotic stimulus. biological_process GO:0002831 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 modulates the frequency, rate, or extent of a response to biotic stimulus. GOC:add 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 biological_process GO:0002832 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. negative regulation of response to biotic stimulus Any process that stops, prevents, or reduces the frequency, rate, or extent of a response to biotic stimulus. GOC:add 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 biological_process GO:0002833 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. positive regulation of response to biotic stimulus Any process that activates or increases the frequency, rate, or extent of a response to biotic stimulus. GOC:add molecular_function 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. GO:0005554 molecular function molecular_function GO:0003674 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. GO:molecular_function molecular_function 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. GOC:pdt Interacting selectively and non-covalently with any nucleic acid. molecular_function GO:0003676 nucleic acid binding Interacting selectively and non-covalently with any nucleic acid. GOC:jl Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0043566 plasmid binding molecular_function microtubule/chromatin interaction structure specific DNA binding structure-specific DNA binding GO:0003677 DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GOC:dph GOC:jl GOC:tb GOC:vw 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. molecular_function B cell receptor activity antibody immunoglobulin opsonin activity GO:0003823 antigen binding 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. GOC:jl ISBN:0198506732 ISBN:0721662544 catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. Wikipedia:Enzyme enzyme activity molecular_function GO:0003824 catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GOC:vw ISBN:0198506732 enzyme activity GOC:dph GOC:tb RNA-directed DNA polymerase activity 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. RNA-directed DNA polymerase activity Catalysis of the hydrolysis of ester linkages within nucleic acids. EC:3.1 molecular_function GO:0004518 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. nuclease activity Catalysis of the hydrolysis of ester linkages within nucleic acids. ISBN:0198547684 Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks. Reactome:REACT_100654 Reactome:REACT_101397 Reactome:REACT_103600 Reactome:REACT_106502 Reactome:REACT_108614 Reactome:REACT_110731 Reactome:REACT_112366 Reactome:REACT_1124 Reactome:REACT_112509 Reactome:REACT_112615 Reactome:REACT_112782 Reactome:REACT_113127 Reactome:REACT_113480 Reactome:REACT_113819 Reactome:REACT_114931 Reactome:REACT_115221 Reactome:REACT_115226 Reactome:REACT_115382 Reactome:REACT_115937 Reactome:REACT_116011 Reactome:REACT_1914 Reactome:REACT_34610 Reactome:REACT_6746 Reactome:REACT_6774 Reactome:REACT_77706 Reactome:REACT_78624 Reactome:REACT_79198 Reactome:REACT_80387 Reactome:REACT_80628 Reactome:REACT_80681 Reactome:REACT_80797 Reactome:REACT_81714 Reactome:REACT_87541 Reactome:REACT_89800 Reactome:REACT_90034 Reactome:REACT_90935 Reactome:REACT_92894 molecular_function GO:0004519 endonuclease activity Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks. GOC:mah ISBN:0198547684 Reactome:REACT_100654 3'- incision of DNA by XPG in GG-NER, Arabidopsis thaliana Reactome:REACT_101397 3'- incision of DNA by XPG in GG-NER, Danio rerio Reactome:REACT_103600 3'- incision of DNA by XPG in GG-NER, Gallus gallus Reactome:REACT_106502 3'- incision of DNA by XPG in GG-NER, Rattus norvegicus Reactome:REACT_108614 3'- incision of DNA by XPG in GG-NER, Taeniopygia guttata Reactome:REACT_110731 3'- incision of DNA by XPG in GG-NER, Xenopus tropicalis Reactome:REACT_112366 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Danio rerio Reactome:REACT_1124 3'- incision of DNA by XPG in GG-NER, Homo sapiens Reactome:REACT_112509 Cleavage of mRNA at the 3'-end, Arabidopsis thaliana Reactome:REACT_112615 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Rattus norvegicus Reactome:REACT_112782 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Xenopus tropicalis Reactome:REACT_113127 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Taeniopygia guttata Reactome:REACT_113480 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Gallus gallus Reactome:REACT_113819 Cleavage of mRNA at the 3'-end, Drosophila melanogaster Reactome:REACT_114931 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Canis familiaris Reactome:REACT_115221 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Mus musculus Reactome:REACT_115226 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Bos taurus Reactome:REACT_115382 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Sus scrofa Reactome:REACT_115937 Displacement of DNA glycosylase and endonucleolytic cleavage by DNA-lyase, Gallus gallus Reactome:REACT_116011 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Gallus gallus Reactome:REACT_1914 Cleavage of mRNA at the 3'-end, Homo sapiens Reactome:REACT_34610 Cleavage of mRNA at the 3'-end, Bos taurus Reactome:REACT_6746 Removal of 3'-phosphate moiety from DSB ends, Homo sapiens Reactome:REACT_6774 Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Homo sapiens Reactome:REACT_77706 Cleavage of mRNA at the 3'-end, Taeniopygia guttata Reactome:REACT_78624 3'- incision of DNA by XPG in GG-NER, Canis familiaris Reactome:REACT_79198 Cleavage of mRNA at the 3'-end, Canis familiaris Reactome:REACT_80387 3'- incision of DNA by XPG in GG-NER, Caenorhabditis elegans Reactome:REACT_80628 3'- incision of DNA by XPG in GG-NER, Saccharomyces cerevisiae Reactome:REACT_80681 3'- incision of DNA by XPG in GG-NER, Bos taurus Reactome:REACT_80797 Cleavage of mRNA at the 3'-end, Mus musculus Reactome:REACT_81714 3'- incision of DNA by XPG in GG-NER, Oryza sativa Reactome:REACT_87541 Cleavage of mRNA at the 3'-end, Xenopus tropicalis Reactome:REACT_89800 3'- incision of DNA by XPG in GG-NER, Schizosaccharomyces pombe Reactome:REACT_90034 3'- incision of DNA by XPG in GG-NER, Mus musculus Reactome:REACT_90935 3'- incision of DNA by XPG in GG-NER, Sus scrofa Reactome:REACT_92894 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. Reactome:REACT_101184 Reactome:REACT_101250 Reactome:REACT_101987 Reactome:REACT_103441 Reactome:REACT_103771 Reactome:REACT_104010 Reactome:REACT_104673 Reactome:REACT_104703 Reactome:REACT_104968 Reactome:REACT_106756 Reactome:REACT_109040 Reactome:REACT_109537 Reactome:REACT_109692 Reactome:REACT_110386 Reactome:REACT_112122 Reactome:REACT_112152 Reactome:REACT_115154 Reactome:REACT_115463 Reactome:REACT_115479 Reactome:REACT_1274 Reactome:REACT_1311 Reactome:REACT_1964 Reactome:REACT_27164 Reactome:REACT_27209 Reactome:REACT_28610 Reactome:REACT_28960 Reactome:REACT_30718 Reactome:REACT_31162 Reactome:REACT_31548 Reactome:REACT_31660 Reactome:REACT_31823 Reactome:REACT_32833 Reactome:REACT_33043 Reactome:REACT_78421 Reactome:REACT_79265 Reactome:REACT_80173 Reactome:REACT_80298 Reactome:REACT_80967 Reactome:REACT_811 Reactome:REACT_81197 Reactome:REACT_82925 Reactome:REACT_83838 Reactome:REACT_85019 Reactome:REACT_88339 Reactome:REACT_90087 Reactome:REACT_92741 Reactome:REACT_94592 Reactome:REACT_94820 Reactome:REACT_95903 Reactome:REACT_97114 Reactome:REACT_98405 Reactome:REACT_98417 Reactome:REACT_99783 molecular_function DNA nicking activity endonuclease G activity GO:0004520 endodeoxyribonuclease activity Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks. GOC:mah ISBN:0198547684 Reactome:REACT_101184 5'-incision of DNA by ERCC1-XPF in GG-NER, Danio rerio Reactome:REACT_101250 5' incision leading to excision of DNA fragment with lesion in TC-NER, Caenorhabditis elegans Reactome:REACT_101987 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Dictyostelium discoideum Reactome:REACT_103441 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Rattus norvegicus Reactome:REACT_103771 3' incision of the lesioned strand of DNA in TC-NER, Xenopus tropicalis Reactome:REACT_104010 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Danio rerio Reactome:REACT_104673 5' incision leading to excision of DNA fragment with lesion in TC-NER, Schizosaccharomyces pombe Reactome:REACT_104703 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Taeniopygia guttata Reactome:REACT_104968 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Sus scrofa Reactome:REACT_106756 3' incision of the lesioned strand of DNA in TC-NER, Drosophila melanogaster Reactome:REACT_109040 3' incision of the lesioned strand of DNA in TC-NER, Canis familiaris Reactome:REACT_109537 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Xenopus tropicalis Reactome:REACT_109692 3' incision of the lesioned strand of DNA in TC-NER, Sus scrofa Reactome:REACT_110386 3' incision of the lesioned strand of DNA in TC-NER, Danio rerio Reactome:REACT_112122 5'-incision of DNA by ERCC1-XPF in GG-NER, Xenopus tropicalis Reactome:REACT_112152 3' incision of the lesioned strand of DNA in TC-NER, Taeniopygia guttata Reactome:REACT_115154 5' incision leading to excision of DNA fragment with lesion in TC-NER, Gallus gallus Reactome:REACT_115463 5' incision leading to excision of DNA fragment with lesion in TC-NER, Taeniopygia guttata Reactome:REACT_115479 3' incision of the lesioned strand of DNA in TC-NER, Gallus gallus Reactome:REACT_1274 3' incision of the lesioned strand of DNA in TC-NER, Homo sapiens Reactome:REACT_1311 5'-incision of DNA by ERCC1-XPF in GG-NER, Homo sapiens Reactome:REACT_1964 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Homo sapiens Reactome:REACT_27164 Removal of SPO11 and Resection of 5' Ends of DNA (yeast), Saccharomyces cerevisiae Reactome:REACT_27209 Removal of SPO11 and Resection of 5' Ends of DNA, Homo sapiens Reactome:REACT_28610 5' incision leading to excision of DNA fragment with lesion in TC-NER, Bos taurus Reactome:REACT_28960 3' incision of the lesioned strand of DNA in TC-NER, Rattus norvegicus Reactome:REACT_30718 3' incision of the lesioned strand of DNA in TC-NER, Dictyostelium discoideum Reactome:REACT_31162 5' incision leading to excision of DNA fragment with lesion in TC-NER, Arabidopsis thaliana Reactome:REACT_31548 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Caenorhabditis elegans Reactome:REACT_31660 3' incision of the lesioned strand of DNA in TC-NER, Schizosaccharomyces pombe Reactome:REACT_31823 5' incision leading to excision of DNA fragment with lesion in TC-NER, Oryza sativa Reactome:REACT_32833 3' incision of the lesioned strand of DNA in TC-NER, Saccharomyces cerevisiae Reactome:REACT_33043 3' incision of the lesioned strand of DNA in TC-NER, Bos taurus Reactome:REACT_78421 5' incision leading to excision of DNA fragment with lesion in TC-NER, Sus scrofa Reactome:REACT_79265 5' incision leading to excision of DNA fragment with lesion in TC-NER, Dictyostelium discoideum Reactome:REACT_80173 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Mus musculus Reactome:REACT_80298 3' incision of the lesioned strand of DNA in TC-NER, Caenorhabditis elegans Reactome:REACT_80967 3' incision of the lesioned strand of DNA in TC-NER, Oryza sativa Reactome:REACT_811 5' incision leading to excision of DNA fragment with lesion in TC-NER, Homo sapiens Reactome:REACT_81197 5' incision leading to excision of DNA fragment with lesion in TC-NER, Mus musculus Reactome:REACT_82925 5' incision leading to excision of DNA fragment with lesion in TC-NER, Canis familiaris Reactome:REACT_83838 5'-incision of DNA by ERCC1-XPF in GG-NER, Rattus norvegicus Reactome:REACT_85019 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Drosophila melanogaster Reactome:REACT_88339 5' incision leading to excision of DNA fragment with lesion in TC-NER, Rattus norvegicus Reactome:REACT_90087 5' incision leading to excision of DNA fragment with lesion in TC-NER, Danio rerio Reactome:REACT_92741 3' incision of the lesioned strand of DNA in TC-NER, Arabidopsis thaliana Reactome:REACT_94592 5' incision leading to excision of DNA fragment with lesion in TC-NER, Drosophila melanogaster Reactome:REACT_94820 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Canis familiaris Reactome:REACT_95903 5'-incision of DNA by ERCC1-XPF in GG-NER, Mus musculus Reactome:REACT_97114 5' incision leading to excision of DNA fragment with lesion in TC-NER, Xenopus tropicalis Reactome:REACT_98405 5' incision leading to excision of DNA fragment with lesion in TC-NER, Saccharomyces cerevisiae Reactome:REACT_98417 APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Bos taurus Reactome:REACT_99783 3' incision of the lesioned strand of DNA in TC-NER, Mus musculus DNA nicking activity GOC:mah Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid. GO:0004537 Reactome:REACT_100642 Reactome:REACT_101208 Reactome:REACT_110575 Reactome:REACT_13702 Reactome:REACT_29722 Reactome:REACT_31853 Reactome:REACT_90424 Reactome:REACT_95359 Reactome:REACT_98682 caspase-activated deoxyribonuclease activity molecular_function GO:0004536 deoxyribonuclease activity Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid. GOC:mah ISBN:0198547684 Reactome:REACT_100642 Cleavage of DNA by DFF40, Xenopus tropicalis Reactome:REACT_101208 Cleavage of DNA by DFF40, Bos taurus Reactome:REACT_110575 Cleavage of DNA by DFF40, Sus scrofa Reactome:REACT_13702 Cleavage of DNA by DFF40, Homo sapiens Reactome:REACT_29722 Cleavage of DNA by DFF40, Danio rerio Reactome:REACT_31853 Cleavage of DNA by DFF40, Taeniopygia guttata Reactome:REACT_90424 Cleavage of DNA by DFF40, Gallus gallus Reactome:REACT_95359 Cleavage of DNA by DFF40, Rattus norvegicus Reactome:REACT_98682 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. GO:0005478 Reactome:REACT_6315 molecular_function carrier GO:0005215 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. transporter activity Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. GOC:ai GOC:dgf Reactome:REACT_6315 Virion-associated M2 protein mediated ion infusion, Homo sapiens ion channel activity 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). molecular_function GO:0005216 ion channel activity 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). GOC:cy GOC:mtg_transport GOC:pr ISBN:0815340729 The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. Wikipedia:Binding_(molecular) ligand molecular_function GO:0005488 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. binding The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. GOC:ceb GOC:mah ISBN:0198506732 cellular_component 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). GO:0008372 NIF_Subcellular:sao-1337158144 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. 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. cellular_component 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). GOC:pdt NIF_Subcellular:sao-1337158144 subcellular entity NIF_Subcellular:nlx_subcell_100315 The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. Wikipedia:Intracellular internal to cell protoplasm cellular_component nucleocytoplasm protoplast GO:0005622 intracellular The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. ISBN:0198506732 nucleocytoplasm GOC:mah protoplast GOC:mah The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. cell and encapsulating structures NIF_Subcellular:sao1813327414 Wikipedia:Cell_(biology) cellular_component GO:0005623 cell The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:go_curators Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GO:0055134 cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process nucleobase, nucleoside and nucleotide metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0006139 nucleobase-containing compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:ai nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. GO:0055132 DNA metabolism cellular DNA metabolism biological_process GO:0006259 DNA metabolic process Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. ISBN:0198506732 The cellular 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. GO:0055133 Reactome:REACT_100559 Reactome:REACT_101280 Reactome:REACT_101497 Reactome:REACT_102679 Reactome:REACT_103614 Reactome:REACT_104547 Reactome:REACT_105292 Reactome:REACT_105467 Reactome:REACT_105835 Reactome:REACT_106018 Reactome:REACT_106104 Reactome:REACT_106382 Reactome:REACT_106434 Reactome:REACT_106732 Reactome:REACT_107075 Reactome:REACT_107423 Reactome:REACT_108461 Reactome:REACT_108634 Reactome:REACT_108739 Reactome:REACT_108768 Reactome:REACT_108929 Reactome:REACT_109137 Reactome:REACT_112472 Reactome:REACT_113703 Reactome:REACT_29423 Reactome:REACT_29444 Reactome:REACT_29691 Reactome:REACT_29764 Reactome:REACT_30149 Reactome:REACT_31024 Reactome:REACT_31919 Reactome:REACT_32546 Reactome:REACT_32932 Reactome:REACT_33572 Reactome:REACT_33874 Reactome:REACT_50018 Reactome:REACT_53588 Reactome:REACT_6729 Reactome:REACT_6738 Reactome:REACT_6750 Reactome:REACT_6769 Reactome:REACT_6798 Reactome:REACT_6869 Reactome:REACT_6936 Reactome:REACT_6939 Reactome:REACT_77532 Reactome:REACT_79188 Reactome:REACT_79450 Reactome:REACT_80432 Reactome:REACT_80571 Reactome:REACT_80896 Reactome:REACT_80988 Reactome:REACT_81803 Reactome:REACT_83095 Reactome:REACT_84829 Reactome:REACT_85561 Reactome:REACT_86410 Reactome:REACT_86739 Reactome:REACT_87233 Reactome:REACT_87449 Reactome:REACT_87590 Reactome:REACT_88085 Reactome:REACT_88384 Reactome:REACT_88529 Reactome:REACT_89355 Reactome:REACT_89439 Reactome:REACT_89725 Reactome:REACT_90512 Reactome:REACT_90809 Reactome:REACT_90838 Reactome:REACT_91184 Reactome:REACT_91302 Reactome:REACT_92527 Reactome:REACT_92644 Reactome:REACT_92706 Reactome:REACT_94983 Reactome:REACT_95253 Reactome:REACT_95329 Reactome:REACT_96115 Reactome:REACT_96804 Reactome:REACT_96998 Reactome:REACT_97204 Reactome:REACT_97726 Reactome:REACT_99948 Wikipedia:DNA_replication biological_process GO:0006260 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'. DNA replication 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. GOC:mah Reactome:REACT_100559 Activation of ATR in response to replication stress, Mus musculus Reactome:REACT_101280 Activation of claspin, Xenopus tropicalis Reactome:REACT_101497 Activation of claspin, Bos taurus Reactome:REACT_102679 Activation of ATR in response to replication stress, Gallus gallus Reactome:REACT_103614 Stalling of DNA replication fork and RPA binding, Taeniopygia guttata Reactome:REACT_104547 Recruitment and activation of Chk1, Gallus gallus Reactome:REACT_105292 Activation of ATR in response to replication stress, Xenopus tropicalis Reactome:REACT_105467 Loading of claspin onto DNA during replication origin firing, Danio rerio Reactome:REACT_105835 Stalling of DNA replication fork and RPA binding, Gallus gallus Reactome:REACT_106018 Recruitment of Rad17-RFC complex to DNA, Gallus gallus Reactome:REACT_106104 Binding of ATR-ATRIP to the RPA-ssDNA complex, Bos taurus Reactome:REACT_106382 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Drosophila melanogaster Reactome:REACT_106434 Activation of claspin, Canis familiaris Reactome:REACT_106732 Recruitment and activation of Chk1, Canis familiaris Reactome:REACT_107075 Activation of ATR in response to replication stress, Danio rerio Reactome:REACT_107423 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Caenorhabditis elegans Reactome:REACT_108461 Recruitment and activation of Chk1, Bos taurus Reactome:REACT_108634 Loading of claspin onto DNA during replication origin firing, Mus musculus Reactome:REACT_108739 Binding of ATR-ATRIP to the RPA-ssDNA complex, Xenopus tropicalis Reactome:REACT_108768 Activation of ATR in response to replication stress, Bos taurus Reactome:REACT_108929 Activation of ATR in response to replication stress, Drosophila melanogaster Reactome:REACT_109137 Stalling of DNA replication fork and RPA binding, Rattus norvegicus Reactome:REACT_112472 Activation of ATR in response to replication stress, Saccharomyces cerevisiae Reactome:REACT_113703 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Gallus gallus Reactome:REACT_29423 Activation of ATR in response to replication stress, Schizosaccharomyces pombe Reactome:REACT_29444 Binding of ATR-ATRIP to the RPA-ssDNA complex, Taeniopygia guttata Reactome:REACT_29691 Activation of ATR in response to replication stress, Rattus norvegicus Reactome:REACT_29764 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Taeniopygia guttata Reactome:REACT_30149 Activation of claspin, Rattus norvegicus Reactome:REACT_31024 Recruitment of Rad17-RFC complex to DNA, Xenopus tropicalis Reactome:REACT_31919 Loading of claspin onto DNA during replication origin firing, Rattus norvegicus Reactome:REACT_32546 Recruitment of Rad17-RFC complex to DNA, Mus musculus Reactome:REACT_32932 Recruitment and activation of Chk1, Taeniopygia guttata Reactome:REACT_33572 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Dictyostelium discoideum Reactome:REACT_33874 Recruitment and activation of Chk1, Xenopus tropicalis Reactome:REACT_50018 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Rattus norvegicus Reactome:REACT_53588 Loading of claspin onto DNA during replication origin firing, Canis familiaris Reactome:REACT_6729 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Homo sapiens Reactome:REACT_6738 Loading of claspin onto DNA during replication origin firing, Homo sapiens Reactome:REACT_6750 Activation of claspin, Homo sapiens Reactome:REACT_6769 Activation of ATR in response to replication stress, Homo sapiens Reactome:REACT_6798 Recruitment of Rad17-RFC complex to DNA, Homo sapiens Reactome:REACT_6869 Recruitment and activation of Chk1, Homo sapiens Reactome:REACT_6936 Stalling of DNA replication fork and RPA binding, Homo sapiens Reactome:REACT_6939 Binding of ATR-ATRIP to the RPA-ssDNA complex, Homo sapiens Reactome:REACT_77532 Stalling of DNA replication fork and RPA binding, Canis familiaris Reactome:REACT_79188 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Canis familiaris Reactome:REACT_79450 Activation of ATR in response to replication stress, Dictyostelium discoideum Reactome:REACT_80432 Loading of claspin onto DNA during replication origin firing, Taeniopygia guttata Reactome:REACT_80571 Activation of claspin, Mus musculus Reactome:REACT_80896 Recruitment and activation of Chk1, Sus scrofa Reactome:REACT_80988 Loading of claspin onto DNA during replication origin firing, Bos taurus Reactome:REACT_81803 Recruitment of Rad17-RFC complex to DNA, Canis familiaris Reactome:REACT_83095 Recruitment of Rad17-RFC complex to DNA, Danio rerio Reactome:REACT_84829 Binding of ATR-ATRIP to the RPA-ssDNA complex, Danio rerio Reactome:REACT_85561 Binding of ATR-ATRIP to the RPA-ssDNA complex, Rattus norvegicus Reactome:REACT_86410 Stalling of DNA replication fork and RPA binding, Mus musculus Reactome:REACT_86739 Recruitment and activation of Chk1, Rattus norvegicus Reactome:REACT_87233 Binding of ATR-ATRIP to the RPA-ssDNA complex, Canis familiaris Reactome:REACT_87449 Recruitment of Rad17-RFC complex to DNA, Rattus norvegicus Reactome:REACT_87590 Recruitment of Rad17-RFC complex to DNA, Bos taurus Reactome:REACT_88085 Binding of ATR-ATRIP to the RPA-ssDNA complex, Gallus gallus Reactome:REACT_88384 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Schizosaccharomyces pombe Reactome:REACT_88529 Activation of claspin, Gallus gallus Reactome:REACT_89355 Activation of claspin, Danio rerio Reactome:REACT_89439 Activation of ATR in response to replication stress, Sus scrofa Reactome:REACT_89725 Loading of claspin onto DNA during replication origin firing, Drosophila melanogaster Reactome:REACT_90512 Stalling of DNA replication fork and RPA binding, Bos taurus Reactome:REACT_90809 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Danio rerio Reactome:REACT_90838 Recruitment of Rad17-RFC complex to DNA, Taeniopygia guttata Reactome:REACT_91184 Recruitment and activation of Chk1, Danio rerio Reactome:REACT_91302 Activation of ATR in response to replication stress, Canis familiaris Reactome:REACT_92527 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Mus musculus Reactome:REACT_92644 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Xenopus tropicalis Reactome:REACT_92706 Stalling of DNA replication fork and RPA binding, Danio rerio Reactome:REACT_94983 Stalling of DNA replication fork and RPA binding, Xenopus tropicalis Reactome:REACT_95253 Activation of ATR in response to replication stress, Taeniopygia guttata Reactome:REACT_95329 Activation of claspin, Taeniopygia guttata Reactome:REACT_96115 Binding of ATR-ATRIP to the RPA-ssDNA complex, Mus musculus Reactome:REACT_96804 Recruitment and activation of Chk1, Mus musculus Reactome:REACT_96998 Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Bos taurus Reactome:REACT_97204 Loading of claspin onto DNA during replication origin firing, Gallus gallus Reactome:REACT_97726 Activation of ATR in response to replication stress, Caenorhabditis elegans Reactome:REACT_99948 Loading of claspin onto DNA during replication origin firing, Xenopus tropicalis Any process that modulates the frequency, rate or extent of DNA replication. biological_process GO:0006275 regulation of DNA replication Any process that modulates the frequency, rate or extent of DNA replication. GOC:go_curators The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division. biological_process GO:0006276 plasmid maintenance The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division. GOC:ai The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties. biological_process GO:0006304 DNA modification The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties. GOC:jl GOC:ma 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. biological_process GO:0006305 DNA alkylation 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. ISBN:0716735970 The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. Wikipedia:DNA_methylation biological_process GO:0006306 DNA methylation The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. GOC:ems ISBN:0198506732 The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. DNA breakdown DNA catabolism DNA degradation biological_process GO:0006308 DNA catabolic process The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. GOC:go_curators ISBN:0198506732 The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments. GO:0008178 DNA fragmentation chromatinolysis Reactome:REACT_102783 Reactome:REACT_105342 Reactome:REACT_110358 Reactome:REACT_113418 Reactome:REACT_1213 Reactome:REACT_28808 Reactome:REACT_33113 Reactome:REACT_92967 Reactome:REACT_94135 Reactome:REACT_98713 Reactome:REACT_99275 Reactome:REACT_99925 DNA catabolic process during apoptosis DNA catabolism during apoptosis DNA fragmentation involved in apoptotic nuclear change endonucleolytic DNA catabolic process involved in apoptosis biological_process GO:0006309 DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases. In human, these include DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in PMID:15723341). Caution is needed when apoptotic DNA laddering assays show presence of fragmented DNA. A positive assay may simply reflect the end point of a whole apoptotic process. Unless clear experimental evidence is available to show that a gene product is directly involved in fragmenting DNA, please do not annotate to GO:0006309 'apoptotic DNA fragmentation' and consider annotating instead to a more upstream process such as, e.g., GO:0042981 'regulation of apoptotic process', GO:0006915 'apoptotic process', GO:0097190 'apoptotic signaling pathway'. Also, note that gene products involved in compartmentalization of apoptotic nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341). apoptotic DNA fragmentation The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments. GOC:dph GOC:mah GOC:mtg_apoptosis GOC:tb ISBN:0721639976 PMID:15723341 PMID:23379520 chromatinolysis GOC:mtg_apoptosis Reactome:REACT_102783 Apoptosis induced DNA fragmentation, Bos taurus Reactome:REACT_105342 Apoptosis induced DNA fragmentation, Sus scrofa Reactome:REACT_110358 Apoptosis induced DNA fragmentation, Xenopus tropicalis Reactome:REACT_113418 Apoptosis induced DNA fragmentation, Plasmodium falciparum Reactome:REACT_1213 Apoptosis induced DNA fragmentation, Homo sapiens Reactome:REACT_28808 Apoptosis induced DNA fragmentation, Rattus norvegicus Reactome:REACT_33113 Apoptosis induced DNA fragmentation, Mus musculus Reactome:REACT_92967 Apoptosis induced DNA fragmentation, Drosophila melanogaster Reactome:REACT_94135 Apoptosis induced DNA fragmentation, Taeniopygia guttata Reactome:REACT_98713 Apoptosis induced DNA fragmentation, Canis familiaris Reactome:REACT_99275 Apoptosis induced DNA fragmentation, Gallus gallus Reactome:REACT_99925 Apoptosis induced DNA fragmentation, Danio rerio DNA fragmentation involved in apoptotic nuclear change GOC:cjm GOC:dph GOC:tb chromatin remodeling 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. chromatin remodeling The cellular synthesis of RNA on a template of DNA. GO:0006350 GO:0061018 GO:0061022 cellular transcription transcription Wikipedia:Transcription_(genetics) DNA-dependent transcription cellular transcription, DNA-dependent transcription, DNA-dependent biological_process transcription regulator activity GO:0006351 transcription, DNA-templated The cellular synthesis of RNA on a template of DNA. GOC:jl GOC:txnOH transcription, DNA-dependent GOC:txnOH Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0032583 GO:0045449 GO:0061019 transcriptional control regulation of cellular transcription, DNA-dependent regulation of transcription, DNA-dependent biological_process regulation of gene-specific transcription GO:0006355 regulation of transcription, DNA-templated Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GOC:go_curators GOC:txnOH regulation of transcription, DNA-dependent GOC:txnOH 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. GO:0006416 GO:0006453 GO:0043037 Reactome:REACT_100338 Reactome:REACT_100851 Reactome:REACT_101045 Reactome:REACT_101324 Reactome:REACT_1014 Reactome:REACT_103420 Reactome:REACT_105544 Reactome:REACT_29980 Reactome:REACT_33559 Reactome:REACT_77710 Reactome:REACT_79784 Reactome:REACT_81734 Reactome:REACT_81833 Reactome:REACT_82171 Reactome:REACT_83429 Reactome:REACT_83530 Reactome:REACT_86996 Reactome:REACT_95535 Reactome:REACT_96394 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis protein biosynthetic process protein formation protein synthesis protein translation biological_process GO:0006412 translation 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. GOC:go_curators Reactome:REACT_100338 Translation, Sus scrofa Reactome:REACT_100851 Translation, Saccharomyces cerevisiae Reactome:REACT_101045 Translation, Dictyostelium discoideum Reactome:REACT_101324 Translation, Canis familiaris Reactome:REACT_1014 Translation, Homo sapiens Reactome:REACT_103420 Translation, Plasmodium falciparum Reactome:REACT_105544 Translation, Arabidopsis thaliana Reactome:REACT_29980 Translation, Bos taurus Reactome:REACT_33559 Translation, Rattus norvegicus Reactome:REACT_77710 Translation, Drosophila melanogaster Reactome:REACT_79784 Translation, Danio rerio Reactome:REACT_81734 Translation, Schizosaccharomyces pombe Reactome:REACT_81833 Translation, Caenorhabditis elegans Reactome:REACT_82171 Translation, Xenopus tropicalis Reactome:REACT_83429 Translation, Taeniopygia guttata Reactome:REACT_83530 Translation, Gallus gallus Reactome:REACT_86996 Translation, Oryza sativa Reactome:REACT_95535 Translation, Mus musculus Reactome:REACT_96394 Translation, Escherichia coli protein biosynthetic process GOC:curators 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. GO:0006440 GO:0006454 biopolymerisation biopolymerization protein synthesis initiation Reactome:REACT_101789 Reactome:REACT_104290 Reactome:REACT_2159 Reactome:REACT_29447 Reactome:REACT_30389 Reactome:REACT_33969 Reactome:REACT_34354 Reactome:REACT_77252 Reactome:REACT_79705 Reactome:REACT_85780 Reactome:REACT_88031 Reactome:REACT_91066 Reactome:REACT_95293 Reactome:REACT_95552 Reactome:REACT_95685 Reactome:REACT_97707 Reactome:REACT_98138 Reactome:REACT_99004 translation initiation biological_process GO:0006413 translational initiation 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. ISBN:019879276X Reactome:REACT_101789 Eukaryotic Translation Initiation, Gallus gallus Reactome:REACT_104290 Eukaryotic Translation Initiation, Xenopus tropicalis Reactome:REACT_2159 Eukaryotic Translation Initiation, Homo sapiens Reactome:REACT_29447 Eukaryotic Translation Initiation, Dictyostelium discoideum Reactome:REACT_30389 Eukaryotic Translation Initiation, Oryza sativa Reactome:REACT_33969 Eukaryotic Translation Initiation, Caenorhabditis elegans Reactome:REACT_34354 Eukaryotic Translation Initiation, Taeniopygia guttata Reactome:REACT_77252 Eukaryotic Translation Initiation, Drosophila melanogaster Reactome:REACT_79705 Eukaryotic Translation Initiation, Rattus norvegicus Reactome:REACT_85780 Eukaryotic Translation Initiation, Bos taurus Reactome:REACT_88031 Eukaryotic Translation Initiation, Schizosaccharomyces pombe Reactome:REACT_91066 Eukaryotic Translation Initiation, Arabidopsis thaliana Reactome:REACT_95293 Eukaryotic Translation Initiation, Plasmodium falciparum Reactome:REACT_95552 Eukaryotic Translation Initiation, Mus musculus Reactome:REACT_95685 Eukaryotic Translation Initiation, Canis familiaris Reactome:REACT_97707 Eukaryotic Translation Initiation, Sus scrofa Reactome:REACT_98138 Eukaryotic Translation Initiation, Saccharomyces cerevisiae Reactome:REACT_99004 Eukaryotic Translation Initiation, Danio rerio The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. GO:0006442 GO:0006455 protein synthesis elongation Reactome:REACT_100207 Reactome:REACT_100561 Reactome:REACT_101290 Reactome:REACT_101737 Reactome:REACT_102082 Reactome:REACT_103580 Reactome:REACT_108124 Reactome:REACT_108677 Reactome:REACT_108858 Reactome:REACT_1477 Reactome:REACT_30678 Reactome:REACT_31079 Reactome:REACT_80015 Reactome:REACT_80831 Reactome:REACT_81624 Reactome:REACT_82124 Reactome:REACT_88049 Reactome:REACT_93503 Reactome:REACT_96070 translation elongation biological_process GO:0006414 translational elongation The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. GOC:ems Reactome:REACT_100207 Eukaryotic Translation Elongation, Dictyostelium discoideum Reactome:REACT_100561 Eukaryotic Translation Elongation, Canis familiaris Reactome:REACT_101290 Eukaryotic Translation Elongation, Gallus gallus Reactome:REACT_101737 Eukaryotic Translation Elongation, Escherichia coli Reactome:REACT_102082 Eukaryotic Translation Elongation, Mus musculus Reactome:REACT_103580 Eukaryotic Translation Elongation, Danio rerio Reactome:REACT_108124 Eukaryotic Translation Elongation, Xenopus tropicalis Reactome:REACT_108677 Eukaryotic Translation Elongation, Taeniopygia guttata Reactome:REACT_108858 Eukaryotic Translation Elongation, Caenorhabditis elegans Reactome:REACT_1477 Eukaryotic Translation Elongation, Homo sapiens Reactome:REACT_30678 Eukaryotic Translation Elongation, Arabidopsis thaliana Reactome:REACT_31079 Eukaryotic Translation Elongation, Sus scrofa Reactome:REACT_80015 Eukaryotic Translation Elongation, Bos taurus Reactome:REACT_80831 Eukaryotic Translation Elongation, Rattus norvegicus Reactome:REACT_81624 Eukaryotic Translation Elongation, Drosophila melanogaster Reactome:REACT_82124 Eukaryotic Translation Elongation, Saccharomyces cerevisiae Reactome:REACT_88049 Eukaryotic Translation Elongation, Schizosaccharomyces pombe Reactome:REACT_93503 Eukaryotic Translation Elongation, Oryza sativa Reactome:REACT_96070 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). GO:0006443 GO:0006456 protein synthesis termination Reactome:REACT_100227 Reactome:REACT_100585 Reactome:REACT_100730 Reactome:REACT_1034 Reactome:REACT_103749 Reactome:REACT_104420 Reactome:REACT_104616 Reactome:REACT_106326 Reactome:REACT_107138 Reactome:REACT_107171 Reactome:REACT_107771 Reactome:REACT_107964 Reactome:REACT_109127 Reactome:REACT_109494 Reactome:REACT_110009 Reactome:REACT_112381 Reactome:REACT_112559 Reactome:REACT_112632 Reactome:REACT_113540 Reactome:REACT_114287 Reactome:REACT_114807 Reactome:REACT_1152 Reactome:REACT_115292 Reactome:REACT_1654 Reactome:REACT_1986 Reactome:REACT_227 Reactome:REACT_28115 Reactome:REACT_28238 Reactome:REACT_28773 Reactome:REACT_29257 Reactome:REACT_31194 Reactome:REACT_31222 Reactome:REACT_32804 Reactome:REACT_33545 Reactome:REACT_34123 Reactome:REACT_34462 Reactome:REACT_389 Reactome:REACT_393 Reactome:REACT_716 Reactome:REACT_78279 Reactome:REACT_78389 Reactome:REACT_78823 Reactome:REACT_80339 Reactome:REACT_81067 Reactome:REACT_81196 Reactome:REACT_81882 Reactome:REACT_83324 Reactome:REACT_83432 Reactome:REACT_84537 Reactome:REACT_84840 Reactome:REACT_84975 Reactome:REACT_86647 Reactome:REACT_86888 Reactome:REACT_87882 Reactome:REACT_88395 Reactome:REACT_88662 Reactome:REACT_91109 Reactome:REACT_92456 Reactome:REACT_92895 Reactome:REACT_93205 Reactome:REACT_93556 Reactome:REACT_94459 Reactome:REACT_94463 Reactome:REACT_97483 translation termination translational complex disassembly biological_process GO:0006415 translational termination 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). GOC:hjd ISBN:019879276X Reactome:REACT_100227 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Taeniopygia guttata Reactome:REACT_100585 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Dictyostelium discoideum Reactome:REACT_100730 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Danio rerio Reactome:REACT_1034 Eukaryotic Translation Termination, Saccharomyces cerevisiae Reactome:REACT_103749 Eukaryotic Translation Termination, Oryza sativa Reactome:REACT_104420 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Caenorhabditis elegans Reactome:REACT_104616 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Taeniopygia guttata Reactome:REACT_106326 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Plasmodium falciparum Reactome:REACT_107138 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Schizosaccharomyces pombe Reactome:REACT_107171 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Danio rerio Reactome:REACT_107771 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Oryza sativa Reactome:REACT_107964 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Schizosaccharomyces pombe Reactome:REACT_109127 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Caenorhabditis elegans Reactome:REACT_109494 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Plasmodium falciparum Reactome:REACT_110009 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Mus musculus Reactome:REACT_112381 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Gallus gallus Reactome:REACT_112559 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Rattus norvegicus Reactome:REACT_112632 Eukaryotic Translation Termination, Rattus norvegicus Reactome:REACT_113540 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Gallus gallus Reactome:REACT_114287 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Gallus gallus Reactome:REACT_114807 Eukaryotic Translation Termination, Gallus gallus Reactome:REACT_1152 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Saccharomyces cerevisiae Reactome:REACT_115292 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Rattus norvegicus Reactome:REACT_1654 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Homo sapiens Reactome:REACT_1986 Eukaryotic Translation Termination, Homo sapiens Reactome:REACT_227 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Homo sapiens Reactome:REACT_28115 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Canis familiaris Reactome:REACT_28238 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Xenopus tropicalis Reactome:REACT_28773 Eukaryotic Translation Termination, Danio rerio Reactome:REACT_29257 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Drosophila melanogaster Reactome:REACT_31194 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Canis familiaris Reactome:REACT_31222 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Oryza sativa Reactome:REACT_32804 Eukaryotic Translation Termination, Drosophila melanogaster Reactome:REACT_33545 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Dictyostelium discoideum Reactome:REACT_34123 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Mus musculus Reactome:REACT_34462 Eukaryotic Translation Termination, Saccharomyces cerevisiae Reactome:REACT_389 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Homo sapiens Reactome:REACT_393 GTP bound eRF3:eRF1 complex binds the peptidyl-tRNA:mRNA:Ribosome complex, Saccharomyces cerevisiae Reactome:REACT_716 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Saccharomyces cerevisiae Reactome:REACT_78279 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Arabidopsis thaliana Reactome:REACT_78389 Eukaryotic Translation Termination, Schizosaccharomyces pombe Reactome:REACT_78823 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Dictyostelium discoideum Reactome:REACT_80339 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Xenopus tropicalis Reactome:REACT_81067 Eukaryotic Translation Termination, Canis familiaris Reactome:REACT_81196 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Arabidopsis thaliana Reactome:REACT_81882 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Caenorhabditis elegans Reactome:REACT_83324 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Xenopus tropicalis Reactome:REACT_83432 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Drosophila melanogaster Reactome:REACT_84537 Eukaryotic Translation Termination, Plasmodium falciparum Reactome:REACT_84840 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Plasmodium falciparum Reactome:REACT_84975 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Arabidopsis thaliana Reactome:REACT_86647 Eukaryotic Translation Termination, Xenopus tropicalis Reactome:REACT_86888 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Taeniopygia guttata Reactome:REACT_87882 Eukaryotic Translation Termination, Dictyostelium discoideum Reactome:REACT_88395 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Canis familiaris Reactome:REACT_88662 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Danio rerio Reactome:REACT_91109 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Oryza sativa Reactome:REACT_92456 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Schizosaccharomyces pombe Reactome:REACT_92895 Eukaryotic Translation Termination, Taeniopygia guttata Reactome:REACT_93205 Eukaryotic Translation Termination, Caenorhabditis elegans Reactome:REACT_93556 Eukaryotic Translation Termination, Mus musculus Reactome:REACT_94459 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Drosophila melanogaster Reactome:REACT_94463 Eukaryotic Translation Termination, Arabidopsis thaliana Reactome:REACT_97483 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. GO:0006445 regulation of protein anabolism regulation of protein biosynthesis regulation of protein formation regulation of protein synthesis biological_process GO:0006417 regulation of translation Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GOC:isa_complete Any process that modulates the frequency, rate or extent of translational initiation. biological_process GO:0006446 regulation of translational initiation Any process that modulates the frequency, rate or extent of translational initiation. GOC:go_curators Any process that modulates the frequency, rate, extent or accuracy of translational elongation. biological_process GO:0006448 regulation of translational elongation Any process that modulates the frequency, rate, extent or accuracy of translational elongation. GOC:go_curators Any process that modulates the frequency, rate or extent of translational termination. biological_process GO:0006449 regulation of translational termination Any process that modulates the frequency, rate or extent of translational termination. GOC:go_curators 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. peptide metabolism biological_process GO:0006518 peptide metabolic process 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. CHEBI:16670 GOC:go_curators The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. aromatic compound metabolism aromatic hydrocarbon metabolic process aromatic hydrocarbon metabolism biological_process GO:0006725 cellular aromatic compound metabolic process The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. GOC:ai ISBN:0198506732 The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. nitrogen compound metabolism biological_process GO:0006807 nitrogen compound metabolic process The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. CHEBI:51143 GOC:go_curators GOC:jl ISBN:0198506732 The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. janelomax 2012-12-13T16:25:32Z GO:0015457 GO:0015460 GO:0044765 small molecule transport solute:solute exchange biological_process single-organism transport GO:0006810 Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. transport The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. GOC:dos GOC:dph GOC:jl GOC:mah The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Reactome:REACT_102356 Reactome:REACT_102895 Reactome:REACT_106972 Reactome:REACT_109067 Reactome:REACT_110862 Reactome:REACT_19397 Reactome:REACT_29110 Reactome:REACT_31978 Reactome:REACT_33992 Reactome:REACT_34201 Reactome:REACT_79109 Reactome:REACT_82618 Reactome:REACT_87822 Reactome:REACT_91472 Reactome:REACT_91958 Reactome:REACT_92903 Reactome:REACT_93485 Reactome:REACT_94357 Reactome:REACT_96078 Reactome:REACT_96919 Reactome:REACT_98077 biological_process GO:0006811 ion transport The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Reactome:REACT_102356 Transport of inorganic cations/anions and amino acids/oligopeptides, Xenopus tropicalis Reactome:REACT_102895 Transport of inorganic cations/anions and amino acids/oligopeptides, Staphylococcus aureus N315 Reactome:REACT_106972 Transport of inorganic cations/anions and amino acids/oligopeptides, Sus scrofa Reactome:REACT_109067 Transport of inorganic cations/anions and amino acids/oligopeptides, Saccharomyces cerevisiae Reactome:REACT_110862 Transport of inorganic cations/anions and amino acids/oligopeptides, Arabidopsis thaliana Reactome:REACT_19397 Transport of inorganic cations/anions and amino acids/oligopeptides, Homo sapiens Reactome:REACT_29110 Transport of inorganic cations/anions and amino acids/oligopeptides, Oryza sativa Reactome:REACT_31978 Transport of inorganic cations/anions and amino acids/oligopeptides, Mus musculus Reactome:REACT_33992 Transport of inorganic cations/anions and amino acids/oligopeptides, Danio rerio Reactome:REACT_34201 Transport of inorganic cations/anions and amino acids/oligopeptides, Gallus gallus Reactome:REACT_79109 Transport of inorganic cations/anions and amino acids/oligopeptides, Caenorhabditis elegans Reactome:REACT_82618 Transport of inorganic cations/anions and amino acids/oligopeptides, Escherichia coli Reactome:REACT_87822 Transport of inorganic cations/anions and amino acids/oligopeptides, Bos taurus Reactome:REACT_91472 Transport of inorganic cations/anions and amino acids/oligopeptides, Dictyostelium discoideum Reactome:REACT_91958 Transport of inorganic cations/anions and amino acids/oligopeptides, Drosophila melanogaster Reactome:REACT_92903 Transport of inorganic cations/anions and amino acids/oligopeptides, Mycobacterium tuberculosis Reactome:REACT_93485 Transport of inorganic cations/anions and amino acids/oligopeptides, Canis familiaris Reactome:REACT_94357 Transport of inorganic cations/anions and amino acids/oligopeptides, Rattus norvegicus Reactome:REACT_96078 Transport of inorganic cations/anions and amino acids/oligopeptides, Plasmodium falciparum Reactome:REACT_96919 Transport of inorganic cations/anions and amino acids/oligopeptides, Taeniopygia guttata Reactome:REACT_98077 Transport of inorganic cations/anions and amino acids/oligopeptides, Schizosaccharomyces pombe The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0006822 biological_process GO:0006820 anion transport The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. biological_process GO:0006869 lipid transport The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. ISBN:0198506732 A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GO:0006917 GO:0008632 cell suicide cellular suicide Reactome:REACT_100045 Reactome:REACT_100962 Reactome:REACT_101249 Reactome:REACT_104187 Reactome:REACT_105149 Reactome:REACT_106405 Reactome:REACT_106672 Reactome:REACT_107264 Reactome:REACT_108651 Reactome:REACT_109165 Reactome:REACT_110081 Reactome:REACT_111964 Reactome:REACT_13526 Reactome:REACT_13638 Reactome:REACT_13643 Reactome:REACT_28087 Reactome:REACT_28795 Reactome:REACT_28816 Reactome:REACT_30266 Reactome:REACT_30361 Reactome:REACT_30371 Reactome:REACT_30548 Reactome:REACT_30763 Reactome:REACT_31349 Reactome:REACT_34139 Reactome:REACT_578 Reactome:REACT_77132 Reactome:REACT_77313 Reactome:REACT_77415 Reactome:REACT_78287 Reactome:REACT_78802 Reactome:REACT_79809 Reactome:REACT_82724 Reactome:REACT_83328 Reactome:REACT_85877 Reactome:REACT_86749 Reactome:REACT_86873 Reactome:REACT_87570 Reactome:REACT_88740 Reactome:REACT_88784 Reactome:REACT_89196 Reactome:REACT_90267 Reactome:REACT_91011 Reactome:REACT_91243 Reactome:REACT_93937 Reactome:REACT_94099 Reactome:REACT_95069 Reactome:REACT_95675 Reactome:REACT_97627 Reactome:REACT_99784 Reactome:REACT_99799 Wikipedia:Apoptosis apoptotic cell death apoptotic programmed cell death programmed cell death by apoptosis activation of apoptosis apoptosis apoptosis signaling apoptotic program type I programmed cell death biological_process apoptosis activator activity caspase-dependent programmed cell death commitment to apoptosis induction of apoptosis induction of apoptosis by p53 signaling (initiator) caspase activity GO:0006915 apoptotic process A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. GOC:cjm GOC:dhl GOC:ecd GOC:go_curators GOC:mtg_apoptosis GOC:tb ISBN:0198506732 PMID:18846107 PMID:21494263 Reactome:REACT_100045 Apoptosis, Drosophila melanogaster Reactome:REACT_100962 Apoptosis, Mus musculus Reactome:REACT_101249 NRIF signals cell death from the nucleus, Danio rerio Reactome:REACT_104187 NRAGE signals death through JNK, Taeniopygia guttata Reactome:REACT_105149 NADE modulates death signalling, Rattus norvegicus Reactome:REACT_106405 NRAGE signals death through JNK, Xenopus tropicalis Reactome:REACT_106672 NADE modulates death signalling, Sus scrofa Reactome:REACT_107264 NRIF signals cell death from the nucleus, Xenopus tropicalis Reactome:REACT_108651 NRAGE signals death through JNK, Mus musculus Reactome:REACT_109165 NRAGE signals death through JNK, Arabidopsis thaliana Reactome:REACT_110081 NRAGE signals death through JNK, Schizosaccharomyces pombe Reactome:REACT_111964 NRAGE signals death through JNK, Dictyostelium discoideum Reactome:REACT_13526 NADE modulates death signalling, Homo sapiens Reactome:REACT_13638 NRAGE signals death through JNK, Homo sapiens Reactome:REACT_13643 NRIF signals cell death from the nucleus, Homo sapiens Reactome:REACT_28087 Apoptosis, Saccharomyces cerevisiae Reactome:REACT_28795 Apoptosis, Oryza sativa Reactome:REACT_28816 Apoptosis, Danio rerio Reactome:REACT_30266 Apoptosis, Arabidopsis thaliana Reactome:REACT_30361 Apoptosis, Canis familiaris Reactome:REACT_30371 NRAGE signals death through JNK, Saccharomyces cerevisiae Reactome:REACT_30548 NRAGE signals death through JNK, Caenorhabditis elegans Reactome:REACT_30763 NRAGE signals death through JNK, Oryza sativa Reactome:REACT_31349 NRAGE signals death through JNK, Canis familiaris Reactome:REACT_34139 NRAGE signals death through JNK, Gallus gallus Reactome:REACT_578 Apoptosis, Homo sapiens Reactome:REACT_77132 NRAGE signals death through JNK, Drosophila melanogaster Reactome:REACT_77313 NADE modulates death signalling, Bos taurus Reactome:REACT_77415 NRIF signals cell death from the nucleus, Canis familiaris Reactome:REACT_78287 Apoptosis, Gallus gallus Reactome:REACT_78802 NADE modulates death signalling, Canis familiaris Reactome:REACT_79809 Apoptosis, Schizosaccharomyces pombe Reactome:REACT_82724 Apoptosis, Taeniopygia guttata Reactome:REACT_83328 Apoptosis, Sus scrofa Reactome:REACT_85877 NRAGE signals death through JNK, Rattus norvegicus Reactome:REACT_86749 Apoptosis, Rattus norvegicus Reactome:REACT_86873 NRIF signals cell death from the nucleus, Gallus gallus Reactome:REACT_87570 NRIF signals cell death from the nucleus, Rattus norvegicus Reactome:REACT_88740 NRIF signals cell death from the nucleus, Sus scrofa Reactome:REACT_88784 NRIF signals cell death from the nucleus, Mus musculus Reactome:REACT_89196 Apoptosis, Dictyostelium discoideum Reactome:REACT_90267 NRIF signals cell death from the nucleus, Taeniopygia guttata Reactome:REACT_91011 Apoptosis, Caenorhabditis elegans Reactome:REACT_91243 NADE modulates death signalling, Mus musculus Reactome:REACT_93937 Apoptosis, Bos taurus Reactome:REACT_94099 NRAGE signals death through JNK, Danio rerio Reactome:REACT_95069 Apoptosis, Xenopus tropicalis Reactome:REACT_95675 Apoptosis, Plasmodium falciparum Reactome:REACT_97627 NRIF signals cell death from the nucleus, Bos taurus Reactome:REACT_99784 NRAGE signals death through JNK, Bos taurus Reactome:REACT_99799 NRAGE signals death through JNK, Sus scrofa apoptotic cell death GOC:sl apoptotic program GOC:add The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis. cellular component disassembly involved in apoptotic process disassembly of cell structures Reactome:REACT_100800 Reactome:REACT_108463 Reactome:REACT_29660 Reactome:REACT_77151 Reactome:REACT_78666 Reactome:REACT_79472 Reactome:REACT_79859 Reactome:REACT_80493 Reactome:REACT_81021 Reactome:REACT_81052 Reactome:REACT_84120 Reactome:REACT_89424 Reactome:REACT_90988 Reactome:REACT_92689 Reactome:REACT_93576 Reactome:REACT_94230 Reactome:REACT_97703 Reactome:REACT_995 cellular component disassembly involved in apoptosis biological_process GO:0006921 cellular component disassembly involved in execution phase of apoptosis The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis. GOC:dph GOC:mah GOC:mtg_apoptosis GOC:tb Reactome:REACT_100800 Apoptotic execution phase, Danio rerio Reactome:REACT_108463 Apoptotic execution phase, Taeniopygia guttata Reactome:REACT_29660 Apoptotic execution phase, Oryza sativa Reactome:REACT_77151 Apoptotic execution phase, Sus scrofa Reactome:REACT_78666 Apoptotic execution phase, Saccharomyces cerevisiae Reactome:REACT_79472 Apoptotic execution phase, Schizosaccharomyces pombe Reactome:REACT_79859 Apoptotic execution phase, Rattus norvegicus Reactome:REACT_80493 Apoptotic execution phase, Dictyostelium discoideum Reactome:REACT_81021 Apoptotic execution phase, Drosophila melanogaster Reactome:REACT_81052 Apoptotic execution phase, Canis familiaris Reactome:REACT_84120 Apoptotic execution phase, Xenopus tropicalis Reactome:REACT_89424 Apoptotic execution phase, Arabidopsis thaliana Reactome:REACT_90988 Apoptotic execution phase, Plasmodium falciparum Reactome:REACT_92689 Apoptotic execution phase, Caenorhabditis elegans Reactome:REACT_93576 Apoptotic execution phase, Gallus gallus Reactome:REACT_94230 Apoptotic execution phase, Bos taurus Reactome:REACT_97703 Apoptotic execution phase, Mus musculus Reactome:REACT_995 Apoptotic execution phase, Homo sapiens The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore. cellular component motion cellular component movement biological_process cell movement GO:0006928 Note that in GO cellular components include whole cells (cell is_a cellular component). movement of cell or subcellular component The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore. GOC:dgh GOC:dph GOC:jl GOC:mlg cellular component motion GOC:dph GOC:jl The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). Wikipedia:Chemotaxis taxis in response to chemical stimulus biological_process GO:0006935 chemotaxis The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). ISBN:0198506732 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). biological_process response to abiotic stress response to biotic stress GO:0006950 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stress Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:mah 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. GO:0034984 response to DNA damage stimulus DNA damage response cellular DNA damage response response to genotoxic stress biological_process GO:0006974 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. GOC:go_curators A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. jl 2013-12-19T15:25:51Z GO:1902589 organelle organisation single organism organelle organization biological_process organelle organization and biogenesis single-organism organelle organization GO:0006996 organelle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah organelle organisation GOC:curators single organism organelle organization GOC:TermGenie organelle organization and biogenesis GOC:dph GOC:jl GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. GO:0048287 nuclear organisation nuclear organization biological_process nuclear morphology nuclear organization and biogenesis nucleus organization and biogenesis GO:0006997 nucleus organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus. GOC:dph GOC:ems GOC:jl GOC:mah nuclear organisation GOC:curators nuclear organization GOC:curators nuclear organization and biogenesis GOC:mah nucleus organization and biogenesis GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus. nucleolus organisation biological_process nucleolus organization and biogenesis GO:0007000 nucleolus organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus. GOC:dph GOC:jid GOC:jl GOC:mah nucleolus organisation GOC:curators nucleolus organization and biogenesis GOC:mah 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. Wikipedia:Cell_signaling biological_process GO:0007154 cell communication 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. GOC:mah 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. GO:0023033 Reactome:REACT_100624 Reactome:REACT_102354 Reactome:REACT_112130 Reactome:REACT_112549 Reactome:REACT_113151 Reactome:REACT_113601 Reactome:REACT_113964 Reactome:REACT_114657 Reactome:REACT_114690 Reactome:REACT_114820 Reactome:REACT_114910 Reactome:REACT_115037 Reactome:REACT_115147 Reactome:REACT_12478 Reactome:REACT_31232 Reactome:REACT_78535 Reactome:REACT_89740 Reactome:REACT_93680 Reactome:REACT_98872 Wikipedia:Signal_transduction signaling cascade signalling cascade biological_process signaling pathway signalling pathway GO:0007165 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. signal transduction 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. GOC:go_curators GOC:mtg_signaling_feb11 Reactome:REACT_100624 EGFR interacts with phospholipase C-gamma, Gallus gallus Reactome:REACT_102354 EGFR interacts with phospholipase C-gamma, Canis familiaris Reactome:REACT_112130 EGFR interacts with phospholipase C-gamma, Oryza sativa Reactome:REACT_112549 EGFR interacts with phospholipase C-gamma, Arabidopsis thaliana Reactome:REACT_113151 EGFR interacts with phospholipase C-gamma, Mycobacterium tuberculosis Reactome:REACT_113601 EGFR interacts with phospholipase C-gamma, Drosophila melanogaster Reactome:REACT_113964 EGFR interacts with phospholipase C-gamma, Bos taurus Reactome:REACT_114657 EGFR interacts with phospholipase C-gamma, Dictyostelium discoideum Reactome:REACT_114690 EGFR interacts with phospholipase C-gamma, Saccharomyces cerevisiae Reactome:REACT_114820 EGFR interacts with phospholipase C-gamma, Sus scrofa Reactome:REACT_114910 EGFR interacts with phospholipase C-gamma, Caenorhabditis elegans Reactome:REACT_115037 EGFR interacts with phospholipase C-gamma, Plasmodium falciparum Reactome:REACT_115147 EGFR interacts with phospholipase C-gamma, Schizosaccharomyces pombe Reactome:REACT_12478 EGFR interacts with phospholipase C-gamma, Homo sapiens Reactome:REACT_31232 EGFR interacts with phospholipase C-gamma, Rattus norvegicus Reactome:REACT_78535 EGFR interacts with phospholipase C-gamma, Xenopus tropicalis Reactome:REACT_89740 EGFR interacts with phospholipase C-gamma, Taeniopygia guttata Reactome:REACT_93680 EGFR interacts with phospholipase C-gamma, Danio rerio Reactome:REACT_98872 EGFR interacts with phospholipase C-gamma, Mus musculus signalling pathway GOC:mah 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). GO:0016280 Wikipedia:Aging ageing biological_process GO:0007568 aging 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). GOC:PO_curators 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). cell ageing biological_process GO:0007569 cell aging 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). GOC:PO_curators The cell aging process that results in the nucleolus breaking down into fragments. GO:0046616 biological_process nucleolar size increase GO:0007576 nucleolar fragmentation The cell aging process that results in the nucleolus breaking down into fragments. GOC:mah PMID:9271578 Any process in which a protein is transported to, or maintained in, a specific location. GO:0008105 protein localisation biological_process asymmetric protein localisation asymmetric protein localization establishment and maintenance of asymmetric protein localization establishment and maintenance of protein localization GO:0008104 protein localization Any process in which a protein is transported to, or maintained in, a specific location. GOC:ai protein localisation GOC:mah asymmetric protein localisation GOC:mah biological_process 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. janelomax 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. 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. biological_process 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. GOC:pdt The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. janelomax 2012-10-17T15:46:40Z GO:0044236 GO:0044710 Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth multicellular organism metabolic process biological_process single-organism metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. GOC:go_curators ISBN:0198547684 Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication. down regulation of DNA replication down-regulation of DNA replication downregulation of DNA replication inhibition of DNA replication biological_process DNA replication inhibitor GO:0008156 negative regulation of DNA replication Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication. GOC:go_curators Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). biological_process accidental cell death necrosis GO:0008219 This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term. cell death Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538). GOC:mah GOC:mtg_apoptosis PMID:25236395 cell proliferation The multiplication or reproduction of cells, resulting in the expansion of a cell population. biological_process GO:0008283 This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms. cell proliferation The multiplication or reproduction of cells, resulting in the expansion of a cell population. GOC:mah GOC:mb Any process that activates or increases the rate or extent of cell proliferation. up regulation of cell proliferation up-regulation of cell proliferation upregulation of cell proliferation activation of cell proliferation stimulation of cell proliferation biological_process GO:0008284 positive regulation of cell proliferation Any process that activates or increases the rate or extent of cell proliferation. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of cell proliferation. down regulation of cell proliferation down-regulation of cell proliferation downregulation of cell proliferation inhibition of cell proliferation biological_process GO:0008285 negative regulation of cell proliferation Any process that stops, prevents or reduces the rate or extent of cell proliferation. GOC:go_curators The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. janelomax 2012-10-17T15:52:35Z GO:0044243 GO:0044712 Wikipedia:Catabolism breakdown catabolism degradation multicellular organismal catabolic process biological_process single-organism catabolic process GO:0009056 catabolic process The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism. ISBN:0198547684 The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0043285 GO:0044266 biopolymer catabolic process macromolecule breakdown macromolecule catabolism macromolecule degradation multicellular organismal macromolecule catabolic process biological_process GO:0009057 macromolecule catabolic process The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. CHEBI:33694 GOC:mah biopolymer catabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. janelomax 2012-10-17T15:52:18Z GO:0044274 GO:0044711 formation Wikipedia:Anabolism anabolism biosynthesis synthesis multicellular organismal biosynthetic process biological_process single-organism biosynthetic process GO:0009058 biosynthetic process The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0043284 biopolymer biosynthetic process macromolecule anabolism macromolecule biosynthesis macromolecule formation macromolecule synthesis biological_process GO:0009059 macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. CHEBI:33694 GOC:mah biopolymer biosynthetic process GOC:mtg_chebi_dec09 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. biological_process GO:0009300 antisense RNA transcription 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. GOC:jl The controlled release of proteins from a cell. GO:0045166 GO:0045731 glycoprotein secretion protein secretion during cell fate commitment protein secretion resulting in cell fate commitment biological_process GO:0009306 protein secretion The controlled release of proteins from a cell. GOC:ai Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. response to environmental stimulus biological_process GO:0009605 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to 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 an external stimulus. GOC:hb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism. response to biotic stress biological_process GO:0009607 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to biotic stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism. GOC:hb Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism. GO:0002245 physiological response to wounding biological_process GO:0009611 response to wounding Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism. GOC:go_curators Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. detoxification response biological_process toxin resistance toxin susceptibility/resistance GO:0009636 response to toxic substance Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. GOC:lr The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. embryogenesis and morphogenesis Wikipedia:Morphogenesis anatomical structure organization morphogenesis biological_process GO:0009653 anatomical structure morphogenesis The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. GOC:go_curators ISBN:0521436125 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. biological_process GO:0009719 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to endogenous stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism. GOC:sm Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. regulation of anabolism regulation of biosynthesis regulation of formation regulation of synthesis biological_process GO:0009889 regulation of biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. down regulation of biosynthetic process down-regulation of biosynthetic process downregulation of biosynthetic process negative regulation of anabolism negative regulation of biosynthesis negative regulation of formation negative regulation of synthesis inhibition of biosynthetic process biological_process GO:0009890 negative regulation of biosynthetic process Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. positive regulation of anabolism positive regulation of biosynthesis positive regulation of formation positive regulation of synthesis up regulation of biosynthetic process up-regulation of biosynthetic process upregulation of biosynthetic process activation of biosynthetic process stimulation of biosynthetic process biological_process GO:0009891 positive regulation of biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044252 down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism negative regulation of organismal metabolism inhibition of metabolic process inhibition of organismal metabolic process negative regulation of multicellular organismal metabolic process biological_process GO:0009892 negative regulation of metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044253 positive regulation of metabolism up regulation of metabolic process up-regulation of metabolic process upregulation of metabolic process activation of metabolic process positive regulation of multicellular organismal metabolic process positive regulation of organismal metabolism stimulation of metabolic process stimulation of organismal metabolic process up-regulation of organismal metabolic process biological_process GO:0009893 positive regulation of metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. regulation of breakdown regulation of catabolism regulation of degradation biological_process GO:0009894 regulation of catabolic process Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. down regulation of catabolic process down-regulation of catabolic process downregulation of catabolic process negative regulation of breakdown negative regulation of catabolism negative regulation of degradation inhibition of catabolic process biological_process GO:0009895 negative regulation of catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. positive regulation of breakdown positive regulation of catabolism positive regulation of degradation up regulation of catabolic process up-regulation of catabolic process upregulation of catabolic process activation of catabolic process stimulation of catabolic process biological_process GO:0009896 positive regulation of catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances. GOC:go_curators Any process that modulates the frequency, rate or extent of signal transduction. GO:0035466 biological_process regulation of signaling pathway regulation of signalling pathway GO:0009966 regulation of signal transduction Any process that modulates the frequency, rate or extent of signal transduction. GOC:sm regulation of signalling pathway GOC:mah Any process that activates or increases the frequency, rate or extent of signal transduction. GO:0035468 Reactome:REACT_6227 up regulation of signal transduction up-regulation of signal transduction upregulation of signal transduction activation of signal transduction stimulation of signal transduction biological_process positive regulation of signaling pathway positive regulation of signalling pathway GO:0009967 positive regulation of signal transduction Any process that activates or increases the frequency, rate or extent of signal transduction. GOC:sm Reactome:REACT_6227 Activated DTOR also phosphorylates D4EBP, Drosophila melanogaster positive regulation of signalling pathway GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GO:0035467 Reactome:REACT_6334 down regulation of signal transduction down-regulation of signal transduction downregulation of signal transduction inhibition of signal transduction biological_process negative regulation of signaling pathway negative regulation of signalling pathway GO:0009968 negative regulation of signal transduction Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GOC:sm Reactome:REACT_6334 DTSC1 AND DTSC2 form a complex, Drosophila melanogaster negative regulation of signalling pathway GOC:mah cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. janelomax 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete 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. biological_process GO:0010033 response to organic substance Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus. GOC:sm 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. biological_process GO:0010046 response to mycotoxin 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. GOC:sm 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. response to organic nitrogen biological_process GO:0010243 response to organonitrogen compound Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond. CHEBI:35352 PMID:9869419 gene expression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. Reactome:REACT_100537 Reactome:REACT_101147 Reactome:REACT_101952 Reactome:REACT_105649 Reactome:REACT_108313 Reactome:REACT_29068 Reactome:REACT_34240 Reactome:REACT_71 Reactome:REACT_78136 Reactome:REACT_78959 Reactome:REACT_79662 Reactome:REACT_85241 Reactome:REACT_85359 Reactome:REACT_86357 Reactome:REACT_89816 Reactome:REACT_91657 Reactome:REACT_91965 Reactome:REACT_93586 Reactome:REACT_93968 Reactome:REACT_94814 Reactome:REACT_98256 Wikipedia:Gene_expression biological_process GO:0010467 gene expression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb Reactome:REACT_100537 Gene Expression, Xenopus tropicalis Reactome:REACT_101147 Gene Expression, Danio rerio Reactome:REACT_101952 Gene Expression, Sus scrofa Reactome:REACT_105649 Gene Expression, Drosophila melanogaster Reactome:REACT_108313 Gene Expression, Caenorhabditis elegans Reactome:REACT_29068 Gene Expression, Escherichia coli Reactome:REACT_34240 Gene Expression, Staphylococcus aureus N315 Reactome:REACT_71 Gene Expression, Homo sapiens Reactome:REACT_78136 Gene Expression, Mus musculus Reactome:REACT_78959 Gene Expression, Taeniopygia guttata Reactome:REACT_79662 Gene Expression, Plasmodium falciparum Reactome:REACT_85241 Gene Expression, Oryza sativa Reactome:REACT_85359 Gene Expression, Gallus gallus Reactome:REACT_86357 Gene Expression, Canis familiaris Reactome:REACT_89816 Gene Expression, Mycobacterium tuberculosis Reactome:REACT_91657 Gene Expression, Arabidopsis thaliana Reactome:REACT_91965 Gene Expression, Rattus norvegicus Reactome:REACT_93586 Gene Expression, Dictyostelium discoideum Reactome:REACT_93968 Gene Expression, Bos taurus Reactome:REACT_94814 Gene Expression, Schizosaccharomyces pombe Reactome:REACT_98256 Gene Expression, Saccharomyces cerevisiae 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. Wikipedia:Regulation_of_gene_expression regulation of protein expression biological_process regulation of gene product expression GO:0010468 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. regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb regulation of protein expression GOC:curators regulation of gene product expression GOC:curators 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. biological_process GO:0010556 regulation of macromolecule biosynthetic process Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb 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. biological_process GO:0010557 positive regulation of macromolecule biosynthetic process Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb 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. biological_process GO:0010558 negative regulation of macromolecule biosynthetic process Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb 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. biological_process GO:0010604 positive regulation of macromolecule metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb 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. biological_process GO:0010605 negative regulation of macromolecule metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. biological_process GO:0010608 posttranscriptional regulation of gene expression Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. GOC:dph GOC:tb 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. biological_process GO:0010628 positive regulation of gene expression Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb 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. biological_process GO:0010629 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. negative regulation of gene expression Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GOC:dph GOC:tb 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 biological_process positive regulation of organelle organization and biogenesis GO:0010638 positive regulation of organelle organization 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. GOC:dph GOC:tb positive regulation of organelle organisation GOC:mah positive regulation of organelle organization and biogenesis GOC:mah 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 biological_process negative regulation of organelle organization and biogenesis GO:0010639 negative 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. GOC:dph GOC:tb negative regulation of organelle organisation GOC:mah negative regulation of organelle organization and biogenesis GOC:mah 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. biological_process GO:0010646 regulation of cell communication 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. GOC:dph GOC:tb 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. biological_process GO:0010647 positive regulation of cell communication 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. GOC:dph GOC:tb 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. biological_process GO:0010648 negative 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. GOC:dph GOC:tb Any process in which a lipid is transported to, or maintained in, a specific location. lipid localisation biological_process GO:0010876 lipid localization Any process in which a lipid is transported to, or maintained in, a specific location. GOC:BHF GOC:dph GOC:tb lipid localisation GOC:mah The cellular component assembly that is part of the initial shaping of the component during its developmental progression. biological_process GO:0010927 cellular component assembly involved in morphogenesis The cellular component assembly that is part of the initial shaping of the component during its developmental progression. GOC:dph GOC:tb 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. biological_process GO:0010941 regulation of cell death 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. GOC:dph GOC:tb 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. biological_process GO:0010942 positive regulation of 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. GOC:dph GOC:tb A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. GO:0016244 regulated cell death Wikipedia:Programmed_cell_death caspase-independent cell death non-apoptotic programmed cell death nonapoptotic programmed cell death biological_process PCD RCD caspase-independent apoptosis GO:0012501 Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children, which are descendants of GO:0034050 'host programmed cell death induced by symbiont'. programmed cell death A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell. GOC:lr GOC:mtg_apoptosis Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus. response to organic cyclic substance biological_process GO:0014070 response to organic cyclic compound Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus. CHEBI:33832 GOC:ef response to organic cyclic substance GOC:mah 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. GO:0015831 enzyme transport biological_process GO:0015031 protein transport 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. GOC:ai Enables the transfer of an ion from one side of a membrane to the other. ion transporter activity molecular_function GO:0015075 ion transmembrane transporter activity Enables the transfer of an ion from one side of a membrane to the other. GOC:dgf GOC:mtg_transport ISBN:0815340729 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. GO:0015249 GO:0015268 pore activity TC:1 channel/pore class transporter activity nonselective channel activity molecular_function alpha-type channel activity channel-forming toxin activity pore class transporter activity GO:0015267 channel activity 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. GOC:mtg_transport ISBN:0815340729 TC:1.-.-.-.- 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 inorganic uptake permease activity molecular_function GO:0015318 Renamed term see https://github.com/geneontology/go-ontology/issues/14372 inorganic molecular entity transmembrane transporter activity 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. GOC:mtg_transport ISBN:0815340729 The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. biological_process GO:0015711 organic anion transport The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage. GOC:ai GOC:krc The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015718 monocarboxylic acid transport The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:krc The directed movement of 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. biological_process GO:0015833 peptide transport 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. GOC:ai The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015849 organic acid transport The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. ISBN:0198506732 The directed movement of fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Fatty acids are aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis. biological_process GO:0015908 fatty acid transport The directed movement of fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Fatty acids are aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis. GOC:ai The directed movement of long-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22. Reactome:REACT_23892 biological_process GO:0015909 long-chain fatty acid transport The directed movement of long-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22. CHEBI:15904 GOC:ai Reactome:REACT_23892 Transport of fatty acids, Homo sapiens A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0044235 GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism biological_process cell organization and biogenesis GO:0016043 cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:ai GOC:jl GOC:mah cellular component organisation at cellular level GOC:mah cellular component organisation in other organism GOC:mah cell organization and biogenesis GOC:mah The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. GO:0048591 cellular growth growth of cell biological_process cell expansion metabolic process resulting in cell growth metabolism resulting in cell growth non-developmental cell growth non-developmental growth of a unicellular organism GO:0016049 cell growth The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. GOC:ai non-developmental cell growth GOC:mah non-developmental growth of a unicellular organism GOC:mah The 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. Reactome:REACT_107259 Reactome:REACT_107652 Reactome:REACT_110289 Reactome:REACT_21257 Reactome:REACT_30579 Reactome:REACT_31367 Reactome:REACT_33720 Reactome:REACT_80071 Reactome:REACT_83630 Reactome:REACT_84169 Reactome:REACT_85788 Reactome:REACT_88316 Reactome:REACT_89992 Reactome:REACT_91556 Reactome:REACT_92152 Reactome:REACT_94876 Reactome:REACT_99403 Reactome:REACT_99885 RNA metabolism biological_process GO:0016070 RNA metabolic process 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. ISBN:0198506732 Reactome:REACT_107259 Metabolism of RNA, Sus scrofa Reactome:REACT_107652 Metabolism of RNA, Schizosaccharomyces pombe Reactome:REACT_110289 Metabolism of RNA, Danio rerio Reactome:REACT_21257 Metabolism of RNA, Homo sapiens Reactome:REACT_30579 Metabolism of RNA, Xenopus tropicalis Reactome:REACT_31367 Metabolism of RNA, Dictyostelium discoideum Reactome:REACT_33720 Metabolism of RNA, Plasmodium falciparum Reactome:REACT_80071 Metabolism of RNA, Caenorhabditis elegans Reactome:REACT_83630 Metabolism of RNA, Taeniopygia guttata Reactome:REACT_84169 Metabolism of RNA, Canis familiaris Reactome:REACT_85788 Metabolism of RNA, Oryza sativa Reactome:REACT_88316 Metabolism of RNA, Mus musculus Reactome:REACT_89992 Metabolism of RNA, Saccharomyces cerevisiae Reactome:REACT_91556 Metabolism of RNA, Bos taurus Reactome:REACT_92152 Metabolism of RNA, Drosophila melanogaster Reactome:REACT_94876 Metabolism of RNA, Arabidopsis thaliana Reactome:REACT_99403 Metabolism of RNA, Rattus norvegicus Reactome:REACT_99885 Metabolism of RNA, Gallus gallus The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes. Wikipedia:RNA_interference RNAi posttranscriptional gene silencing by siRNA biological_process GO:0016246 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'. RNA interference 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. GOC:ems PMID:11201747 PMID:11713190 PMID:18771919 posttranscriptional gene silencing by siRNA GOC:mah The inactivation of gene expression by a posttranscriptional mechanism. Wikipedia:Post_transcriptional_gene_silencing PTGS post-transcriptional gene silencing quelling biological_process cosuppression GO:0016441 posttranscriptional gene silencing The inactivation of gene expression by a posttranscriptional mechanism. GOC:mah PMID:15020054 post-transcriptional gene silencing GOC:vw 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. Wikipedia:Gene_silencing long-term maintenance of gene inactivation biological_process GO:0016458 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. gene silencing Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression. GOC:dos GOC:dph GOC:jid GOC:tb The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. Wikipedia:Cell_migration biological_process GO:0016477 cell migration The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms. GOC:cjm GOC:dph GOC:ems GOC:pf http://en.wikipedia.org/wiki/Cell_migration 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. EC:3 Reactome:REACT_110436 Reactome:REACT_111159 Reactome:REACT_15331 Reactome:REACT_83734 Reactome:REACT_84047 Reactome:REACT_87959 Reactome:REACT_88159 Reactome:REACT_90118 Reactome:REACT_91045 Reactome:REACT_98572 molecular_function GO:0016787 hydrolase activity 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. ISBN:0198506732 Reactome:REACT_110436 Hydrolysis of phosphatidylcholine, Bos taurus Reactome:REACT_111159 Partial proteolysis of antigen in phagolysosomes, Homo sapiens Reactome:REACT_15331 Hydrolysis of phosphatidylcholine, Homo sapiens Reactome:REACT_83734 Hydrolysis of phosphatidylcholine, Danio rerio Reactome:REACT_84047 Hydrolysis of phosphatidylcholine, Xenopus tropicalis Reactome:REACT_87959 Hydrolysis of phosphatidylcholine, Gallus gallus Reactome:REACT_88159 Hydrolysis of phosphatidylcholine, Canis familiaris Reactome:REACT_90118 Hydrolysis of phosphatidylcholine, Mus musculus Reactome:REACT_91045 Hydrolysis of phosphatidylcholine, Taeniopygia guttata Reactome:REACT_98572 Hydrolysis of phosphatidylcholine, Rattus norvegicus Catalysis of the hydrolysis of any ester bond. EC:3.1 Reactome:REACT_106563 Reactome:REACT_109748 Reactome:REACT_112177 Reactome:REACT_19294 Reactome:REACT_1978 Reactome:REACT_45174 Reactome:REACT_77112 Reactome:REACT_81282 Reactome:REACT_83347 Reactome:REACT_88228 Reactome:REACT_88314 Reactome:REACT_89615 Reactome:REACT_92446 Reactome:REACT_94475 esterase activity molecular_function GO:0016788 hydrolase activity, acting on ester bonds Catalysis of the hydrolysis of any ester bond. GOC:jl Reactome:REACT_106563 Deacylation of Acyl Ghrelin, Mus musculus Reactome:REACT_109748 Deacylation of Acyl Ghrelin, Bos taurus Reactome:REACT_112177 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Xenopus tropicalis Reactome:REACT_19294 Deacylation of Acyl Ghrelin, Homo sapiens Reactome:REACT_1978 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Homo sapiens Reactome:REACT_45174 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Mus musculus Reactome:REACT_77112 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Danio rerio Reactome:REACT_81282 Deacylation of Acyl Ghrelin, Rattus norvegicus Reactome:REACT_83347 Deacylation of Acyl Ghrelin, Gallus gallus Reactome:REACT_88228 Deacylation of Acyl Ghrelin, Canis familiaris Reactome:REACT_88314 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Sus scrofa Reactome:REACT_89615 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Rattus norvegicus Reactome:REACT_92446 uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Canis familiaris Reactome:REACT_94475 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. GO:0016478 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 biological_process protein biosynthesis inhibitor activity protein biosynthetic process inhibitor activity GO:0017148 negative regulation of translation Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA. GOC:isa_complete The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle anabolism heterocycle biosynthesis heterocycle formation heterocycle synthesis biological_process GO:0018130 heterocycle biosynthetic process The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). ISBN:0198547684 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 biological_process regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0019219 regulation of nucleobase-containing compound metabolic process Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044246 regulation of metabolism regulation of multicellular organismal metabolic process regulation of organismal metabolic process biological_process GO:0019222 regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators regulation of organismal metabolic process GOC:tb The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. aromatic compound anabolism aromatic compound biosynthesis aromatic compound formation aromatic compound synthesis aromatic hydrocarbon biosynthesis aromatic hydrocarbon biosynthetic process biological_process GO:0019438 aromatic compound biosynthetic process The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring. GOC:ai The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. aromatic compound breakdown aromatic compound catabolism aromatic compound degradation aromatic hydrocarbon catabolic process aromatic hydrocarbon catabolism biological_process GO:0019439 aromatic compound catabolic process The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. GOC:ai The chemical reactions and pathways involving a protein. Includes protein modification. GO:0006411 GO:0044268 Wikipedia:Protein_metabolism protein metabolic process and modification protein metabolism protein metabolism and modification multicellular organismal protein metabolic process biological_process GO:0019538 protein metabolic process The chemical reactions and pathways involving a protein. Includes protein modification. GOC:ma immunoglobulin complex 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. immunoglobulin complex B cell receptor complex 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. B cell receptor complex A cellular process that results in the breakdown of a cellular component. GO:0071845 cell structure disassembly cellular component disassembly at cellular level biological_process GO:0022411 cellular component disassembly A cellular process that results in the breakdown of a cellular component. GOC:isa_complete Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis. regulation of morphogenesis biological_process GO:0022603 regulation of anatomical structure morphogenesis Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis. GOC:mah The aggregation, arrangement and bonding together of a cellular component. GO:0071844 cell structure assembly cellular component assembly at cellular level biological_process GO:0022607 cellular component assembly The aggregation, arrangement and bonding together of a cellular component. GOC:isa_complete A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex. RNA-protein complex biogenesis ribonucleoprotein complex biogenesis and assembly biological_process GO:0022613 ribonucleoprotein complex biogenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex. GOC:isa_complete GOC:mah RNA-protein complex biogenesis GOC:mah ribonucleoprotein complex biogenesis and assembly GOC:mah The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. RNA-protein complex assembly RNP complex assembly protein-RNA complex assembly biological_process GO:0022618 ribonucleoprotein complex assembly The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. GOC:jl 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. GO:0022814 porters Reactome:REACT_118066 Reactome:REACT_118091 Reactome:REACT_118204 Reactome:REACT_118231 Reactome:REACT_118327 Reactome:REACT_118347 Reactome:REACT_118350 Reactome:REACT_118478 Reactome:REACT_118490 Reactome:REACT_118544 Reactome:REACT_19251 Wikipedia:Facilitated_diffusion uniporter activity z molecular_function facilitated diffusion GO:0022803 passive transmembrane transporter activity 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. GOC:mtg_transport ISBN:0815340729 Reactome:REACT_118066 Passive I- efflux mediated by SMCT1, Staphylococcus aureus N315 Reactome:REACT_118091 Passive I- efflux mediated by SMCT1, Xenopus tropicalis Reactome:REACT_118204 Passive I- efflux mediated by SMCT1, Mus musculus Reactome:REACT_118231 Passive I- efflux mediated by SMCT1, Bos taurus Reactome:REACT_118327 Passive I- efflux mediated by SMCT1, Taeniopygia guttata Reactome:REACT_118347 Passive I- efflux mediated by SMCT1, Rattus norvegicus Reactome:REACT_118350 Passive I- efflux mediated by SMCT1, Canis familiaris Reactome:REACT_118478 Passive I- efflux mediated by SMCT1, Sus scrofa Reactome:REACT_118490 Passive I- efflux mediated by SMCT1, Gallus gallus Reactome:REACT_118544 Passive I- efflux mediated by SMCT1, Danio rerio Reactome:REACT_19251 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. molecular_function GO:0022838 substrate-specific channel activity 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. GOC:mtg_transport 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. GO:0005386 GO:0015563 GO:0015646 GO:0022891 GO:0022892 Reactome:REACT_100033 Reactome:REACT_106735 Reactome:REACT_111088 Reactome:REACT_111933 Reactome:REACT_113047 Reactome:REACT_113116 Reactome:REACT_113829 Reactome:REACT_114161 Reactome:REACT_19288 Reactome:REACT_77235 Reactome:REACT_81225 Reactome:REACT_88503 Reactome:REACT_91849 Reactome:REACT_94185 substrate-specific transporter activity molecular_function substrate-specific transmembrane transporter activity uptake permease activity uptake transmembrane transporter activity GO:0022857 transmembrane transporter activity 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. GOC:jid GOC:mtg_transport ISBN:0815340729 Reactome:REACT_100033 GLUT9 transports glucose, fructose and urate, Gallus gallus Reactome:REACT_106735 GLUT9 transports glucose, fructose and urate, Xenopus tropicalis Reactome:REACT_111088 Egress of internalized antigen to the cytosol via sec61, Homo sapiens Reactome:REACT_111933 GLUT9 transports glucose, fructose and urate, Plasmodium falciparum Reactome:REACT_113047 GLUT9 transports glucose, fructose and urate, Dictyostelium discoideum Reactome:REACT_113116 GLUT9 transports glucose, fructose and urate, Mycobacterium tuberculosis Reactome:REACT_113829 GLUT9 transports glucose, fructose and urate, Arabidopsis thaliana Reactome:REACT_114161 GLUT9 transports glucose, fructose and urate, Oryza sativa Reactome:REACT_19288 GLUT9 transports glucose, fructose and urate, Homo sapiens Reactome:REACT_77235 GLUT9 transports glucose, fructose and urate, Canis familiaris Reactome:REACT_81225 GLUT9 transports glucose, fructose and urate, Bos taurus Reactome:REACT_88503 GLUT9 transports glucose, fructose and urate, Taeniopygia guttata Reactome:REACT_91849 GLUT9 transports glucose, fructose and urate, Mus musculus Reactome:REACT_94185 GLUT9 transports glucose, fructose and urate, Rattus norvegicus Any process that modulates the frequency, rate or extent of transmembrane transporter activity. biological_process GO:0022898 regulation of transmembrane transporter activity Any process that modulates the frequency, rate or extent of transmembrane transporter activity. GOC:dph GOC:mtg_cardio GOC:mtg_transport 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. 2010-02-16T09:30:50Z biological_process regulation of gene expression as a consequence of signal transmission GO:0023019 signal transduction involved in regulation of gene expression 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. GOC:mtg_signal regulation of gene expression as a consequence of signal transmission GOC:bf Any process that modulates the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process regulation of signaling process regulation of signalling process GO:0023051 regulation of signaling Any process that modulates the frequency, rate or extent of a signaling process. GOC:mtg_signal regulation of signaling process GOC:bf regulation of signalling process GOC:mah 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. janelomax 2010-02-16T09:30:50Z GO:0023046 GO:0044700 biological signaling signaling process signalling biological_process signalling process single organism signaling GO:0023052 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. signaling 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. GOC:mtg_signal GOC:mtg_signaling_feb11 GOC:signaling signalling process GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z positive regulation of signalling process biological_process positive regulation of signaling process GO:0023056 positive regulation of signaling Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. GOC:mtg_signal positive regulation of signalling process GOC:mah positive regulation of signaling process GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process negative regulation of signaling process negative regulation of signalling process GO:0023057 negative regulation of signaling Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. GOC:mtg_signal negative regulation of signaling process GOC:bf negative regulation of signalling process GOC:mah 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 organisation biological_process cell projection organization and biogenesis cell surface structure organization and biogenesis GO:0030030 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 prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection organisation GOC:curators cell projection organization and biogenesis GOC:mah cell surface structure organization and biogenesis GOC:mah Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. formation of a cell surface projection biological_process cell projection biogenesis GO:0030031 cell projection assembly Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah http://www.cogsci.princeton.edu/~wn/ cell projection biogenesis GOC:mah actin filament polymerization Assembly of actin filaments by the addition of actin monomers to a filament. actin filament polymerization hemopoiesis 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. hemopoiesis Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis. apoptotic nuclear change biological_process GO:0030262 apoptotic nuclear changes Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis. GOC:mah GOC:mtg_apoptosis Any process that activates or increases the frequency, rate, extent or direction of cell growth. up regulation of cell growth up-regulation of cell growth upregulation of cell growth activation of cell growth stimulation of cell growth biological_process GO:0030307 positive regulation of cell growth Any process that activates or increases the frequency, rate, extent or direction of cell growth. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth. Reactome:REACT_6328 down regulation of cell growth down-regulation of cell growth downregulation of cell growth inhibition of cell growth biological_process GO:0030308 negative regulation of cell growth Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth. GOC:go_curators Reactome:REACT_6328 DRheb is inhibited by the TSC1/2 complex, Drosophila melanogaster Any process that modulates the frequency, rate or extent of cell migration. biological_process GO:0030334 regulation of cell migration Any process that modulates the frequency, rate or extent of cell migration. GOC:go_curators Any process that activates or increases the frequency, rate or extent of cell migration. up regulation of cell migration up-regulation of cell migration upregulation of cell migration activation of cell migration stimulation of cell migration biological_process GO:0030335 positive regulation of cell migration Any process that activates or increases the frequency, rate or extent of cell migration. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. down regulation of cell migration down-regulation of cell migration downregulation of cell migration inhibition of cell migration biological_process GO:0030336 negative regulation of cell migration Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration. GOC:go_curators Any process in which RNA molecules inactivate expression of target genes. RNA-mediated gene silencing biological_process GO:0031047 gene silencing by RNA Any process in which RNA molecules inactivate expression of target genes. GOC:dph GOC:mah GOC:tb PMID:15020054 RNA-mediated gene silencing GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. regulation of cellular metabolism biological_process GO:0031323 regulation of cellular metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah 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 biological_process GO:0031324 negative regulation of cellular metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. Reactome:REACT_101225 Reactome:REACT_102187 Reactome:REACT_102331 Reactome:REACT_105293 Reactome:REACT_108571 Reactome:REACT_109170 Reactome:REACT_2122 Reactome:REACT_28360 Reactome:REACT_31270 Reactome:REACT_79603 Reactome:REACT_80902 Reactome:REACT_83058 Reactome:REACT_84314 Reactome:REACT_86633 Reactome:REACT_87840 Reactome:REACT_88060 Reactome:REACT_91293 Reactome:REACT_91429 Reactome:REACT_91906 Reactome:REACT_92487 Reactome:REACT_99393 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 biological_process GO:0031325 positive regulation of cellular metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Reactome:REACT_101225 ChREBP activates metabolic gene expression, Mus musculus Reactome:REACT_102187 ChREBP activates metabolic gene expression, Escherichia coli Reactome:REACT_102331 ChREBP activates metabolic gene expression, Caenorhabditis elegans Reactome:REACT_105293 ChREBP activates metabolic gene expression, Plasmodium falciparum Reactome:REACT_108571 ChREBP activates metabolic gene expression, Drosophila melanogaster Reactome:REACT_109170 ChREBP activates metabolic gene expression, Xenopus tropicalis Reactome:REACT_2122 ChREBP activates metabolic gene expression, Homo sapiens Reactome:REACT_28360 ChREBP activates metabolic gene expression, Arabidopsis thaliana Reactome:REACT_31270 ChREBP activates metabolic gene expression, Mycobacterium tuberculosis Reactome:REACT_79603 ChREBP activates metabolic gene expression, Canis familiaris Reactome:REACT_80902 ChREBP activates metabolic gene expression, Saccharomyces cerevisiae Reactome:REACT_83058 ChREBP activates metabolic gene expression, Taeniopygia guttata Reactome:REACT_84314 ChREBP activates metabolic gene expression, Oryza sativa Reactome:REACT_86633 ChREBP activates metabolic gene expression, Dictyostelium discoideum Reactome:REACT_87840 ChREBP activates metabolic gene expression, Danio rerio Reactome:REACT_88060 ChREBP activates metabolic gene expression, Rattus norvegicus Reactome:REACT_91293 ChREBP activates metabolic gene expression, Staphylococcus aureus N315 Reactome:REACT_91429 ChREBP activates metabolic gene expression, Gallus gallus Reactome:REACT_91906 ChREBP activates metabolic gene expression, Schizosaccharomyces pombe Reactome:REACT_92487 ChREBP activates metabolic gene expression, Bos taurus Reactome:REACT_99393 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 anabolism regulation of cellular biosynthesis regulation of cellular formation regulation of cellular synthesis biological_process GO:0031326 regulation of cellular biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah 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 biological_process GO:0031327 negative regulation of cellular biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah 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 biological_process GO:0031328 positive regulation of cellular biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. regulation of cellular breakdown regulation of cellular catabolism regulation of cellular degradation biological_process GO:0031329 regulation of cellular catabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:mah 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 biological_process GO:0031330 negative regulation of cellular catabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:mah 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 biological_process GO:0031331 positive regulation of cellular catabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:mah 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 inhibition of protein complex assembly biological_process GO:0031333 negative regulation of protein complex assembly Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly. GOC:mah 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 activation of protein complex assembly stimulation of protein complex assembly biological_process GO:0031334 positive regulation of protein complex assembly Any process that activates or increases the frequency, rate or extent of protein complex assembly. GOC:mah 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. biological_process GO:0031341 regulation of cell killing 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. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of cell killing. down regulation of cell killing down-regulation of cell killing downregulation of cell killing inhibition of cell killing biological_process GO:0031342 negative regulation of cell killing Any process that stops, prevents, or reduces the frequency, rate or extent of cell killing. GOC:mah Any process that activates or increases the frequency, rate or extent of cell killing. up regulation of cell killing up-regulation of cell killing upregulation of cell killing activation of cell killing stimulation of cell killing biological_process GO:0031343 positive regulation of cell killing Any process that activates or increases the frequency, rate or extent of cell killing. GOC:mah 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 biological_process regulation of cell projection organization and biogenesis GO:0031344 regulation of cell projection organization 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. GOC:mah regulation of cell projection organisation GOC:curators regulation of cell projection organization and biogenesis GOC:mah 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 biological_process negative regulation of cell projection organization and biogenesis GO:0031345 negative 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. GOC:mah down regulation of cell projection organization GOC:mah negative regulation of cell projection organisation GOC:curators negative regulation of cell projection organization and biogenesis GOC:mah 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 biological_process positive regulation of cell projection organization and biogenesis GO:0031346 positive 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. GOC:mah positive regulation of cell projection organisation GOC:curators positive regulation of cell projection organization and biogenesis GOC:mah 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. blebbing membrane blebbing cell blebbing plasma membrane bleb assembly plasma membrane blebbing biological_process GO:0032060 bleb assembly 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. GOC:mah GOC:mtg_apoptosis PMID:12083798 PMID:16624291 http://en.wikipedia.org/wiki/Bleb_(cell_biology) blebbing GOC:pr membrane blebbing GOC:pr plasma membrane bleb assembly GOC:pr plasma membrane blebbing GOC:pr Any process that modulates the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids. biological_process nuclease regulator activity GO:0032069 regulation of nuclease activity Any process that modulates the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids. GOC:mah Any process that modulates the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. biological_process DNase regulator deoxyribonuclease regulator GO:0032070 regulation of deoxyribonuclease activity Any process that modulates the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. GOC:mah Any process that modulates the frequency, rate or extent of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks. biological_process endodeoxyribonuclease regulator GO:0032071 regulation of endodeoxyribonuclease 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. GOC:mah Any process that stops or reduces the rate of nuclease activity, the hydrolysis of ester linkages within nucleic acids. down regulation of nuclease activity down-regulation of nuclease activity downregulation of nuclease activity inhibition of nuclease activity biological_process nuclease inhibitor GO:0032074 negative regulation of nuclease activity Any process that stops or reduces the rate of nuclease activity, the hydrolysis of ester linkages within nucleic acids. GOC:mah Any process that activates or increases the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids. up regulation of nuclease activity up-regulation of nuclease activity upregulation of nuclease activity activation of nuclease activity stimulation of nuclease activity biological_process nuclease activator GO:0032075 positive 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. GOC:mah 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 biological_process DNase inhibitor deoxyribonuclease inhibitor GO:0032076 negative regulation of deoxyribonuclease activity Any process that stops or reduces the rate of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid. GOC:mah 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 biological_process DNase activator deoxyribonuclease activator GO:0032077 positive 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. GOC:mah 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 biological_process endodeoxyribonuclease inhibitor GO:0032078 negative regulation of endodeoxyribonuclease activity Any process that stops or reduces the rate of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks. GOC:mah 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 biological_process endodeoxyribonuclease activator GO:0032079 positive 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. GOC:mah Any process that modulates the frequency, rate or extent of a response to an external stimulus. biological_process GO:0032101 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 external stimulus Any process that modulates the frequency, rate or extent of a response to an external stimulus. GOC:mah 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 biological_process GO:0032102 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. negative 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. GOC:mah 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 biological_process GO:0032103 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. positive regulation of response to external stimulus Any process that activates, maintains or increases the rate of a response to an external stimulus. GOC:mah The process in which a methyl group is covalently attached to a molecule. Reactome:REACT_100463 Reactome:REACT_104378 Reactome:REACT_106986 Reactome:REACT_107353 Reactome:REACT_107808 Reactome:REACT_110691 Reactome:REACT_34638 Reactome:REACT_6946 Reactome:REACT_77304 Reactome:REACT_78116 Reactome:REACT_87183 Reactome:REACT_88148 Reactome:REACT_90436 Reactome:REACT_92149 Reactome:REACT_92596 Reactome:REACT_93357 Reactome:REACT_95391 Reactome:REACT_98332 Reactome:REACT_99471 Reactome:REACT_99529 Wikipedia:Methylation biological_process GO:0032259 methylation The process in which a methyl group is covalently attached to a molecule. GOC:mah Reactome:REACT_100463 Methylation, Rattus norvegicus Reactome:REACT_104378 Methylation, Staphylococcus aureus N315 Reactome:REACT_106986 Methylation, Schizosaccharomyces pombe Reactome:REACT_107353 Methylation, Taeniopygia guttata Reactome:REACT_107808 Methylation, Caenorhabditis elegans Reactome:REACT_110691 Methylation, Gallus gallus Reactome:REACT_34638 Methylation, Mus musculus Reactome:REACT_6946 Methylation, Homo sapiens Reactome:REACT_77304 Methylation, Oryza sativa Reactome:REACT_78116 Methylation, Xenopus tropicalis Reactome:REACT_87183 Methylation, Drosophila melanogaster Reactome:REACT_88148 Methylation, Canis familiaris Reactome:REACT_90436 Methylation, Danio rerio Reactome:REACT_92149 Methylation, Sus scrofa Reactome:REACT_92596 Methylation, Escherichia coli Reactome:REACT_93357 Methylation, Mycobacterium tuberculosis Reactome:REACT_95391 Methylation, Saccharomyces cerevisiae Reactome:REACT_98332 Methylation, Arabidopsis thaliana Reactome:REACT_99471 Methylation, Bos taurus Reactome:REACT_99529 Methylation, Dictyostelium discoideum 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 biological_process GO:0032268 regulation of cellular protein metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. GOC:mah 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 biological_process GO:0032269 negative regulation of cellular protein metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell. GOC:mah 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 biological_process GO:0032270 positive 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. GOC:mah Any process that modulates the frequency, rate or extent of the controlled release of an icosanoid from a cell. regulation of eicosanoid secretion biological_process GO:0032303 regulation of icosanoid secretion Any process that modulates the frequency, rate or extent of the controlled release of an icosanoid from a cell. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of an icosanoid from a cell. down regulation of icosanoid secretion down-regulation of icosanoid secretion downregulation of icosanoid secretion negative regulation of eicosanoid secretion inhibition of icosanoid secretion biological_process GO:0032304 negative regulation of icosanoid secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of an icosanoid from a cell. GOC:mah 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 up regulation of icosanoid secretion up-regulation of icosanoid secretion upregulation of icosanoid secretion activation of icosanoid secretion stimulation of icosanoid secretion biological_process GO:0032305 positive 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. GOC:mah The controlled release of icosanoids, any of a group of C20 polyunsaturated fatty acids from a cell or a tissue. eicosanoid secretion biological_process GO:0032309 icosanoid secretion The controlled release of icosanoids, any of a group of C20 polyunsaturated fatty acids from a cell or a tissue. GOC:mah 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. biological_process GO:0032368 regulation of lipid transport 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. GOC:mah 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. down regulation of lipid transport down-regulation of lipid transport downregulation of lipid transport inhibition of lipid transport biological_process GO:0032369 negative regulation of lipid transport 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. GOC:mah 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. up regulation of lipid transport up-regulation of lipid transport upregulation of lipid transport activation of lipid transport stimulation of lipid transport biological_process GO:0032370 positive regulation of lipid transport 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. GOC:mah Any process that modulates the activity of a transporter. biological_process GO:0032409 regulation of transporter activity Any process that modulates the activity of a transporter. GOC:mah Any process that stops or reduces the activity of a transporter. down regulation of transporter activity down-regulation of transporter activity downregulation of transporter activity inhibition of transporter activity biological_process GO:0032410 negative regulation of transporter activity Any process that stops or reduces the activity of a transporter. GOC:mah Any process that activates or increases the activity of a transporter. up regulation of transporter activity up-regulation of transporter activity upregulation of transporter activity activation of transporter activity stimulation of transporter activity biological_process GO:0032411 positive regulation of transporter activity Any process that activates or increases the activity of a transporter. GOC:mah Any process that modulates the activity of an ion transporter. regulation of ion transporter activity biological_process GO:0032412 regulation of ion transmembrane transporter activity Any process that modulates the activity of an ion transporter. GOC:mah GOC:tb regulation of ion transporter activity GOC:tb 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 inhibition of ion transporter activity biological_process GO:0032413 negative regulation of ion transmembrane transporter activity Any process that stops or reduces the activity of an ion transporter. GOC:mah GOC:tb negative regulation of ion transporter activity GOC:tb 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 activation of ion transporter activity stimulation of ion transporter activity biological_process GO:0032414 positive regulation of ion transmembrane transporter activity Any process that activates or increases the activity of an ion transporter. GOC:mah GOC:tb positive regulation of ion transporter activity GOC:tb Any biological process, occurring at the level of a multicellular organism, pertinent to its function. janelomax 2012-09-19T16:07:47Z GO:0044707 GO:0050874 organismal physiological process biological_process single-multicellular organism process GO:0032501 multicellular organismal process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GOC:curators GOC:dph GOC:isa_complete GOC:tb 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. janelomax 2012-12-19T12:21:31Z GO:0044767 development biological_process single-organism developmental process GO:0032502 developmental process 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. GOC:isa_complete 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. TNF production TNF-alpha production tumor necrosis factor-alpha production biological_process GO:0032640 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'). tumor necrosis factor production 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. GOC:mah Any process that modulates the frequency, rate, or extent of tumor necrosis factor production. regulation of TNF production regulation of TNF-alpha production regulation of tumor necrosis factor-alpha production biological_process GO:0032680 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'). regulation of tumor necrosis factor production Any process that modulates the frequency, rate, or extent of tumor necrosis factor production. GOC:mah 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 production negative regulation TNF-alpha production negative regulation tumor necrosis factor-alpha production inhibition of tumor necrosis factor production biological_process GO:0032720 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'). negative regulation of tumor necrosis factor production Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production. GOC:mah Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production. positive regulation of TNF 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 biological_process GO:0032760 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'). positive regulation of tumor necrosis factor production Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production. GOC:mah 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. RNA anabolism RNA biosynthesis RNA formation RNA synthesis biological_process GO:0032774 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. RNA biosynthetic process 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. GOC:mah GOC:txnOH 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. regulation of localisation biological_process GO:0032879 regulation of localization 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. GOC:mah regulation of localisation GOC:mah 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. regulation of protein localisation biological_process GO:0032880 regulation of protein localization 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. GOC:dph GOC:mah GOC:tb regulation of protein localisation GOC:mah 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. biological_process GO:0032890 regulation of organic acid transport 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. GOC:mah 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 inhibition of organic acid transport biological_process GO:0032891 negative regulation of organic acid transport 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. GOC:mah 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. up regulation of organic acid transport up-regulation of organic acid transport upregulation of organic acid transport activation of organic acid transport stimulation of organic acid transport biological_process GO:0032892 positive 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. GOC:mah The controlled release of a substance by a cell. Wikipedia:Secretion cellular secretion biological_process GO:0032940 secretion by cell The controlled release of a substance by a cell. GOC:mah The disaggregation of a protein-containing macromolecular complex into its constituent components. GO:0034623 GO:0043241 protein complex disassembly biological_process cellular macromolecule complex disassembly macromolecule complex disassembly GO:0032984 protein-containing complex disassembly The disaggregation of a protein-containing macromolecular complex into its constituent components. GOC:mah The process in which cellular structures, including whole cells or cell parts, are generated and organized. cellular structure morphogenesis biological_process GO:0032989 cellular component morphogenesis The process in which cellular structures, including whole cells or cell parts, are generated and organized. GOC:dph GOC:mah GOC:tb cellular structure morphogenesis GOC:dph GOC:tb 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. GO:0043234 macromolecular complex macromolecule complex protein containing complex protein complex protein-protein complex cellular_component GO:0032991 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. protein-containing complex 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. GOC:dos GOC:mah macromolecule localization Any process in which a macromolecule is transported to, or maintained in, a specific location. macromolecule localisation biological_process GO:0033036 macromolecule localization Any process in which a macromolecule is transported to, or maintained in, a specific location. GOC:mah macromolecule localisation GOC:mah 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 organisation biological_process regulation of organelle organization and biogenesis GO:0033043 regulation of organelle organization 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. GOC:mah regulation of organelle organisation GOC:mah regulation of organelle organization and biogenesis GOC:mah 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 organisation biological_process regulation of chromosome organization and biogenesis GO:0033044 regulation of chromosome organization 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. GOC:mah regulation of chromosome organisation GOC:mah regulation of chromosome organization and biogenesis GOC:mah 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). biological_process GO:0033554 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. cellular response to stress 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). GOC:mah DNA polymerase activity 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. DNA polymerase activity A process in which an ion is transported across a membrane. Reactome:REACT_100497 Reactome:REACT_101721 Reactome:REACT_103924 Reactome:REACT_107347 Reactome:REACT_108844 Reactome:REACT_109050 Reactome:REACT_25149 Reactome:REACT_25300 Reactome:REACT_25387 Reactome:REACT_28672 Reactome:REACT_30601 Reactome:REACT_31166 Reactome:REACT_32763 Reactome:REACT_33389 Reactome:REACT_34584 Reactome:REACT_77153 Reactome:REACT_77267 Reactome:REACT_78982 Reactome:REACT_79679 Reactome:REACT_81685 Reactome:REACT_82102 Reactome:REACT_89671 Reactome:REACT_89674 Reactome:REACT_89758 Reactome:REACT_89890 Reactome:REACT_92146 Reactome:REACT_93475 Reactome:REACT_94109 Reactome:REACT_94939 Reactome:REACT_94986 Reactome:REACT_97506 Reactome:REACT_97619 Reactome:REACT_98518 ion membrane transport transmembrane ion transport biological_process GO:0034220 Note that this term is not intended for use in annotating lateral movement within membranes. ion transmembrane transport A process in which an ion is transported across a membrane. GOC:mah Reactome:REACT_100497 Ion channel transport, Rattus norvegicus Reactome:REACT_101721 Ion transport by P-type ATPases, Canis familiaris Reactome:REACT_103924 Ion transport by P-type ATPases, Taeniopygia guttata Reactome:REACT_107347 Ion channel transport, Caenorhabditis elegans Reactome:REACT_108844 Ion transport by P-type ATPases, Drosophila melanogaster Reactome:REACT_109050 Ion channel transport, Gallus gallus Reactome:REACT_25149 Ion transport by P-type ATPases, Homo sapiens Reactome:REACT_25300 Ion channel transport, Homo sapiens Reactome:REACT_25387 Ligand-gated ion channel transport, Homo sapiens Reactome:REACT_28672 Ion transport by P-type ATPases, Arabidopsis thaliana Reactome:REACT_30601 Ion channel transport, Danio rerio Reactome:REACT_31166 Ion channel transport, Sus scrofa Reactome:REACT_32763 Ion channel transport, Plasmodium falciparum Reactome:REACT_33389 Ion channel transport, Mycobacterium tuberculosis Reactome:REACT_34584 Ion channel transport, Oryza sativa Reactome:REACT_77153 Ion channel transport, Arabidopsis thaliana Reactome:REACT_77267 Ion channel transport, Taeniopygia guttata Reactome:REACT_78982 Ion transport by P-type ATPases, Bos taurus Reactome:REACT_79679 Ion transport by P-type ATPases, Xenopus tropicalis Reactome:REACT_81685 Ion channel transport, Bos taurus Reactome:REACT_82102 Ion channel transport, Canis familiaris Reactome:REACT_89671 Ion channel transport, Xenopus tropicalis Reactome:REACT_89674 Ion transport by P-type ATPases, Caenorhabditis elegans Reactome:REACT_89758 Ion transport by P-type ATPases, Sus scrofa Reactome:REACT_89890 Ion transport by P-type ATPases, Oryza sativa Reactome:REACT_92146 Ion transport by P-type ATPases, Mus musculus Reactome:REACT_93475 Ion transport by P-type ATPases, Rattus norvegicus Reactome:REACT_94109 Ion channel transport, Mus musculus Reactome:REACT_94939 Ion transport by P-type ATPases, Mycobacterium tuberculosis Reactome:REACT_94986 Ion transport by P-type ATPases, Plasmodium falciparum Reactome:REACT_97506 Ion transport by P-type ATPases, Danio rerio Reactome:REACT_97619 Ion channel transport, Drosophila melanogaster Reactome:REACT_98518 Ion transport by P-type ATPases, Gallus gallus transmembrane ion transport GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides. regulation of amide metabolism biological_process GO:0034248 regulation of cellular amide metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides. negative regulation of amide metabolism biological_process GO:0034249 negative 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. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides. positive regulation of amide metabolism biological_process GO:0034250 positive 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. GOC:mah 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. GO:0016249 cellular protein localisation channel localizer activity biological_process GO:0034613 cellular protein localization 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. GOC:mah cellular protein localisation GOC:mah channel localizer activity GOC:mah The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell. GO:0043623 cellular protein complex assembly biological_process cellular macromolecule complex assembly GO:0034622 cellular protein-containing complex assembly The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell. GOC:jl The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. Reactome:REACT_102000 Reactome:REACT_103710 Reactome:REACT_107293 Reactome:REACT_108179 Reactome:REACT_109042 Reactome:REACT_13 Reactome:REACT_28699 Reactome:REACT_29108 Reactome:REACT_32429 Reactome:REACT_33347 Reactome:REACT_34326 Reactome:REACT_55564 Reactome:REACT_77741 Reactome:REACT_82379 Reactome:REACT_86268 Reactome:REACT_90299 Reactome:REACT_91959 Reactome:REACT_93580 Reactome:REACT_95666 Reactome:REACT_98086 Reactome:REACT_99241 cellular nitrogen compound metabolism biological_process GO:0034641 cellular nitrogen compound metabolic process The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. GOC:mah Reactome:REACT_102000 Metabolism of amino acids and derivatives, Mycobacterium tuberculosis Reactome:REACT_103710 Metabolism of amino acids and derivatives, Escherichia coli Reactome:REACT_107293 Metabolism of amino acids and derivatives, Arabidopsis thaliana Reactome:REACT_108179 Metabolism of amino acids and derivatives, Xenopus tropicalis Reactome:REACT_109042 Metabolism of amino acids and derivatives, Sus scrofa Reactome:REACT_13 Metabolism of amino acids and derivatives, Homo sapiens Reactome:REACT_28699 Metabolism of amino acids and derivatives, Saccharomyces cerevisiae Reactome:REACT_29108 Metabolism of amino acids and derivatives, Caenorhabditis elegans Reactome:REACT_32429 Metabolism of amino acids and derivatives, Rattus norvegicus Reactome:REACT_33347 Metabolism of amino acids and derivatives, Mus musculus Reactome:REACT_34326 Metabolism of amino acids and derivatives, Staphylococcus aureus N315 Reactome:REACT_55564 Metabolism of amino acids and derivatives, Gallus gallus Reactome:REACT_77741 Metabolism of amino acids and derivatives, Taeniopygia guttata Reactome:REACT_82379 Metabolism of amino acids and derivatives, Bos taurus Reactome:REACT_86268 Metabolism of amino acids and derivatives, Drosophila melanogaster Reactome:REACT_90299 Metabolism of amino acids and derivatives, Oryza sativa Reactome:REACT_91959 Metabolism of amino acids and derivatives, Plasmodium falciparum Reactome:REACT_93580 Metabolism of amino acids and derivatives, Danio rerio Reactome:REACT_95666 Metabolism of amino acids and derivatives, Canis familiaris Reactome:REACT_98086 Metabolism of amino acids and derivatives, Dictyostelium discoideum Reactome:REACT_99241 Metabolism of amino acids and derivatives, Schizosaccharomyces pombe The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells. GO:0034961 cellular biopolymer biosynthetic process cellular macromolecule anabolism cellular macromolecule biosynthesis cellular macromolecule formation cellular macromolecule synthesis biological_process GO:0034645 cellular macromolecule biosynthetic process The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells. CHEBI:33694 GOC:mah cellular biopolymer biosynthetic process GOC:mtg_chebi_dec09 cellular macromolecule anabolism GOC:mah cellular macromolecule biosynthesis GOC:mah cellular macromolecule formation GOC:mah cellular macromolecule synthesis GOC:mah The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase, nucleoside, nucleotide and nucleic acid anabolism nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis nucleobase, nucleoside, nucleotide and nucleic acid formation nucleobase, nucleoside, nucleotide and nucleic acid synthesis biological_process GO:0034654 nucleobase-containing compound biosynthetic process The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids. GOC:mah The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. nucleobase, nucleoside, nucleotide and nucleic acid breakdown nucleobase, nucleoside, nucleotide and nucleic acid catabolism nucleobase, nucleoside, nucleotide and nucleic acid degradation biological_process nucleobase, nucleoside, nucleotide and nucleic acid catabolic process GO:0034655 nucleobase-containing compound catabolic process The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids. GOC:mah nucleobase, nucleoside, nucleotide and nucleic acid catabolic process GOC:dph GOC:tb The chemical reactions and pathways involving non-coding RNA transcripts (ncRNAs). Reactome:REACT_104424 Reactome:REACT_107260 Reactome:REACT_11052 Reactome:REACT_31743 Reactome:REACT_34395 Reactome:REACT_77416 Reactome:REACT_82057 Reactome:REACT_87487 Reactome:REACT_91823 Reactome:REACT_92649 Reactome:REACT_94145 ncRNA metabolism biological_process GO:0034660 ncRNA metabolic process The chemical reactions and pathways involving non-coding RNA transcripts (ncRNAs). GOC:mah Reactome:REACT_104424 Metabolism of non-coding RNA, Sus scrofa Reactome:REACT_107260 Metabolism of non-coding RNA, Canis familiaris Reactome:REACT_11052 Metabolism of non-coding RNA, Homo sapiens Reactome:REACT_31743 Metabolism of non-coding RNA, Rattus norvegicus Reactome:REACT_34395 Metabolism of non-coding RNA, Taeniopygia guttata Reactome:REACT_77416 Metabolism of non-coding RNA, Gallus gallus Reactome:REACT_82057 Metabolism of non-coding RNA, Drosophila melanogaster Reactome:REACT_87487 Metabolism of non-coding RNA, Danio rerio Reactome:REACT_91823 Metabolism of non-coding RNA, Xenopus tropicalis Reactome:REACT_92649 Metabolism of non-coding RNA, Bos taurus Reactome:REACT_94145 Metabolism of non-coding RNA, Mus musculus A protein complex that possesses methyltransferase activity. cellular_component GO:0034708 methyltransferase complex A protein complex that possesses methyltransferase activity. GOC:mah 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. regulation of membrane transport biological_process GO:0034762 regulation of transmembrane transport 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. GOC:mah 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 inhibition of transmembrane transport biological_process GO:0034763 negative regulation of transmembrane transport 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. GOC:mah 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 upregulation of transmembrane transport activation of transmembrane transport stimulation of transmembrane transport biological_process GO:0034764 positive 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. GOC:mah 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 ion membrane transport regulation of transmembrane ion transport biological_process GO:0034765 regulation of ion 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. GOC:mah regulation of transmembrane ion transport GOC:dph GOC:tb 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 biological_process GO:0034766 negative 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. GOC:mah negative regulation of transmembrane ion transport GOC:dph GOC:tb 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 biological_process GO:0034767 positive 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. GOC:mah 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 biological_process sense-PTGS GO:0035194 posttranscriptional gene silencing by RNA Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation. GOC:mah PMID:15020054 PMID:15066275 PMID:15066283 RNA-mediated posttranscriptional gene silencing GOC:dph GOC:tb 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. rfoulger 2011-02-24T03:37:26Z biological_process GO:0035690 cellular response to drug 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. GOC:sl 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. rfoulger 2012-03-12T11:08:22Z biological_process GO:0036146 cellular response to mycotoxin 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. GOC:di PMID:20548963 The increase in size or mass of an entire organism, a part of an organism or a cell. GO:0048590 biological_process growth pattern non-developmental growth GO:0040007 See also the biological process term 'cell growth ; GO:0016049'. growth The increase in size or mass of an entire organism, a part of an organism or a cell. GOC:bf GOC:ma non-developmental growth GOC:mah 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. biological_process GO:0040008 regulation of growth 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. GOC:ems GOC:mah Self-propelled movement of a cell or organism from one location to another. biological_process GO:0040011 locomotion Self-propelled movement of a cell or organism from one location to another. GOC:dgh Any process that modulates the frequency, rate or extent of locomotion of a cell or organism. biological_process GO:0040012 regulation of locomotion Any process that modulates the frequency, rate or extent of locomotion of a cell or organism. GOC:ems Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism. down regulation of locomotion down-regulation of locomotion downregulation of locomotion inhibition of locomotion biological_process GO:0040013 negative regulation of locomotion Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism. up regulation of locomotion up-regulation of locomotion upregulation of locomotion activation of locomotion stimulation of locomotion biological_process GO:0040017 positive regulation of locomotion Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism. GOC:go_curators 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. biological_process GO:0040029 regulation of gene expression, epigenetic 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. PMID:10521337 PMID:11498582 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. regulation of molecular function, epigenetic 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 biological_process GO:0040033 negative regulation of translation, ncRNA-mediated Any process, mediated by small non-coding RNAs, that stops, prevents or reduces the rate that mRNAs are effectively translated into protein. GOC:dph GOC:ems GOC:tb The series of events that restore integrity to a damaged tissue, following an injury. Wikipedia:Wound_healing biological_process GO:0042060 wound healing The series of events that restore integrity to a damaged tissue, following an injury. GOC:bf PMID:15269788 T cell receptor complex 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. T cell receptor complex Any process that modulates the frequency, rate or extent of cell proliferation. biological_process GO:0042127 regulation of cell proliferation Any process that modulates the frequency, rate or extent of cell proliferation. GOC:jl Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. response to chemical stimulus response to chemical substance biological_process GO:0042221 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to chemical Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. GOC:jl response to chemical stimulus GOC:dos The directed movement of a motile cell or organism in response to an external stimulus. Wikipedia:Taxis directed movement in response to stimulus biological_process GO:0042330 taxis The directed movement of a motile cell or organism in response to an external stimulus. GOC:jl ISBN:0192801023 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. biological_process GO:0042391 regulation of membrane potential 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. GOC:jl GOC:mtg_cardio GOC:tb ISBN:0198506732 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease. GO:0017035 biological_process drug resistance drug susceptibility/resistance GO:0042493 response to drug 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. GOC:jl immunoglobulin complex, circulating 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. antibody antibody immunoglobulin complex, circulating DNA polymerase complex A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. DNA polymerase complex A process in which planktonically growing microorganisms grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription. biological_process GO:0042710 biofilm formation A process in which planktonically growing microorganisms grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription. GOC:di PMID:11932229 The chemical reactions and pathways involving 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. antisense RNA metabolism biological_process GO:0042868 antisense RNA metabolic process 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. GOC:jl 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. biological_process GO:0042886 amide transport 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. GOC:jl ISBN:0198506732 Any process that modulates the occurrence or rate of cell death by apoptotic process. Reactome:REACT_106248 Reactome:REACT_109234 Reactome:REACT_109339 Reactome:REACT_13648 Reactome:REACT_29911 Reactome:REACT_30641 Reactome:REACT_79698 Reactome:REACT_85908 Reactome:REACT_86575 Reactome:REACT_95946 Reactome:REACT_96201 Reactome:REACT_99944 regulation of apoptosis biological_process apoptosis regulator activity GO:0042981 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 apoptotic process Any process that modulates the occurrence or rate of cell death by apoptotic process. GOC:jl GOC:mtg_apoptosis Reactome:REACT_106248 Regulation of Apoptosis, Mus musculus Reactome:REACT_109234 Regulation of Apoptosis, Rattus norvegicus Reactome:REACT_109339 Regulation of Apoptosis, Sus scrofa Reactome:REACT_13648 Regulation of Apoptosis, Homo sapiens Reactome:REACT_29911 Regulation of Apoptosis, Danio rerio Reactome:REACT_30641 Regulation of Apoptosis, Drosophila melanogaster Reactome:REACT_79698 Regulation of Apoptosis, Taeniopygia guttata Reactome:REACT_85908 Regulation of Apoptosis, Bos taurus Reactome:REACT_86575 Regulation of Apoptosis, Xenopus tropicalis Reactome:REACT_95946 Regulation of Apoptosis, Caenorhabditis elegans Reactome:REACT_96201 Regulation of Apoptosis, Canis familiaris Reactome:REACT_99944 Regulation of Apoptosis, Gallus gallus 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. peptide anabolism peptide biosynthesis peptide formation peptide synthesis biological_process GO:0043043 peptide biosynthetic process 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. CHEBI:16670 GOC:dph GOC:jl Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process. up regulation of apoptosis up-regulation of apoptosis upregulation of apoptosis activation of apoptosis positive regulation of apoptosis stimulation of apoptosis biological_process pro-apoptosis GO:0043065 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 activates or increases the frequency, rate or extent of cell death by apoptotic process. GOC:jl GOC:mtg_apoptosis Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. GO:0006916 Reactome:REACT_13537 Reactome:REACT_29981 Reactome:REACT_77563 Reactome:REACT_81263 Reactome:REACT_83278 Reactome:REACT_84567 Reactome:REACT_91585 Reactome:REACT_93662 Reactome:REACT_95215 Reactome:REACT_95867 Reactome:REACT_98500 anti-apoptosis down regulation of apoptosis down-regulation of apoptosis downregulation of apoptosis inhibition of apoptosis negative regulation of apoptosis biological_process apoptosis inhibitor activity pro-survival GO:0043066 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 Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process. GOC:jl GOC:mtg_apoptosis Reactome:REACT_13537 p75NTR signals via NF-kB, Homo sapiens Reactome:REACT_29981 p75NTR signals via NF-kB, Canis familiaris Reactome:REACT_77563 p75NTR signals via NF-kB, Sus scrofa Reactome:REACT_81263 p75NTR signals via NF-kB, Taeniopygia guttata Reactome:REACT_83278 p75NTR signals via NF-kB, Drosophila melanogaster Reactome:REACT_84567 p75NTR signals via NF-kB, Gallus gallus Reactome:REACT_91585 p75NTR signals via NF-kB, Danio rerio Reactome:REACT_93662 p75NTR signals via NF-kB, Rattus norvegicus Reactome:REACT_95215 p75NTR signals via NF-kB, Mus musculus Reactome:REACT_95867 p75NTR signals via NF-kB, Xenopus tropicalis Reactome:REACT_98500 p75NTR signals via NF-kB, Bos taurus Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043070 regulation of non-apoptotic programmed cell death biological_process GO:0043067 regulation of programmed cell death Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GOC:jl Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. GO:0043071 up regulation of programmed cell death up-regulation of programmed cell death upregulation of programmed cell death activation of programmed cell death positive regulation of non-apoptotic programmed cell death stimulation of programmed cell death biological_process GO:0043068 positive regulation of 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. GOC:jl 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. GO:0043072 down regulation of programmed cell death down-regulation of programmed cell death downregulation of programmed cell death inhibition of programmed cell death negative regulation of non-apoptotic programmed cell death biological_process GO:0043069 negative 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. GOC:jl Any process that activates or increases the activity of an enzyme. GO:0048554 positive regulation of enzyme activity up regulation of enzyme activity up-regulation of enzyme activity upregulation of enzyme activity activation of enzyme activity activation of metalloenzyme activity positive regulation of metalloenzyme activity stimulation of enzyme activity stimulation of metalloenzyme activity up regulation of metalloenzyme activity up-regulation of metalloenzyme activity upregulation of metalloenzyme activity biological_process GO:0043085 positive regulation of catalytic activity Any process that activates or increases the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw positive regulation of enzyme activity GOC:tb Any process that stops or reduces the activity of an enzyme. GO:0048553 down regulation of enzyme activity down-regulation of enzyme activity down-regulation of metalloenzyme activity downregulation of enzyme activity negative regulation of enzyme activity down regulation of metalloenzyme activity downregulation of metalloenzyme activity inhibition of enzyme activity inhibition of metalloenzyme activity negative regulation of metalloenzyme activity biological_process GO:0043086 negative regulation of catalytic activity Any process that stops or reduces the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw negative regulation of enzyme activity GOC:tb 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 translational machinery localization translational protein localization biological_process GO:0043143 regulation of translation by machinery localization Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location. GOC:jl regulation of translation by machinery localisation GOC:mah translational machinery localization GOC:dph GOC:tb The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0043283 GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism multicellular organismal macromolecule metabolic process biological_process GO:0043170 macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. CHEBI:33694 GOC:mah biopolymer metabolic process GOC:mtg_chebi_dec09 protein complex A ribosome is a protein complex 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. protein complex 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 biological_process GO:0043242 negative regulation of protein complex disassembly 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. GOC:jl 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 biological_process GO:0043243 positive 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. GOC:jl Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components. biological_process GO:0043244 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. GOC:jl Any process that modulates the frequency, rate or extent of protein complex assembly. biological_process GO:0043254 regulation of protein complex assembly Any process that modulates the frequency, rate or extent of protein complex assembly. GOC:jl 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. biological_process GO:0043269 regulation of ion transport 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. GOC:jl 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. up regulation of ion transport up-regulation of ion transport upregulation of ion transport activation of ion transport stimulation of ion transport biological_process GO:0043270 positive regulation of ion transport 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. GOC:jl 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. down regulation of ion transport down-regulation of ion transport downregulation of ion transport inhibition of ion transport biological_process GO:0043271 negative regulation of ion transport 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. GOC:jl 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). up regulation of DNA binding up-regulation of DNA binding upregulation of DNA binding activation of DNA binding stimulation of DNA binding biological_process GO:0043388 positive regulation of DNA binding 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). GOC:dph GOC:jl GOC:tb 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). down regulation of DNA binding down-regulation of DNA binding downregulation of DNA binding inhibition of DNA binding biological_process GO:0043392 negative regulation of DNA binding 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). GOC:dph GOC:jl GOC:tb 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. biological_process GO:0043412 macromolecule modification 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. GOC:go_curators The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule. biological_process GO:0043414 macromolecule methylation The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule. GOC:go_curators sequence-specific DNA binding 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. sequence specific DNA binding molecular_function GO:0043565 sequence-specific DNA binding 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. GOC:jl 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. amide metabolism biological_process GO:0043603 cellular amide metabolic process 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. CHEBI:32988 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. biological_process GO:0043604 amide biosynthetic process 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. CHEBI:32988 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. biological_process GO:0043624 cellular protein complex disassembly 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. GOC:jl 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. biological_process GO:0043900 regulation of multi-organism process 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. GOC:jl 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. biological_process GO:0043901 negative regulation of multi-organism process 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. GOC:jl 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. biological_process GO:0043902 positive 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. GOC:jl Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. midori 2010-09-08T10:01:42Z GO:0034600 GO:0034621 GO:0071822 protein complex subunit organisation protein complex subunit organization biological_process cellular macromolecular complex organization cellular macromolecular complex subunit organisation cellular macromolecular complex subunit organization macromolecular complex organization macromolecular complex subunit organisation macromolecular complex subunit organization GO:0043933 protein-containing complex subunit organization Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. GOC:mah protein complex subunit organisation GOC:mah cellular macromolecular complex subunit organisation GOC:curators macromolecular complex subunit organisation GOC:curators regulation of DNA methylation 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. biological_process GO:0044030 regulation of DNA methylation 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. GOC:jl 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. biological_process GO:0044070 regulation of anion transport 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. GOC:jl 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. GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 cellular component biogenesis 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. GOC:jl GOC:mah 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. biological_process GO:0044087 regulation of cellular component biogenesis 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. GOC:jl 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. biological_process GO:0044089 positive 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. GOC:jl 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. jane 2009-04-21T04:07:27Z biological_process GO:0044092 negative regulation of molecular function 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. GO:jl 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. jane 2009-04-21T04:11:06Z biological_process GO:0044093 positive 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. GO:jl 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. kchris 2009-11-04T12:58:25Z GO:0000975 regulatory region DNA binding molecular_function GO:0044212 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 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. GOC:jl GOC:txnOH SO:0005836 The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism biological_process intermediary metabolism GO:0044237 cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. GOC:go_curators intermediary metabolism GOC:mah The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. primary metabolism biological_process GO:0044238 primary metabolic process The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators http://www.metacyc.org The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. cellular breakdown cellular catabolism cellular degradation biological_process GO:0044248 cellular catabolic process The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells. GOC:jl The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. cellular anabolism cellular biosynthesis cellular formation cellular synthesis biological_process GO:0044249 cellular biosynthetic process The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:jl The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells. GO:0034960 cellular biopolymer metabolic process cellular macromolecule metabolism biological_process GO:0044260 cellular macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells. CHEBI:33694 GOC:mah cellular biopolymer metabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells. GO:0034962 cellular biopolymer catabolic process cellular macromolecule breakdown cellular macromolecule catabolism cellular macromolecule degradation biological_process GO:0044265 cellular macromolecule catabolic process The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells. CHEBI:33694 GOC:jl cellular biopolymer catabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification. Reactome:REACT_101554 Reactome:REACT_102155 Reactome:REACT_105825 Reactome:REACT_106151 Reactome:REACT_108005 Reactome:REACT_109022 Reactome:REACT_17015 Reactome:REACT_32904 Reactome:REACT_34473 Reactome:REACT_80561 Reactome:REACT_81994 Reactome:REACT_82523 Reactome:REACT_85873 Reactome:REACT_86658 Reactome:REACT_89852 Reactome:REACT_91052 Reactome:REACT_93132 Reactome:REACT_96466 Reactome:REACT_99179 cellular protein metabolism biological_process GO:0044267 cellular protein metabolic 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. GOC:jl Reactome:REACT_101554 Metabolism of proteins, Gallus gallus Reactome:REACT_102155 Metabolism of proteins, Arabidopsis thaliana Reactome:REACT_105825 Metabolism of proteins, Dictyostelium discoideum Reactome:REACT_106151 Metabolism of proteins, Xenopus tropicalis Reactome:REACT_108005 Metabolism of proteins, Bos taurus Reactome:REACT_109022 Metabolism of proteins, Schizosaccharomyces pombe Reactome:REACT_17015 Metabolism of proteins, Homo sapiens Reactome:REACT_32904 Metabolism of proteins, Canis familiaris Reactome:REACT_34473 Metabolism of proteins, Taeniopygia guttata Reactome:REACT_80561 Metabolism of proteins, Escherichia coli Reactome:REACT_81994 Metabolism of proteins, Sus scrofa Reactome:REACT_82523 Metabolism of proteins, Danio rerio Reactome:REACT_85873 Metabolism of proteins, Saccharomyces cerevisiae Reactome:REACT_86658 Metabolism of proteins, Drosophila melanogaster Reactome:REACT_89852 Metabolism of proteins, Rattus norvegicus Reactome:REACT_91052 Metabolism of proteins, Caenorhabditis elegans Reactome:REACT_93132 Metabolism of proteins, Mus musculus Reactome:REACT_96466 Metabolism of proteins, Plasmodium falciparum Reactome:REACT_99179 Metabolism of proteins, Oryza sativa The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. nitrogen compound breakdown nitrogen compound catabolism nitrogen compound degradation biological_process GO:0044270 cellular nitrogen compound catabolic process The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds. GOC:jl ISBN:0198506732 The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. nitrogen compound anabolism nitrogen compound biosynthesis nitrogen compound formation nitrogen compound synthesis biological_process GO:0044271 cellular nitrogen compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds. GOC:jl ISBN:0198506732 Any 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. cellular_component GO:0044424 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. intracellular part Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. GOC:jl Any constituent part of a cell, the basic structural and functional unit of all organisms. NIF_Subcellular:sao628508602 cellular subcomponent cellular_component protoplast GO:0044464 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. cell part Any constituent part of a cell, the basic structural and functional unit of all organisms. GOC:jl cellular subcomponent NIF_Subcellular:sao628508602 protoplast GOC:mah The process of adding or removing a methyl group from one or more nucleotides within an DNA molecule. janelomax 2012-10-24T14:49:41Z biological_process changes in DNA methylation GO:0044728 DNA methylation or demethylation The process of adding or removing a methyl group from one or more nucleotides within an DNA molecule. GOC:jl Any process that is carried out at the cellular level which involves another organism of the same or different species. janelomax 2012-12-11T17:00:50Z biological_process GO:0044764 multi-organism cellular process Any process that is carried out at the cellular level which involves another organism of the same or different species. GOC:jl Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome. translation factor activity molecular_function GO:0045182 translation regulator activity Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome. GOC:ai The directed movement of a protein to a specific location. establishment of protein localisation protein positioning protein recruitment biological_process GO:0045184 establishment of protein localization The directed movement of a protein to a specific location. GOC:bf establishment of protein localisation GOC:mah 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. GO:0045946 Reactome:REACT_6236 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 biological_process GO:0045727 positive regulation of translation 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. GOC:dph GOC:go_curators GOC:tb Reactome:REACT_6236 Activated DTOR phosphorylates DS6K, Drosophila melanogaster positive regulation of protein biosynthetic process GOC:tb Any process that activates or increases the frequency, rate or extent of DNA replication. up regulation of DNA replication up-regulation of DNA replication upregulation of DNA replication activation of DNA replication stimulation of DNA replication biological_process GO:0045740 positive regulation of DNA replication Any process that activates or increases the frequency, rate or extent of DNA replication. GOC:go_curators 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. down regulation of action potential down-regulation of action potential downregulation of action potential inhibition of action potential biological_process GO:0045759 negative regulation of action potential 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. GOC:go_curators 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. up regulation of action potential up-regulation of action potential upregulation of action potential activation of action potential stimulation of action potential biological_process GO:0045760 positive regulation of action potential 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. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. GO:0016481 GO:0032582 GO:0061021 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 biological_process 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 transcription repressor activity GO:0045892 negative regulation of transcription, DNA-templated Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription. GOC:go_curators GOC:txnOH negative regulation of transcription, DNA-dependent GOC:txnOH Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. GO:0043193 GO:0045941 GO:0061020 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 biological_process activation of gene-specific transcription positive regulation of gene-specific transcription transcription activator activity up regulation of gene-specific transcription up-regulation of gene-specific transcription upregulation of gene-specific transcription GO:0045893 positive regulation of transcription, DNA-templated Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. GOC:go_curators GOC:txnOH positive regulation of transcription, DNA-dependent GOC:txnOH 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 inhibition of translational elongation biological_process GO:0045900 negative regulation of translational elongation Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation. GOC:go_curators 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 activation of translational elongation stimulation of translational elongation biological_process GO:0045901 positive regulation of translational elongation Any process that activates or increases the frequency, rate or extent of translational elongation. GOC:go_curators 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 inhibition of translational termination biological_process GO:0045904 negative regulation of translational termination Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination. GOC:go_curators 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 activation of translational termination stimulation of translational termination biological_process GO:0045905 positive regulation of translational termination Any process that activates or increases the frequency, rate or extent of translational termination. GOC:go_curators 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. down regulation of growth down-regulation of growth downregulation of growth inhibition of growth biological_process GO:0045926 negative regulation of growth 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. GOC:go_curators 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. up regulation of growth up-regulation of growth upregulation of growth activation of growth stimulation of growth biological_process GO:0045927 positive regulation of growth 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. GOC:go_curators 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 biological_process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0045934 negative regulation of nucleobase-containing compound metabolic process Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb 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 biological_process positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0045935 positive regulation of nucleobase-containing compound metabolic process Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb 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 inhibition of translational initiation biological_process GO:0045947 negative regulation of translational initiation Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation. GOC:go_curators 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 activation of translational initiation stimulation of translational initiation biological_process GO:0045948 positive regulation of translational initiation Any process that activates or increases the frequency, rate or extent of translational initiation. GOC:go_curators Any process, mediated by small non-coding RNAs, that modulates the frequency, rate or extent that mRNAs are effectively translated into protein. biological_process GO:0045974 regulation of translation, ncRNA-mediated Any process, mediated by small non-coding RNAs, that modulates the frequency, rate or extent that mRNAs are effectively translated into protein. GOC:dph GOC:go_curators GOC:tb The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle metabolism biological_process GO:0046483 heterocycle metabolic process The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). CHEBI:5686 ISBN:0198506732 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms. biological_process antibiotic susceptibility/resistance GO:0046677 response to antibiotic Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms. GOC:ai GOC:ef The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle breakdown heterocycle catabolism heterocycle degradation biological_process GO:0046700 heterocycle catabolic process The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). GOC:ai The controlled release of acid by a cell or a tissue. biological_process GO:0046717 acid secretion The controlled release of acid by a cell or a tissue. GOC:ai The controlled release of a substance by a cell or a tissue. biological_process GO:0046903 secretion The controlled release of a substance by a cell or a tissue. GOC:ai The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-). biological_process GO:0046942 carboxylic acid transport The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-). GOC:ai Any process 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. GO:0043119 positive regulation of physiological process up regulation of biological process up-regulation of biological process upregulation of biological process activation of biological process stimulation of biological process biological_process GO:0048518 positive regulation of biological process Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid 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. GO:0043118 down regulation of biological process down-regulation of biological process downregulation of biological process negative regulation of physiological process inhibition of biological process biological_process GO:0048519 negative regulation of biological process Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid 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. GO:0051242 positive regulation of cellular physiological process up regulation of cellular process up-regulation of cellular process upregulation of cellular process activation of cellular process stimulation of cellular process biological_process GO:0048522 positive regulation of cellular process Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid 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. GO:0051243 down regulation of cellular process down-regulation of cellular process downregulation of cellular process negative regulation of cellular physiological process inhibition of cellular process biological_process GO:0048523 negative regulation of cellular process Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid 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 organization anatomical structure structural organization organization of an anatomical structure structural organization biological_process GO:0048532 anatomical structure arrangement 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. GOC:go_curators 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. biological_process GO:0048583 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 stimulus Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. up regulation of response to stimulus up-regulation of response to stimulus upregulation of response to stimulus activation of response to stimulus stimulation of response to stimulus biological_process GO:0048584 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. positive regulation of response to stimulus Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. down regulation of response to stimulus down-regulation of response to stimulus downregulation of response to stimulus inhibition of response to stimulus biological_process GO:0048585 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. negative regulation of response to stimulus Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid 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 biological_process GO:0048646 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 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. GOC:dph GOC:jid GOC:tb formation of an anatomical structure involved in morphogenesis GOC:dph GOC:tb 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. development of an anatomical structure biological_process GO:0048856 This term was added by GO_REF:0000021. anatomical structure development 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. GOC:mtg_15jun06 GO_REF:0000021 A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. biological_process GO:0048869 cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. GOC:isa_complete Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. cell locomotion movement of a cell biological_process cell movement GO:0048870 cell motility Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. GOC:dgh GOC:dph GOC:isa_complete GOC:mlg The controlled release of arachidonic acid from a cell or a tissue. biological_process GO:0050482 This term should be used to annotate release of arachidonic acid from the cell. For the hydrolytic release of arachidonic acid from a phospholipid, consider instead annotating to 'phospholipase A2 activity ; GO:0004623'. arachidonic acid secretion The controlled release of arachidonic acid from a cell or a tissue. GOC:ai 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. interferon secretion interleukin secretion biological_process GO:0050663 cytokine secretion 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. GOC:ai GOC:bf ISBN:0198599471 interferon secretion GOC:add GOC:mah interleukin secretion GOC:add GOC:mah http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F Any process that modulates the frequency, rate or extent of the regulated release of cytokines from a cell. biological_process GO:0050707 regulation of cytokine secretion Any process that modulates the frequency, rate or extent of the regulated release of cytokines from a cell. GOC:ai Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell. biological_process GO:0050708 regulation of protein secretion Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell. down regulation of protein secretion down-regulation of protein secretion downregulation of protein secretion inhibition of protein secretion biological_process GO:0050709 negative regulation of protein secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of cytokines from a cell. down regulation of cytokine secretion down-regulation of cytokine secretion downregulation of cytokine secretion inhibition of cytokine secretion biological_process GO:0050710 negative regulation of cytokine secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of cytokines from a cell. GOC:ai Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell. up regulation of protein secretion up-regulation of protein secretion upregulation of protein secretion activation of protein secretion stimulation of protein secretion biological_process GO:0050714 positive regulation of protein secretion Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that activates or increases the frequency, rate or extent of the regulated release of cytokines from a cell. up regulation of cytokine secretion up-regulation of cytokine secretion upregulation of cytokine secretion activation of cytokine secretion stimulation of cytokine secretion biological_process GO:0050715 positive regulation of cytokine secretion Any process that activates or increases the frequency, rate or extent of the regulated release of cytokines from a cell. GOC:ai 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. GO:0050791 regulation of physiological process biological_process GO:0050789 regulation of biological process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:ai GOC:go_curators Any process that modulates the activity of an enzyme. GO:0048552 regulation of enzyme activity regulation of metalloenzyme activity biological_process GO:0050790 regulation of catalytic activity Any process that modulates the activity of an enzyme. GOC:ai GOC:ebc GOC:vw 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). biological_process GO:0050793 regulation of developmental process 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). GOC:go_curators 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. GO:0051244 regulation of cellular physiological process biological_process GO:0050794 regulation of cellular process Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0051869 physiological response to stimulus biological_process GO:0050896 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GOC:ai GOC:bf Any process 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. biological_process GO:0050920 regulation of chemotaxis 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. GOC:ai 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. up regulation of chemotaxis up-regulation of chemotaxis upregulation of chemotaxis activation of chemotaxis stimulation of chemotaxis biological_process GO:0050921 positive regulation of chemotaxis 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. GOC:ai 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. down regulation of chemotaxis down-regulation of chemotaxis downregulation of chemotaxis inhibition of chemotaxis biological_process GO:0050922 negative regulation of chemotaxis 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. GOC:ai Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. biological_process GO:0051046 regulation of secretion Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. up regulation of secretion up-regulation of secretion upregulation of secretion activation of secretion stimulation of secretion biological_process GO:0051047 positive regulation of secretion Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai 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. down regulation of secretion down-regulation of secretion downregulation of secretion inhibition of secretion biological_process GO:0051048 negative regulation of secretion 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. GOC:ai 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. biological_process GO:0051049 regulation of transport 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. GOC:ai 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. up regulation of transport up-regulation of transport upregulation of transport activation of transport stimulation of transport biological_process GO:0051050 positive regulation of transport 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. GOC:ai 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. down regulation of transport down-regulation of transport downregulation of transport inhibition of transport biological_process GO:0051051 negative regulation of transport 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. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. regulation of DNA metabolism biological_process GO:0051052 regulation of DNA metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai 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 downregulation of DNA metabolic process negative regulation of DNA metabolism inhibition of DNA metabolic process biological_process GO:0051053 negative regulation of DNA metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA. positive regulation of DNA metabolism up regulation of DNA metabolic process up-regulation of DNA metabolic process upregulation of DNA metabolic process activation of DNA metabolic process stimulation of DNA metabolic process biological_process GO:0051054 positive regulation of DNA metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA. GOC:ai 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 downregulation of developmental process inhibition of developmental process biological_process GO:0051093 negative regulation of developmental 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). GOC:ai 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). up regulation of developmental process up-regulation of developmental process upregulation of developmental process activation of developmental process stimulation of developmental process biological_process GO:0051094 positive 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). GOC:ai 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. biological_process GO:0051098 regulation of binding 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. GOC:ai 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. up regulation of binding up-regulation of binding upregulation of binding activation of binding stimulation of binding biological_process GO:0051099 positive regulation of binding 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. GOC:ai 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. down regulation of binding down-regulation of binding downregulation of binding inhibition of binding biological_process GO:0051100 negative regulation of binding 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. GOC:ai 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). biological_process GO:0051101 regulation of DNA binding 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). GOC:ai GOC:dph GOC:tb 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 biological_process regulation of cell organisation regulation of cell organization regulation of cellular component organization and biogenesis GO:0051128 regulation of cellular component organization 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. GOC:ai regulation of cellular component organisation GOC:curators regulation of cell organisation GOC:mah regulation of cell organization GOC:mah regulation of cellular component organization and biogenesis GOC:mah 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. down regulation of cell organization down-regulation of cell organization downregulation of cell organization inhibition of cell organization biological_process negative regulation of cell organisation negative regulation of cellular component organization and biogenesis GO:0051129 negative 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. GOC:ai negative regulation of cell organisation GOC:mah negative regulation of cellular component organization and biogenesis GOC:mah 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 up regulation of cell organization up-regulation of cell organization upregulation of cell organization activation of cell organization stimulation of cell organization biological_process positive regulation of cellular component organization and biogenesis GO:0051130 positive 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. GOC:ai positive regulation of cellular component organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. regulation of nitrogen metabolic process regulation of nitrogen metabolism biological_process GO:0051171 regulation of nitrogen compound metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb regulation of nitrogen metabolic process GOC:tb 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 biological_process GO:0051172 negative regulation of nitrogen compound metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb negative regulation of nitrogen metabolic process GOC:tb 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 biological_process GO:0051173 positive regulation of nitrogen compound metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb positive regulation of nitrogen metabolic process GOC:tb Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. jl 2013-12-18T13:51:04Z GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location biological_process single organism localization single-organism localization GO:0051179 localization Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. GOC:ai GOC:dos localisation GOC:mah single organism localization GOC:TermGenie Any process that 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. up regulation of protein transport up-regulation of protein transport upregulation of protein transport activation of protein transport stimulation of protein transport biological_process GO:0051222 positive regulation of protein transport 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. GOC:ai 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. biological_process GO:0051223 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. GOC:ai 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. down regulation of protein transport down-regulation of protein transport downregulation of protein transport inhibition of protein transport biological_process GO:0051224 negative regulation of protein transport 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. GOC:ai Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation biological_process GO:0051234 establishment of localization Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos establishment of localisation GOC:mah 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. biological_process GO:0051239 regulation of multicellular organismal process 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. GOC:ai GOC:dph GOC:tb 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 biological_process GO:0051240 positive 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. GOC:ai 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 biological_process GO:0051241 negative 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. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein. regulation of protein metabolism biological_process GO:0051246 regulation of protein metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein. GOC:ai 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 activation of protein metabolic process stimulation of protein metabolic process biological_process GO:0051247 positive regulation of protein metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein. GOC:ai 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 inhibition of protein metabolic process biological_process GO:0051248 negative regulation of protein metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA. regulation of RNA metabolism biological_process GO:0051252 regulation of RNA metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA. down regulation of RNA metabolic process down-regulation of RNA metabolic process downregulation of RNA metabolic process negative regulation of RNA metabolism inhibition of RNA metabolic process biological_process GO:0051253 negative regulation of RNA metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA. positive regulation of RNA metabolism up regulation of RNA metabolic process up-regulation of RNA metabolic process upregulation of RNA metabolic process activation of RNA metabolic process stimulation of RNA metabolic process biological_process GO:0051254 positive regulation of RNA metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA. GOC:ai Any process that modulates the frequency, rate or extent of the movement of a cellular component. regulation of cellular component motion biological_process regulation of cell movement GO:0051270 regulation of cellular component movement Any process that modulates the frequency, rate or extent of the movement of a cellular component. GOC:ai GOC:dph GOC:jl regulation of cellular component motion GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component. down regulation of cell motility down-regulation of cell motility downregulation of cell motility negative regulation of cellular component motion inhibition of cell motility biological_process negative regulation of cell movement GO:0051271 negative regulation of cellular component movement Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component. GOC:ai GOC:dph GOC:jl negative regulation of cellular component motion GOC:mah Any process that activates or increases the frequency, rate or extent of the movement of a cellular component. positive regulation of cellular component motion up regulation of cell motility up-regulation of cell motility upregulation of cell motility activation of cell motility stimulation of cell motility biological_process positive regulation of cell movement GO:0051272 positive regulation of cellular component movement Any process that activates or increases the frequency, rate or extent of the movement of a cellular component. GOC:ai GOC:dph GOC:jl positive regulation of cellular component motion GOC:mah chromosome organization 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. GO:0007001 GO:0051277 chromosome organisation biological_process chromosome organization and biogenesis maintenance of genome integrity nuclear genome maintenance GO:0051276 chromosome organization 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. GOC:ai GOC:dph GOC:jl GOC:mah chromosome organization and biogenesis GOC:mah 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. hydrolase regulator biological_process GO:0051336 regulation of hydrolase activity 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. EC:3.-.-.- GOC:ai Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds. hydrolase activator up regulation of hydrolase activity up-regulation of hydrolase activity upregulation of hydrolase activity activation of hydrolase activity stimulation of hydrolase activity biological_process GO:0051345 positive regulation of hydrolase activity Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds. GOC:ai Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds. down regulation of hydrolase activity down-regulation of hydrolase activity downregulation of hydrolase activity hydrolase inhibitor inhibition of hydrolase activity biological_process GO:0051346 negative regulation of hydrolase activity Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds. GOC:ai 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. jl 2013-12-18T14:04:32Z GO:1902580 cellular localisation establishment and maintenance of cellular localization establishment and maintenance of localization in cell or cell membrane single organism cellular localization intracellular localization localization within cell biological_process single-organism cellular localization GO:0051641 cellular localization 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. GOC:tb GOC:vw cellular localisation GOC:mah single organism cellular localization GOC:TermGenie Any process in which a cell is transported to, and/or maintained in, a specific location. cell localization establishment and maintenance of cell localization establishment and maintenance of localization of cell localisation of cell biological_process GO:0051674 localization of cell Any process in which a cell is transported to, and/or maintained in, a specific location. GOC:ai localisation of cell GOC:mah A biological process which involves another organism of the same or different species. GO:0051706 interaction between organisms physiological interaction between organisms physiological interaction with other organism biological_process GO:0051704 multi-organism process A biological process which involves another organism of the same or different species. GOC:jl 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. biological_process GO:0051716 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. cellular response to stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. GOC:bf GOC:jl The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. Reactome:REACT_100480 Reactome:REACT_101577 Reactome:REACT_101877 Reactome:REACT_101975 Reactome:REACT_102348 Reactome:REACT_102897 Reactome:REACT_102974 Reactome:REACT_104555 Reactome:REACT_108243 Reactome:REACT_109832 Reactome:REACT_110770 Reactome:REACT_114546 Reactome:REACT_114763 Reactome:REACT_114890 Reactome:REACT_115378 Reactome:REACT_15480 Reactome:REACT_15518 Reactome:REACT_19118 Reactome:REACT_29093 Reactome:REACT_29184 Reactome:REACT_29635 Reactome:REACT_30969 Reactome:REACT_32055 Reactome:REACT_32223 Reactome:REACT_32423 Reactome:REACT_32713 Reactome:REACT_33571 Reactome:REACT_61245 Reactome:REACT_79086 Reactome:REACT_79921 Reactome:REACT_80022 Reactome:REACT_80510 Reactome:REACT_80848 Reactome:REACT_80977 Reactome:REACT_81024 Reactome:REACT_81153 Reactome:REACT_82725 Reactome:REACT_83770 Reactome:REACT_86135 Reactome:REACT_86409 Reactome:REACT_86576 Reactome:REACT_87124 Reactome:REACT_88059 Reactome:REACT_88521 Reactome:REACT_88894 Reactome:REACT_89376 Reactome:REACT_91272 Reactome:REACT_91803 Reactome:REACT_92006 Reactome:REACT_92624 Reactome:REACT_93747 Reactome:REACT_94160 Reactome:REACT_94393 Reactome:REACT_94944 Reactome:REACT_94972 Reactome:REACT_96633 Reactome:REACT_96636 Reactome:REACT_97365 Reactome:REACT_97867 Reactome:REACT_98509 Reactome:REACT_98716 Reactome:REACT_99579 Reactome:REACT_99829 membrane transport biological_process GO:0055085 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. transmembrane transport The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GOC:dph GOC:jid Reactome:REACT_100480 SLC-mediated transmembrane transport, Taeniopygia guttata Reactome:REACT_101577 SLC-mediated transmembrane transport, Caenorhabditis elegans Reactome:REACT_101877 SLC-mediated transmembrane transport, Escherichia coli Reactome:REACT_101975 SLC-mediated transmembrane transport, Sus scrofa Reactome:REACT_102348 Transmembrane transport of small molecules, Staphylococcus aureus N315 Reactome:REACT_102897 Transmembrane transport of small molecules, Caenorhabditis elegans Reactome:REACT_102974 SLC-mediated transmembrane transport, Canis familiaris Reactome:REACT_104555 SLC-mediated transmembrane transport, Xenopus tropicalis Reactome:REACT_108243 SLC-mediated transmembrane transport, Staphylococcus aureus N315 Reactome:REACT_109832 Transmembrane transport of small molecules, Plasmodium falciparum Reactome:REACT_110770 ABC-family proteins mediated transport, Mus musculus Reactome:REACT_114546 ABC-family proteins mediated transport, Staphylococcus aureus N315 Reactome:REACT_114763 ABC-family proteins mediated transport, Escherichia coli Reactome:REACT_114890 ABC-family proteins mediated transport, Plasmodium falciparum Reactome:REACT_115378 ABC-family proteins mediated transport, Mycobacterium tuberculosis Reactome:REACT_15480 ABC-family proteins mediated transport, Homo sapiens Reactome:REACT_15518 Transmembrane transport of small molecules, Homo sapiens Reactome:REACT_19118 SLC-mediated transmembrane transport, Homo sapiens Reactome:REACT_29093 ABC-family proteins mediated transport, Taeniopygia guttata Reactome:REACT_29184 SLC-mediated transmembrane transport, Gallus gallus Reactome:REACT_29635 Transmembrane transport of small molecules, Canis familiaris Reactome:REACT_30969 ABC-family proteins mediated transport, Canis familiaris Reactome:REACT_32055 Transmembrane transport of small molecules, Saccharomyces cerevisiae Reactome:REACT_32223 Transmembrane transport of small molecules, Rattus norvegicus Reactome:REACT_32423 SLC-mediated transmembrane transport, Bos taurus Reactome:REACT_32713 ABC-family proteins mediated transport, Sus scrofa Reactome:REACT_33571 SLC-mediated transmembrane transport, Danio rerio Reactome:REACT_61245 Transmembrane transport of small molecules, Bos taurus Reactome:REACT_79086 SLC-mediated transmembrane transport, Plasmodium falciparum Reactome:REACT_79921 SLC-mediated transmembrane transport, Saccharomyces cerevisiae Reactome:REACT_80022 ABC-family proteins mediated transport, Bos taurus Reactome:REACT_80510 ABC-family proteins mediated transport, Rattus norvegicus Reactome:REACT_80848 ABC-family proteins mediated transport, Schizosaccharomyces pombe Reactome:REACT_80977 ABC-family proteins mediated transport, Caenorhabditis elegans Reactome:REACT_81024 Transmembrane transport of small molecules, Oryza sativa Reactome:REACT_81153 SLC-mediated transmembrane transport, Mus musculus Reactome:REACT_82725 SLC-mediated transmembrane transport, Rattus norvegicus Reactome:REACT_83770 Transmembrane transport of small molecules, Escherichia coli Reactome:REACT_86135 ABC-family proteins mediated transport, Oryza sativa Reactome:REACT_86409 Transmembrane transport of small molecules, Drosophila melanogaster Reactome:REACT_86576 Transmembrane transport of small molecules, Schizosaccharomyces pombe Reactome:REACT_87124 SLC-mediated transmembrane transport, Oryza sativa Reactome:REACT_88059 ABC-family proteins mediated transport, Xenopus tropicalis Reactome:REACT_88521 Transmembrane transport of small molecules, Taeniopygia guttata Reactome:REACT_88894 Transmembrane transport of small molecules, Gallus gallus Reactome:REACT_89376 SLC-mediated transmembrane transport, Schizosaccharomyces pombe Reactome:REACT_91272 ABC-family proteins mediated transport, Arabidopsis thaliana Reactome:REACT_91803 SLC-mediated transmembrane transport, Mycobacterium tuberculosis Reactome:REACT_92006 Transmembrane transport of small molecules, Mycobacterium tuberculosis Reactome:REACT_92624 ABC-family proteins mediated transport, Gallus gallus Reactome:REACT_93747 Transmembrane transport of small molecules, Dictyostelium discoideum Reactome:REACT_94160 Transmembrane transport of small molecules, Mus musculus Reactome:REACT_94393 ABC-family proteins mediated transport, Drosophila melanogaster Reactome:REACT_94944 ABC-family proteins mediated transport, Danio rerio Reactome:REACT_94972 SLC-mediated transmembrane transport, Dictyostelium discoideum Reactome:REACT_96633 Transmembrane transport of small molecules, Sus scrofa Reactome:REACT_96636 SLC-mediated transmembrane transport, Arabidopsis thaliana Reactome:REACT_97365 Transmembrane transport of small molecules, Arabidopsis thaliana Reactome:REACT_97867 ABC-family proteins mediated transport, Saccharomyces cerevisiae Reactome:REACT_98509 Transmembrane transport of small molecules, Xenopus tropicalis Reactome:REACT_98716 SLC-mediated transmembrane transport, Drosophila melanogaster Reactome:REACT_99579 Transmembrane transport of small molecules, Danio rerio Reactome:REACT_99829 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. biological_process GO:0060147 regulation of posttranscriptional gene silencing Any process that modulates the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism. GOC:dph Any process that increases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism. biological_process GO:0060148 positive regulation of posttranscriptional gene silencing Any process that increases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism. GOC:dph Any process that decreases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism. biological_process GO:0060149 negative regulation of posttranscriptional gene silencing Any process that decreases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism. GOC:dph 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. biological_process GO:0060194 regulation of antisense RNA transcription 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. GOC:dph GOC:jp GOC:tb PMID:18075583 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. biological_process GO:0060195 negative 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. GOC:dph GOC:tb PMID:18075583 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. biological_process GO:0060196 positive 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. GOC:dph GOC:tb PMID:18075583 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. biological_process GO:0060255 regulation of macromolecule metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:dph GOC:tb The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). biological_process GO:0060326 cell chemotaxis The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis). GOC:dph 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. regulation of cellular localisation biological_process GO:0060341 regulation of cellular localization 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. GOC:dph GOC:tb regulation of cellular localisation GOC:mah Any process that modulates the rate, frequency, or extent of cell projection assembly. biological_process regulation of cell projection formation GO:0060491 regulation of cell projection assembly Any process that modulates the rate, frequency, or extent of cell projection assembly. GOC:dph GOC:tb regulation of cell projection formation GOC:dph GOC:tb 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. dph 2009-04-13T01:56:10Z biological_process GO:0060548 negative regulation of cell death 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. GOC:BHF GOC:dph GOC:tb Any apoptotic process that contributes to the shaping of an anatomical structure. dph 2009-04-28T09:17:27Z apoptosis involved in morphogenesis biological_process apoptosis involved in development morphogenetic apoptosis GO:0060561 apoptotic process involved in morphogenesis Any apoptotic process that contributes to the shaping of an anatomical structure. GOC:dph GOC:mtg_apoptosis morphogenetic apoptosis GOC:dph 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. dph 2009-10-05T03:17:02Z biological_process GO:0060966 regulation of gene silencing by RNA Any process that regulates the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes. GOC:dph GOC:tb 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. dph 2009-10-05T03:21:05Z biological_process GO:0060967 negative regulation of gene silencing by RNA Any process that decreases the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes. GOC:dph GOC:tb 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. dph 2009-10-05T03:23:56Z biological_process GO:0060968 regulation of gene silencing Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation. GOC:dph GOC:tb 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. dph 2009-10-05T03:26:19Z biological_process GO:0060969 negative regulation of gene silencing Any process that decreases the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. dph 2010-02-25T10:14:37Z biological_process GO:0061041 regulation of wound healing Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. GOC:BHF GOC:dph Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. dph 2010-02-25T10:33:30Z biological_process GO:0061045 negative regulation of wound healing Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. GOC:dph 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. dph 2012-11-07T09:09:37Z biological_process GO:0061478 response to platelet aggregation inhibitor 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. GOC:dph The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. GO:0006461 biological_process chaperone activity macromolecular complex assembly macromolecule complex assembly protein complex assembly protein complex formation GO:0065003 protein-containing complex assembly The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. GOC:jl Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological_process GO:0065007 biological regulation Any process that modulates a measurable attribute of any biological process, quality or function. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw 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. regulation of biological attribute regulation of biological characteristic biological_process GO:0065008 regulation of biological quality 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. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw 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. regulation of a molecular function biological_process GO:0065009 regulation of molecular function 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. GOC:isa_complete 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 biological_process GO:0070201 regulation of establishment of protein localization Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. GOC:BHF GOC:mah regulation of establishment of protein localisation GOC:mah 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 biological_process GO:0070549 negative regulation of translation involved in RNA interference A process of negative regulation of translation that is mediated by the association of small interfering RNAs (siRNAs) with a cognate target mRNA. GOC:mah PMID:18771919 RNA interference, negative regulation of translation GOC:mah down regulation of translation involved in RNA interference GOC:mah down-regulation of translation involved in RNA interference GOC:mah downregulation of translation involved in RNA interference GOC:mah inhibition of translation involved in RNA interference GOC:mah 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. midori 2009-06-16T04:08:29Z cellular macromolecule localisation biological_process GO:0070727 cellular macromolecule localization 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. GOC:mah cellular macromolecule localisation GOC:mah 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. midori 2009-08-27T04:41:45Z biological_process GO:0070887 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. cellular response to chemical stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus. GOC:mah 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. midori 2009-12-10T04:46:04Z biological_process GO:0071310 cellular response to organic substance Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus. GOC:mah 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. midori 2009-12-14T02:55:58Z cellular response to organic cyclic substance biological_process GO:0071407 cellular response to organic cyclic compound Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus. GOC:mah cellular response to organic cyclic substance GOC:mah 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. midori 2009-12-14T04:07:27Z cellular response to organic nitrogen biological_process GO:0071417 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 an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond. CHEBI:35352 GOC:mah cellular response to organic nitrogen GOC:mah 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. midori 2009-12-18T02:25:40Z biological_process GO:0071495 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. cellular response to endogenous 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 arising within the organism. GOC:mah The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. midori 2010-03-08T02:15:14Z biological_process GO:0071702 organic substance transport The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. CHEBI:50860 GOC:mah The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. midori 2010-03-08T03:32:18Z organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism biological_process GO:0071704 organic substance metabolic process The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. CHEBI:50860 GOC:mah The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. midori 2010-03-08T03:56:28Z biological_process GO:0071705 nitrogen compound transport 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. CHEBI:51143 GOC:mah 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. midori 2010-03-09T02:40:35Z TNFSF cytokine production biological_process TNF superfamily production GO:0071706 tumor necrosis factor superfamily cytokine production 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. GOC:add TNFSF cytokine production GOC:add TNF superfamily production GOC:rv The directed movement of icosanoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Icosanoids are unsaturated C20 fatty acids and skeletally related compounds. midori 2010-03-10T02:47:22Z eicosanoid transport biological_process GO:0071715 icosanoid transport The directed movement of icosanoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Icosanoids are unsaturated C20 fatty acids and skeletally related compounds. CHEBI:23899 GOC:mah eicosanoid transport GOC:sl Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. midori 2010-09-08T10:10:35Z RNA-protein complex subunit organization protein-RNA complex subunit organization ribonucleoprotein complex subunit organisation biological_process GO:0071826 ribonucleoprotein complex subunit organization Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. GOC:mah RNA-protein complex subunit organization GOC:mah protein-RNA complex subunit organization GOC:mah ribonucleoprotein complex subunit organisation GOC:mah A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. midori 2010-09-10T01:39:16Z GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level biological_process GO:0071840 cellular component organization or biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:mah cellular component organisation or biogenesis GOC:mah cellular component organisation or biogenesis at cellular level GOC:mah The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. midori 2010-09-15T02:14:33Z DNA anabolism DNA biosynthesis DNA formation DNA synthesis biological_process GO:0071897 DNA biosynthetic process The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. GOC:mah DNA anabolism GOC:mah DNA biosynthesis GOC:mah DNA formation GOC:mah DNA synthesis GOC:mah Any 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. midori 2012-08-31T12:37:15Z biological_process GO:0072749 cellular response to cytochalasin B 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. GOC:mah 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. donghui 2009-04-22T04:30:52Z biological_process GO:0080090 regulation of primary metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. PMID:19211694 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). donghui 2009-05-06T04:51:28Z biological_process GO:0080134 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 stress 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). GOC:dhl 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). donghui 2009-05-06T05:02:52Z biological_process GO:0080135 regulation of cellular response to stress 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). GOC:dhl 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. tanyaberardini 2009-10-23T11:21:38Z biological_process GO:0090087 regulation of peptide transport 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. GOC:dph GOC:tb 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. tanyaberardini 2010-01-20T03:32:22Z biological_process GO:0090237 regulation of arachidonic acid secretion 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. GOC:dph GOC:tb 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. tanyaberardini 2010-01-20T03:32:22Z biological_process GO:0090238 positive 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. GOC:BHF GOC:dph GOC:tb Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. tanyaberardini 2010-03-22T02:12:03Z biological_process GO:0090303 positive regulation of wound healing Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury. GOC:BHF Any cellular metabolic process involving nucleic acids. tanyaberardini 2010-04-07T10:18:47Z biological_process GO:0090304 nucleic acid metabolic process Any cellular metabolic process involving nucleic acids. GOC:dph GOC:tb The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis. tanyaberardini 2010-04-07T10:26:30Z nucleic acid cleavage biological_process GO:0090305 nucleic acid phosphodiester bond hydrolysis The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis. GOC:dph GOC:tb nucleic acid cleavage GOC:dph GOC:tb 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. tanyaberardini 2010-06-02T10:12:37Z biological_process GO:0090342 regulation of cell aging 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. GOC:BHF GOC:dph GOC:tb 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. tanyaberardini 2010-06-02T10:12:37Z biological_process GO:0090343 positive regulation of cell aging 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. GOC:BHF GOC:dph GOC:tb 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. tanyaberardini 2010-06-02T10:12:37Z biological_process GO:0090344 negative regulation of cell aging 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. GOC:BHF GOC:dph GOC:tb Synthesis of DNA that is a part of the process of duplicating one or more molecules of DNA. tanyaberardini 2014-06-06T13:54:36Z biological_process GO:0090592 DNA synthesis involved in DNA replication Synthesis of DNA that is a part of the process of duplicating one or more molecules of DNA. GOC:vw Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure. paola 2011-09-23T02:31:01Z molecular_function GO:0097159 organic cyclic compound binding Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure. CHEBI:33832 GOC:sjw PMID:7583672 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. paola 2011-11-23T09:30:23Z GO:0008624 Reactome:REACT_101039 Reactome:REACT_101287 Reactome:REACT_101722 Reactome:REACT_102105 Reactome:REACT_102682 Reactome:REACT_103565 Reactome:REACT_104430 Reactome:REACT_104446 Reactome:REACT_104880 Reactome:REACT_105789 Reactome:REACT_1059 Reactome:REACT_106019 Reactome:REACT_106417 Reactome:REACT_107145 Reactome:REACT_107277 Reactome:REACT_108226 Reactome:REACT_108738 Reactome:REACT_108954 Reactome:REACT_110327 Reactome:REACT_110777 Reactome:REACT_113012 Reactome:REACT_113720 Reactome:REACT_114928 Reactome:REACT_115331 Reactome:REACT_13720 Reactome:REACT_13806 Reactome:REACT_1426 Reactome:REACT_1619 Reactome:REACT_28136 Reactome:REACT_30777 Reactome:REACT_32035 Reactome:REACT_33023 Reactome:REACT_33363 Reactome:REACT_47012 Reactome:REACT_78512 Reactome:REACT_78709 Reactome:REACT_79738 Reactome:REACT_81353 Reactome:REACT_81381 Reactome:REACT_82611 Reactome:REACT_83750 Reactome:REACT_84151 Reactome:REACT_85830 Reactome:REACT_86320 Reactome:REACT_86807 Reactome:REACT_88410 Reactome:REACT_88562 Reactome:REACT_89305 Reactome:REACT_89421 Reactome:REACT_900 Reactome:REACT_90409 Reactome:REACT_90414 Reactome:REACT_90980 Reactome:REACT_91488 Reactome:REACT_92659 Reactome:REACT_92947 Reactome:REACT_93354 Reactome:REACT_93927 Reactome:REACT_94832 Reactome:REACT_94837 Reactome:REACT_95750 Reactome:REACT_95777 Reactome:REACT_96066 Reactome:REACT_96229 Reactome:REACT_96867 Reactome:REACT_97301 Reactome:REACT_98119 Reactome:REACT_98804 Reactome:REACT_99367 Reactome:REACT_99865 apoptotic signalling pathway induction of apoptosis by extracellular signals biological_process GO:0097190 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. apoptotic signaling pathway 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. GOC:mtg_apoptosis Reactome:REACT_101039 Ceramide signalling, Canis familiaris Reactome:REACT_101287 Death Receptor Signalling, Xenopus tropicalis Reactome:REACT_101722 FasL/ CD95L signaling, Rattus norvegicus Reactome:REACT_102105 FASL binds FAS Receptor, Taeniopygia guttata Reactome:REACT_102682 Ceramide signalling, Bos taurus Reactome:REACT_103565 Death Receptor Signalling, Danio rerio Reactome:REACT_104430 Ceramide signalling, Gallus gallus Reactome:REACT_104446 Death Receptor Signalling, Bos taurus Reactome:REACT_104880 Cell death signalling via NRAGE, NRIF and NADE, Drosophila melanogaster Reactome:REACT_105789 Cell death signalling via NRAGE, NRIF and NADE, Canis familiaris Reactome:REACT_1059 Extrinsic Pathway for Apoptosis, Homo sapiens Reactome:REACT_106019 Ceramide signalling, Caenorhabditis elegans Reactome:REACT_106417 Cell death signalling via NRAGE, NRIF and NADE, Oryza sativa Reactome:REACT_107145 FASL binds FAS Receptor, Rattus norvegicus Reactome:REACT_107277 Cell death signalling via NRAGE, NRIF and NADE, Rattus norvegicus Reactome:REACT_108226 Ceramide signalling, Rattus norvegicus Reactome:REACT_108738 FASL binds FAS Receptor, Canis familiaris Reactome:REACT_108954 Cell death signalling via NRAGE, NRIF and NADE, Sus scrofa Reactome:REACT_110327 FASL binds FAS Receptor, Gallus gallus Reactome:REACT_110777 Extrinsic Pathway for Apoptosis, Canis familiaris Reactome:REACT_113012 Extrinsic Pathway for Apoptosis, Caenorhabditis elegans Reactome:REACT_113720 FasL/ CD95L signaling, Xenopus tropicalis Reactome:REACT_114928 Cell death signalling via NRAGE, NRIF and NADE, Dictyostelium discoideum Reactome:REACT_115331 FASL binds FAS Receptor, Xenopus tropicalis Reactome:REACT_13720 Cell death signalling via NRAGE, NRIF and NADE, Homo sapiens Reactome:REACT_13806 Ceramide signalling, Homo sapiens Reactome:REACT_1426 FASL binds FAS Receptor, Homo sapiens Reactome:REACT_1619 Death Receptor Signalling, Homo sapiens Reactome:REACT_28136 Death Receptor Signalling, Taeniopygia guttata Reactome:REACT_30777 Death Receptor Signalling, Sus scrofa Reactome:REACT_32035 FasL/ CD95L signaling, Danio rerio Reactome:REACT_33023 Ceramide signalling, Xenopus tropicalis Reactome:REACT_33363 Death Receptor Signalling, Gallus gallus Reactome:REACT_47012 Death Receptor Signalling, Mus musculus Reactome:REACT_78512 Ceramide signalling, Taeniopygia guttata Reactome:REACT_78709 Ceramide signalling, Drosophila melanogaster Reactome:REACT_79738 Extrinsic Pathway for Apoptosis, Xenopus tropicalis Reactome:REACT_81353 Ceramide signalling, Mus musculus Reactome:REACT_81381 FasL/ CD95L signaling, Gallus gallus Reactome:REACT_82611 Cell death signalling via NRAGE, NRIF and NADE, Taeniopygia guttata Reactome:REACT_83750 Extrinsic Pathway for Apoptosis, Gallus gallus Reactome:REACT_84151 Extrinsic Pathway for Apoptosis, Bos taurus Reactome:REACT_85830 Cell death signalling via NRAGE, NRIF and NADE, Danio rerio Reactome:REACT_86320 Cell death signalling via NRAGE, NRIF and NADE, Gallus gallus Reactome:REACT_86807 Death Receptor Signalling, Canis familiaris Reactome:REACT_88410 Cell death signalling via NRAGE, NRIF and NADE, Schizosaccharomyces pombe Reactome:REACT_88562 Ceramide signalling, Danio rerio Reactome:REACT_89305 FASL binds FAS Receptor, Bos taurus Reactome:REACT_89421 Cell death signalling via NRAGE, NRIF and NADE, Xenopus tropicalis Reactome:REACT_900 FasL/ CD95L signaling, Homo sapiens Reactome:REACT_90409 Ceramide signalling, Schizosaccharomyces pombe Reactome:REACT_90414 Cell death signalling via NRAGE, NRIF and NADE, Arabidopsis thaliana Reactome:REACT_90980 FasL/ CD95L signaling, Canis familiaris Reactome:REACT_91488 Cell death signalling via NRAGE, NRIF and NADE, Bos taurus Reactome:REACT_92659 Extrinsic Pathway for Apoptosis, Sus scrofa Reactome:REACT_92947 Extrinsic Pathway for Apoptosis, Danio rerio Reactome:REACT_93354 Ceramide signalling, Sus scrofa Reactome:REACT_93927 Cell death signalling via NRAGE, NRIF and NADE, Caenorhabditis elegans Reactome:REACT_94832 Ceramide signalling, Saccharomyces cerevisiae Reactome:REACT_94837 Extrinsic Pathway for Apoptosis, Taeniopygia guttata Reactome:REACT_95750 FASL binds FAS Receptor, Danio rerio Reactome:REACT_95777 FasL/ CD95L signaling, Taeniopygia guttata Reactome:REACT_96066 Death Receptor Signalling, Rattus norvegicus Reactome:REACT_96229 Extrinsic Pathway for Apoptosis, Rattus norvegicus Reactome:REACT_96867 Cell death signalling via NRAGE, NRIF and NADE, Saccharomyces cerevisiae Reactome:REACT_97301 Extrinsic Pathway for Apoptosis, Mus musculus Reactome:REACT_98119 Cell death signalling via NRAGE, NRIF and NADE, Mus musculus Reactome:REACT_98804 FasL/ CD95L signaling, Bos taurus Reactome:REACT_99367 FASL binds FAS Receptor, Mus musculus Reactome:REACT_99865 FasL/ CD95L signaling, Mus musculus apoptotic signalling pathway GOC:mah 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. paola 2011-11-23T09:45:24Z execution phase of apoptotic process apoptosis biological_process GO:0097194 execution phase of apoptosis 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. GOC:mtg_apoptosis PMID:21760595 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. paola 2012-02-02T12:23:31Z biological_process GO:0097237 cellular response to toxic substance Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. GOC:pr neuron part 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. neuron part The cellular synthesis of RNA on a template of nucleic acid (DNA or RNA). paola 2014-10-01T13:49:27Z biological_process GO:0097659 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. nucleic acid-templated transcription The cellular synthesis of RNA on a template of nucleic acid (DNA or RNA). GOC:pr GOC:txnOH GOC:vw 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. biological_process GO:0098900 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. regulation of action potential 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. GOC:dos GOC:dph GOC:go_curators GOC:tb ISBN:978-0-07-139011-8 Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. kchris 2017-04-24T23:56:08Z biological_process GO:0120031 plasma membrane bounded cell projection assembly Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. GOC:krc Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly. kchris 2017-04-26T04:27:04Z biological_process GO:0120032 regulation of plasma membrane bounded cell projection assembly Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly. GOC:krc Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly. kchris 2017-04-26T04:34:31Z biological_process GO:0120033 negative 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. GOC:krc Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly. kchris 2017-04-26T04:34:45Z biological_process GO:0120034 positive 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. GOC:krc 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. kchris 2017-04-26T16:02:06Z biological_process GO:0120035 regulation of plasma membrane bounded cell projection organization 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. GOC:krc 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. kchris 2017-04-26T16:07:02Z biological_process GO:0120036 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. GOC:krc Catalytic activity that acts to modify DNA. pg 2017-09-14T12:03:51Z molecular_function GO:0140097 https://github.com/geneontology/go-ontology/issues/14225 catalytic activity, acting on DNA Catalytic activity that acts to modify DNA. GOC:pdt Any process that modulates the frequency, rate or extent of execution phase of apoptosis. pr 2012-02-22T11:26:20Z biological_process GO:1900117 regulation of execution phase of apoptosis Any process that modulates the frequency, rate or extent of execution phase of apoptosis. GOC:TermGenie GOC:mtg_apoptosis Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis. pr 2012-02-22T11:26:24Z 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 biological_process GO:1900118 negative regulation of execution phase of apoptosis Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis. GOC:TermGenie GOC:mtg_apoptosis down regulation of execution phase of apoptosis GOC:TermGenie down-regulation of execution phase of apoptosis GOC:TermGenie downregulation of execution phase of apoptosis GOC:TermGenie inhibition of execution phase of apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis. pr 2012-02-22T11:26:27Z 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 biological_process GO:1900119 positive regulation of execution phase of apoptosis Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis. GOC:TermGenie GOC:mtg_apoptosis up regulation of execution phase of apoptosis GOC:TermGenie up-regulation of execution phase of apoptosis GOC:TermGenie upregulation of execution phase of apoptosis GOC:TermGenie activation of execution phase of apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of arachidonic acid secretion. rph 2012-03-01T09:21:19Z down regulation of arachidonic acid secretion down-regulation of arachidonic acid secretion downregulation of arachidonic acid secretion inhibition of arachidonic acid secretion biological_process GO:1900139 negative regulation of arachidonic acid secretion Any process that stops, prevents or reduces the frequency, rate or extent of arachidonic acid secretion. GOC:TermGenie down regulation of arachidonic acid secretion GOC:TermGenie down-regulation of arachidonic acid secretion GOC:TermGenie downregulation of arachidonic acid secretion GOC:TermGenie inhibition of arachidonic acid secretion GOC:TermGenie Any process that modulates the frequency, rate or extent of RNA interference. kmv 2012-04-13T08:28:39Z regulation of RNAi regulation of posttranscriptional gene silencing by siRNA biological_process GO:1900368 regulation of RNA interference Any process that modulates the frequency, rate or extent of RNA interference. GOC:TermGenie GOC:kmv PMID:22412382 regulation of RNAi GOC:TermGenie regulation of posttranscriptional gene silencing by siRNA GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of RNA interference. kmv 2012-04-13T08:28:50Z down regulation of RNA interference down regulation of RNAi down regulation of posttranscriptional gene silencing by siRNA down-regulation of RNA interference down-regulation of RNAi down-regulation of posttranscriptional gene silencing by siRNA downregulation of RNA interference downregulation of RNAi downregulation of posttranscriptional gene silencing by siRNA inhibition of RNAi inhibition of posttranscriptional gene silencing by siRNA negative regulation of RNAi negative regulation of posttranscriptional gene silencing by siRNA inhibition of RNA interference biological_process GO:1900369 negative regulation of RNA interference Any process that stops, prevents or reduces the frequency, rate or extent of RNA interference. GOC:TermGenie GOC:kmv PMID:22412382 down regulation of RNA interference GOC:TermGenie down regulation of RNAi GOC:TermGenie down regulation of posttranscriptional gene silencing by siRNA GOC:TermGenie down-regulation of RNA interference GOC:TermGenie down-regulation of RNAi GOC:TermGenie down-regulation of posttranscriptional gene silencing by siRNA GOC:TermGenie downregulation of RNA interference GOC:TermGenie downregulation of RNAi GOC:TermGenie downregulation of posttranscriptional gene silencing by siRNA GOC:TermGenie inhibition of RNAi GOC:TermGenie inhibition of posttranscriptional gene silencing by siRNA GOC:TermGenie negative regulation of RNAi GOC:TermGenie negative regulation of posttranscriptional gene silencing by siRNA GOC:TermGenie inhibition of RNA interference GOC:TermGenie Any process that activates or increases the frequency, rate or extent of RNA interference. kmv 2012-04-13T08:29:00Z activation of RNAi activation of posttranscriptional gene silencing by siRNA positive regulation of RNAi positive regulation of posttranscriptional gene silencing by siRNA up regulation of RNA interference up regulation of RNAi up regulation of posttranscriptional gene silencing by siRNA up-regulation of RNA interference up-regulation of RNAi up-regulation of posttranscriptional gene silencing by siRNA upregulation of RNA interference upregulation of RNAi upregulation of posttranscriptional gene silencing by siRNA activation of RNA interference biological_process GO:1900370 positive regulation of RNA interference Any process that activates or increases the frequency, rate or extent of RNA interference. GOC:TermGenie GOC:kmv PMID:22412382 activation of RNAi GOC:TermGenie activation of posttranscriptional gene silencing by siRNA GOC:TermGenie positive regulation of RNAi GOC:TermGenie positive regulation of posttranscriptional gene silencing by siRNA GOC:TermGenie up regulation of RNA interference GOC:TermGenie up regulation of RNAi GOC:TermGenie up regulation of posttranscriptional gene silencing by siRNA GOC:TermGenie up-regulation of RNA interference GOC:TermGenie up-regulation of RNAi GOC:TermGenie up-regulation of posttranscriptional gene silencing by siRNA GOC:TermGenie upregulation of RNA interference GOC:TermGenie upregulation of RNAi GOC:TermGenie upregulation of posttranscriptional gene silencing by siRNA GOC:TermGenie activation of RNA interference GOC:TermGenie Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex. ss 2012-07-25T02:26:58Z regulation of translation initiation ternary complex assembly biological_process GO:1901190 regulation of formation of translation initiation ternary complex Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex. GOC:TermGenie regulation of translation initiation ternary complex assembly GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation initiation ternary complex. ss 2012-07-25T02:27:21Z 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 biological_process GO:1901191 negative 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. GOC:TermGenie down regulation of formation of translation initiation ternary complex GOC:TermGenie down regulation of translation initiation ternary complex assembly GOC:TermGenie down-regulation of formation of translation initiation ternary complex GOC:TermGenie down-regulation of translation initiation ternary complex assembly GOC:TermGenie downregulation of formation of translation initiation ternary complex GOC:TermGenie downregulation of translation initiation ternary complex assembly GOC:TermGenie inhibition of translation initiation ternary complex assembly GOC:TermGenie negative regulation of translation initiation ternary complex assembly GOC:TermGenie inhibition of formation of translation initiation ternary complex GOC:TermGenie Any process that activates or increases the frequency, rate or extent of formation of translation initiation ternary complex. ss 2012-07-25T02:27:29Z 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 biological_process GO:1901192 positive 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. GOC:TermGenie activation of translation initiation ternary complex assembly GOC:TermGenie positive regulation of translation initiation ternary complex assembly GOC:TermGenie up regulation of formation of translation initiation ternary complex GOC:TermGenie up regulation of translation initiation ternary complex assembly GOC:TermGenie up-regulation of formation of translation initiation ternary complex GOC:TermGenie up-regulation of translation initiation ternary complex assembly GOC:TermGenie upregulation of formation of translation initiation ternary complex GOC:TermGenie upregulation of translation initiation ternary complex assembly GOC:TermGenie activation of formation of translation initiation ternary complex GOC:TermGenie 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. mah 2012-08-30T16:36:35Z biological_process GO:1901328 response to cytochalasin B 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. GOC:TermGenie The chemical reactions and pathways involving organic cyclic compound. bf 2012-09-14T09:03:51Z organic cyclic compound metabolism biological_process GO:1901360 organic cyclic compound metabolic process The chemical reactions and pathways involving organic cyclic compound. GOC:TermGenie organic cyclic compound metabolism GOC:TermGenie The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. bf 2012-09-14T09:05:04Z organic cyclic compound breakdown organic cyclic compound catabolism organic cyclic compound degradation biological_process GO:1901361 organic cyclic compound catabolic process The chemical reactions and pathways resulting in the breakdown of organic cyclic compound. GOC:TermGenie organic cyclic compound breakdown GOC:TermGenie organic cyclic compound catabolism GOC:TermGenie organic cyclic compound degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of organic cyclic compound. bf 2012-09-14T09:05:22Z organic cyclic compound anabolism organic cyclic compound biosynthesis organic cyclic compound formation organic cyclic compound synthesis biological_process GO:1901362 organic cyclic compound biosynthetic process The chemical reactions and pathways resulting in the formation of organic cyclic compound. GOC:TermGenie organic cyclic compound anabolism GOC:TermGenie organic cyclic compound biosynthesis GOC:TermGenie organic cyclic compound formation GOC:TermGenie organic cyclic compound synthesis GOC:TermGenie Interacting selectively and non-covalently with heterocyclic compound. bf 2012-09-14T13:53:50Z molecular_function GO:1901363 heterocyclic compound binding Interacting selectively and non-covalently with heterocyclic compound. GOC:TermGenie The chemical reactions and pathways involving organonitrogen compound. pr 2012-11-04T15:17:52Z organonitrogen compound metabolism biological_process GO:1901564 organonitrogen compound metabolic process The chemical reactions and pathways involving organonitrogen compound. GOC:TermGenie GOC:pr organonitrogen compound metabolism GOC:TermGenie The chemical reactions and pathways resulting in the formation of organonitrogen compound. pr 2012-11-04T15:18:00Z organonitrogen compound anabolism organonitrogen compound biosynthesis organonitrogen compound formation organonitrogen compound synthesis biological_process GO:1901566 organonitrogen compound biosynthetic process The chemical reactions and pathways resulting in the formation of organonitrogen compound. GOC:TermGenie GOC:pr organonitrogen compound anabolism GOC:TermGenie organonitrogen compound biosynthesis GOC:TermGenie organonitrogen compound formation GOC:TermGenie organonitrogen compound synthesis GOC:TermGenie The directed movement of a fatty acid derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. pr 2012-11-04T17:13:49Z biological_process GO:1901571 fatty acid derivative transport The directed movement of a fatty acid derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:TermGenie GOC:pr The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon. pr 2012-11-05T11:04:36Z organic molecular entity breakdown organic molecular entity catabolic process organic molecular entity catabolism organic molecular entity degradation organic substance breakdown organic substance catabolism organic substance degradation biological_process GO:1901575 organic substance catabolic process The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon. GOC:TermGenie GOC:pr organic molecular entity breakdown GOC:TermGenie organic molecular entity catabolism GOC:TermGenie organic molecular entity degradation GOC:TermGenie The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. pr 2012-11-05T11:04:40Z organic molecular entity anabolism organic molecular entity biosynthesis organic molecular entity biosynthetic process organic molecular entity formation organic molecular entity synthesis organic substance anabolism organic substance biosynthesis organic substance formation organic substance synthesis biological_process GO:1901576 organic substance biosynthetic process The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. GOC:TermGenie GOC:pr organic molecular entity anabolism GOC:TermGenie organic molecular entity biosynthesis GOC:TermGenie organic molecular entity formation GOC:TermGenie organic molecular entity synthesis GOC:TermGenie 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. pr 2012-12-13T15:06:08Z response to nitrogen molecular entity biological_process GO:1901698 response to nitrogen compound Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus. GOC:TermGenie GOC:pr 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. pr 2012-12-13T15:06:13Z cellular response to nitrogen molecular entity biological_process GO:1901699 cellular response to nitrogen compound Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus. GOC:TermGenie GOC:pr 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. pr 2012-12-13T15:11:37Z response to oxygen molecular entity biological_process GO:1901700 response to oxygen-containing compound Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus. GOC:TermGenie GOC:pr 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. pr 2012-12-13T15:11:42Z cellular response to oxygen molecular entity biological_process GO:1901701 cellular response to oxygen-containing 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 oxygen-containing compound stimulus. GOC:TermGenie GOC:pr Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis. sart 2013-07-29T15:03:16Z regulation of apoptosis involved in morphogenesis biological_process regulation of apoptosis involved in development regulation of morphogenetic apoptosis GO:1902337 regulation of apoptotic process involved in morphogenesis Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis. GOC:TermGenie GOC:sart PMID:12202035 regulation of apoptosis involved in morphogenesis GOC:TermGenie regulation of apoptosis involved in development GOC:TermGenie regulation of morphogenetic apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis. sart 2013-07-29T15:03:25Z 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 biological_process 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 inhibition of morphogenetic apoptosis negative regulation of apoptosis involved in development negative regulation of morphogenetic apoptosis GO:1902338 negative 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. GOC:TermGenie GOC:sart PMID:12202035 down regulation of apoptotic process involved in morphogenesis GOC:TermGenie down-regulation of apoptotic process involved in morphogenesis GOC:TermGenie downregulation of apoptotic process involved in morphogenesis GOC:TermGenie down regulation of apoptosis involved in morphogenesis GOC:TermGenie down-regulation of apoptosis involved in morphogenesis GOC:TermGenie downregulation of apoptosis involved in morphogenesis GOC:TermGenie inhibition of apoptosis involved in morphogenesis GOC:TermGenie inhibition of apoptotic process involved in morphogenesis GOC:TermGenie negative regulation of apoptosis involved in morphogenesis GOC:TermGenie down regulation of apoptosis involved in development GOC:TermGenie down regulation of morphogenetic apoptosis GOC:TermGenie down-regulation of apoptosis involved in development GOC:TermGenie down-regulation of morphogenetic apoptosis GOC:TermGenie downregulation of apoptosis involved in development GOC:TermGenie downregulation of morphogenetic apoptosis GOC:TermGenie inhibition of apoptosis involved in development GOC:TermGenie inhibition of morphogenetic apoptosis GOC:TermGenie negative regulation of apoptosis involved in development GOC:TermGenie negative regulation of morphogenetic apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis. sart 2013-07-29T15:03:33Z 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 biological_process activation of apoptosis involved in development activation of morphogenetic apoptosis 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 upregulation of morphogenetic apoptosis GO:1902339 positive regulation of apoptotic process involved in morphogenesis Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis. GOC:TermGenie GOC:sart PMID:12202035 up regulation of apoptotic process involved in morphogenesis GOC:TermGenie up-regulation of apoptotic process involved in morphogenesis GOC:TermGenie upregulation of apoptotic process involved in morphogenesis GOC:TermGenie activation of apoptosis involved in morphogenesis GOC:TermGenie activation of apoptotic process involved in morphogenesis GOC:TermGenie positive regulation of apoptosis involved in morphogenesis GOC:TermGenie up regulation of apoptosis involved in morphogenesis GOC:TermGenie up-regulation of apoptosis involved in morphogenesis GOC:TermGenie upregulation of apoptosis involved in morphogenesis GOC:TermGenie activation of apoptosis involved in development GOC:TermGenie activation of morphogenetic apoptosis GOC:TermGenie positive regulation of apoptosis involved in development GOC:TermGenie positive regulation of morphogenetic apoptosis GOC:TermGenie up regulation of apoptosis involved in development GOC:TermGenie up regulation of morphogenetic apoptosis GOC:TermGenie up-regulation of apoptosis involved in development GOC:TermGenie up-regulation of morphogenetic apoptosis GOC:TermGenie upregulation of apoptosis involved in development GOC:TermGenie upregulation of morphogenetic apoptosis GOC:TermGenie A protein complex which is capable of catalytic activity. bhm 2013-11-13T16:18:47Z enzyme complex cellular_component GO:1902494 catalytic complex A protein complex which is capable of catalytic activity. GOC:TermGenie GOC:bhm PMID:8077207 enzyme complex GOC:bhm GOC:jl Any process that modulates the frequency, rate or extent of apoptotic DNA fragmentation. hjd 2013-11-15T18:28:32Z regulation of DNA fragmentation regulation of chromatinolysis 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 biological_process GO:1902510 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 modulates the frequency, rate or extent of apoptotic DNA fragmentation. GOC:TermGenie GOC:hjd PMID:15572351 PMID:15723341 regulation of DNA fragmentation GOC:TermGenie regulation of chromatinolysis GOC:TermGenie regulation of DNA catabolic process during apoptosis GOC:TermGenie regulation of DNA catabolism during apoptosis GOC:TermGenie regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic DNA fragmentation. hjd 2013-11-15T18:28:41Z 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 biological_process GO:1902511 negative regulation of apoptotic DNA fragmentation Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic DNA fragmentation. GOC:TermGenie GOC:hjd PMID:15572351 down regulation of DNA catabolic process during apoptosis GOC:TermGenie down regulation of DNA catabolism during apoptosis GOC:TermGenie down regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie down regulation of apoptotic DNA fragmentation GOC:TermGenie down regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie down-regulation of DNA catabolic process during apoptosis GOC:TermGenie down-regulation of DNA catabolism during apoptosis GOC:TermGenie down-regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie down-regulation of apoptotic DNA fragmentation GOC:TermGenie down-regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie downregulation of DNA catabolic process during apoptosis GOC:TermGenie downregulation of DNA catabolism during apoptosis GOC:TermGenie downregulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie downregulation of apoptotic DNA fragmentation GOC:TermGenie downregulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie negative regulation of DNA catabolic process during apoptosis GOC:TermGenie negative regulation of DNA catabolism during apoptosis GOC:TermGenie negative regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie negative regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie inhibition of DNA catabolic process during apoptosis GOC:TermGenie inhibition of DNA catabolism during apoptosis GOC:TermGenie inhibition of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie inhibition of apoptotic DNA fragmentation GOC:TermGenie inhibition of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of apoptotic DNA fragmentation. hjd 2013-11-15T18:28:50Z 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 biological_process GO:1902512 positive regulation of apoptotic DNA fragmentation Any process that activates or increases the frequency, rate or extent of apoptotic DNA fragmentation. GOC:TermGenie GOC:hjd PMID:15572351 positive regulation of DNA catabolic process during apoptosis GOC:TermGenie positive regulation of DNA catabolism during apoptosis GOC:TermGenie positive regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie positive regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie up regulation of DNA catabolic process during apoptosis GOC:TermGenie up regulation of DNA catabolism during apoptosis GOC:TermGenie up regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie up regulation of apoptotic DNA fragmentation GOC:TermGenie up regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie up-regulation of DNA catabolic process during apoptosis GOC:TermGenie up-regulation of DNA catabolism during apoptosis GOC:TermGenie up-regulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie up-regulation of apoptotic DNA fragmentation GOC:TermGenie up-regulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie upregulation of DNA catabolic process during apoptosis GOC:TermGenie upregulation of DNA catabolism during apoptosis GOC:TermGenie upregulation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie upregulation of apoptotic DNA fragmentation GOC:TermGenie upregulation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie activation of DNA catabolic process during apoptosis GOC:TermGenie activation of DNA catabolism during apoptosis GOC:TermGenie activation of DNA fragmentation involved in apoptotic nuclear change GOC:TermGenie activation of apoptotic DNA fragmentation GOC:TermGenie activation of endonucleolytic DNA catabolic process involved in apoptosis GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process. jl 2014-02-05T16:32:01Z down regulation of RNA anabolism down regulation of RNA biosynthesis down regulation of RNA biosynthetic process down regulation of RNA formation down regulation of RNA synthesis down-regulation of RNA anabolism down-regulation of RNA biosynthesis down-regulation of RNA biosynthetic process down-regulation of RNA formation down-regulation of RNA synthesis downregulation of RNA anabolism downregulation of RNA biosynthesis downregulation of RNA biosynthetic process downregulation of RNA formation downregulation of RNA synthesis negative regulation of RNA anabolism negative regulation of RNA biosynthesis negative regulation of RNA formation negative regulation of RNA synthesis inhibition of RNA anabolism inhibition of RNA biosynthesis inhibition of RNA biosynthetic process inhibition of RNA formation inhibition of RNA synthesis biological_process GO:1902679 negative regulation of RNA biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process. GO:jl GOC:TermGenie GO_REF:0000058 down regulation of RNA anabolism GOC:TermGenie down regulation of RNA biosynthesis GOC:TermGenie down regulation of RNA biosynthetic process GOC:TermGenie down regulation of RNA formation GOC:TermGenie down regulation of RNA synthesis GOC:TermGenie down-regulation of RNA anabolism GOC:TermGenie down-regulation of RNA biosynthesis GOC:TermGenie down-regulation of RNA biosynthetic process GOC:TermGenie down-regulation of RNA formation GOC:TermGenie down-regulation of RNA synthesis GOC:TermGenie downregulation of RNA anabolism GOC:TermGenie downregulation of RNA biosynthesis GOC:TermGenie downregulation of RNA biosynthetic process GOC:TermGenie downregulation of RNA formation GOC:TermGenie downregulation of RNA synthesis GOC:TermGenie negative regulation of RNA anabolism GOC:TermGenie negative regulation of RNA biosynthesis GOC:TermGenie negative regulation of RNA formation GOC:TermGenie negative regulation of RNA synthesis GOC:TermGenie inhibition of RNA anabolism GOC:TermGenie inhibition of RNA biosynthesis GOC:TermGenie inhibition of RNA biosynthetic process GOC:TermGenie inhibition of RNA formation GOC:TermGenie inhibition of RNA synthesis GOC:TermGenie Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process. jl 2014-02-05T16:32:10Z positive regulation of RNA anabolism positive regulation of RNA biosynthesis positive regulation of RNA formation positive regulation of RNA synthesis up regulation of RNA anabolism up regulation of RNA biosynthesis up regulation of RNA biosynthetic process up regulation of RNA formation up regulation of RNA synthesis up-regulation of RNA anabolism up-regulation of RNA biosynthesis up-regulation of RNA biosynthetic process up-regulation of RNA formation up-regulation of RNA synthesis upregulation of RNA anabolism upregulation of RNA biosynthesis upregulation of RNA biosynthetic process upregulation of RNA formation upregulation of RNA synthesis activation of RNA anabolism activation of RNA biosynthesis activation of RNA biosynthetic process activation of RNA formation activation of RNA synthesis biological_process GO:1902680 positive regulation of RNA biosynthetic process Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process. GO:jl GOC:TermGenie GO_REF:0000058 positive regulation of RNA anabolism GOC:TermGenie positive regulation of RNA biosynthesis GOC:TermGenie positive regulation of RNA formation GOC:TermGenie positive regulation of RNA synthesis GOC:TermGenie up regulation of RNA anabolism GOC:TermGenie up regulation of RNA biosynthesis GOC:TermGenie up regulation of RNA biosynthetic process GOC:TermGenie up regulation of RNA formation GOC:TermGenie up regulation of RNA synthesis GOC:TermGenie up-regulation of RNA anabolism GOC:TermGenie up-regulation of RNA biosynthesis GOC:TermGenie up-regulation of RNA biosynthetic process GOC:TermGenie up-regulation of RNA formation GOC:TermGenie up-regulation of RNA synthesis GOC:TermGenie upregulation of RNA anabolism GOC:TermGenie upregulation of RNA biosynthesis GOC:TermGenie upregulation of RNA biosynthetic process GOC:TermGenie upregulation of RNA formation GOC:TermGenie upregulation of RNA synthesis GOC:TermGenie activation of RNA anabolism GOC:TermGenie activation of RNA biosynthesis GOC:TermGenie activation of RNA biosynthetic process GOC:TermGenie activation of RNA formation GOC:TermGenie activation of RNA synthesis GOC:TermGenie Any apoptotic process that is involved in anatomical structure development. pr 2014-02-28T13:09:43Z 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 biological_process 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 GO:1902742 apoptotic process involved in development Any apoptotic process that is involved in anatomical structure development. GOC:TermGenie GOC:mtg_apoptosis GOC:pg GO_REF:0000060 apoptotic cell death involved in anatomical structure development GOC:TermGenie apoptotic cell death involved in development of an anatomical structure GOC:TermGenie apoptotic process involved in development of an anatomical structure GOC:TermGenie apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie activation of apoptosis involved in anatomical structure development GOC:TermGenie activation of apoptosis involved in development of an anatomical structure GOC:TermGenie apoptosis involved in anatomical structure development GOC:TermGenie apoptosis involved in development of an anatomical structure GOC:TermGenie apoptosis signaling involved in anatomical structure development GOC:TermGenie apoptosis signaling involved in development of an anatomical structure GOC:TermGenie apoptotic program involved in anatomical structure development GOC:TermGenie apoptotic program involved in development of an anatomical structure GOC:TermGenie type I programmed cell death involved in anatomical structure development GOC:TermGenie type I programmed cell death involved in development of an anatomical structure GOC:TermGenie apoptosis activator activity involved in anatomical structure development GOC:TermGenie apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie commitment to apoptosis involved in anatomical structure development GOC:TermGenie commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie induction of apoptosis involved in anatomical structure development GOC:TermGenie induction of apoptosis involved in development of an anatomical structure GOC:TermGenie signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that modulates the frequency, rate or extent of response to wounding. kmv 2014-05-18T01:28:46Z regulation of physiological response to wounding biological_process GO:1903034 regulation of response to wounding Any process that modulates the frequency, rate or extent of response to wounding. GOC:TermGenie GOC:kmv GO_REF:0000058 pmid:19164535 regulation of physiological response to wounding GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding. kmv 2014-05-18T01:28:52Z down regulation of physiological response to wounding down regulation of response to wounding down-regulation of physiological response to wounding down-regulation of response to wounding downregulation of physiological response to wounding downregulation of response to wounding negative regulation of physiological response to wounding inhibition of physiological response to wounding inhibition of response to wounding biological_process GO:1903035 negative regulation of response to wounding Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding. GOC:TermGenie GOC:kmv GO_REF:0000058 pmid:19164535 down regulation of physiological response to wounding GOC:TermGenie down regulation of response to wounding GOC:TermGenie down-regulation of physiological response to wounding GOC:TermGenie down-regulation of response to wounding GOC:TermGenie downregulation of physiological response to wounding GOC:TermGenie downregulation of response to wounding GOC:TermGenie negative regulation of physiological response to wounding GOC:TermGenie inhibition of physiological response to wounding GOC:TermGenie inhibition of response to wounding GOC:TermGenie Any process that activates or increases the frequency, rate or extent of response to wounding. kmv 2014-05-18T01:28:58Z positive regulation of physiological response to wounding up regulation of physiological response to wounding up regulation of response to wounding up-regulation of physiological response to wounding up-regulation of response to wounding upregulation of physiological response to wounding upregulation of response to wounding activation of physiological response to wounding activation of response to wounding biological_process GO:1903036 positive regulation of response to wounding Any process that activates or increases the frequency, rate or extent of response to wounding. GOC:TermGenie GOC:kmv GO_REF:0000058 pmid:19164535 positive regulation of physiological response to wounding GOC:TermGenie up regulation of physiological response to wounding GOC:TermGenie up regulation of response to wounding GOC:TermGenie up-regulation of physiological response to wounding GOC:TermGenie up-regulation of response to wounding GOC:TermGenie upregulation of physiological response to wounding GOC:TermGenie upregulation of response to wounding GOC:TermGenie activation of physiological response to wounding GOC:TermGenie activation of response to wounding GOC:TermGenie Any process that modulates the frequency, rate or extent of nucleus organization. hjd 2014-08-20T19:36:16Z regulation of nuclear organisation regulation of nuclear organization biological_process regulation of nuclear morphology regulation of nuclear organization and biogenesis regulation of nucleus organization and biogenesis GO:1903353 regulation of nucleus organization Any process that modulates the frequency, rate or extent of nucleus organization. GOC:TermGenie GO_REF:0000058 PMID:16943282 regulation of nuclear organisation GOC:TermGenie regulation of nuclear organization GOC:TermGenie regulation of nuclear morphology GOC:TermGenie regulation of nuclear organization and biogenesis GOC:TermGenie regulation of nucleus organization and biogenesis GOC:TermGenie Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription. pr 2014-10-01T14:44:47Z biological_process GO:1903506 regulation of nucleic acid-templated transcription Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription. GOC:TermGenie GOC:pr GOC:txnOH GOC:vw GO_REF:0000058 Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription. pr 2014-10-01T14:44:56Z 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 biological_process GO:1903507 negative regulation of nucleic acid-templated transcription Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription. GOC:TermGenie GOC:pr GOC:txnOH GOC:vw GO_REF:0000058 down regulation of nucleic acid-templated transcription GOC:TermGenie down-regulation of nucleic acid-templated transcription GOC:TermGenie downregulation of nucleic acid-templated transcription GOC:TermGenie inhibition of nucleic acid-templated transcription GOC:TermGenie Any process that activates or increases the frequency, rate or extent of nucleic acid-templated transcription. pr 2014-10-01T14:45:04Z 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 biological_process GO:1903508 positive regulation of nucleic acid-templated transcription Any process that activates or increases the frequency, rate or extent of nucleic acid-templated transcription. GOC:TermGenie GOC:pr GOC:txnOH GOC:vw GO_REF:0000058 up regulation of nucleic acid-templated transcription GOC:TermGenie up-regulation of nucleic acid-templated transcription GOC:TermGenie upregulation of nucleic acid-templated transcription GOC:TermGenie activation of nucleic acid-templated transcription GOC:TermGenie Any process that modulates the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:24:59Z regulation of cellular secretion biological_process GO:1903530 regulation of secretion by cell Any process that modulates the frequency, rate or extent of secretion by cell. GOC:TermGenie GOC:pm GO_REF:0000058 PMID:12130530 regulation of cellular secretion GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:25:08Z down regulation of cellular secretion down regulation of secretion by cell down-regulation of cellular secretion down-regulation of secretion by cell downregulation of cellular secretion downregulation of secretion by cell negative regulation of cellular secretion inhibition of cellular secretion inhibition of secretion by cell biological_process GO:1903531 negative regulation of secretion by cell Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell. GOC:TermGenie GOC:pm GO_REF:0000058 PMID:12130530 down regulation of cellular secretion GOC:TermGenie down regulation of secretion by cell GOC:TermGenie down-regulation of cellular secretion GOC:TermGenie down-regulation of secretion by cell GOC:TermGenie downregulation of cellular secretion GOC:TermGenie downregulation of secretion by cell GOC:TermGenie negative regulation of cellular secretion GOC:TermGenie inhibition of cellular secretion GOC:TermGenie inhibition of secretion by cell GOC:TermGenie Any process that activates or increases the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:25:17Z positive regulation of cellular secretion up regulation of cellular secretion up regulation of secretion by cell up-regulation of cellular secretion up-regulation of secretion by cell upregulation of cellular secretion upregulation of secretion by cell activation of cellular secretion activation of secretion by cell biological_process GO:1903532 positive regulation of secretion by cell Any process that activates or increases the frequency, rate or extent of secretion by cell. GOC:TermGenie GOC:pm GO_REF:0000058 PMID:12130530 positive regulation of cellular secretion GOC:TermGenie up regulation of cellular secretion GOC:TermGenie up regulation of secretion by cell GOC:TermGenie up-regulation of cellular secretion GOC:TermGenie up-regulation of secretion by cell GOC:TermGenie upregulation of cellular secretion GOC:TermGenie upregulation of secretion by cell GOC:TermGenie activation of cellular secretion GOC:TermGenie activation of secretion by cell GOC:TermGenie Any process that modulates the frequency, rate or extent of tumor necrosis factor superfamily cytokine production. pga 2014-10-21T10:26:05Z regulation of TNFSF cytokine production biological_process regulation of TNF superfamily production GO:1903555 regulation of tumor necrosis factor superfamily cytokine production Any process that modulates the frequency, rate or extent of tumor necrosis factor superfamily cytokine production. GOC:TermGenie GO_REF:0000058 PMID:24187568 regulation of TNFSF cytokine production GOC:TermGenie regulation of TNF superfamily production GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor superfamily cytokine production. pga 2014-10-21T10:26:14Z 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 TNFSF cytokine production inhibition of tumor necrosis factor superfamily cytokine production biological_process 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 GO:1903556 negative 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. GOC:TermGenie GO_REF:0000058 PMID:24187568 down regulation of TNFSF cytokine production GOC:TermGenie down regulation of tumor necrosis factor superfamily cytokine production GOC:TermGenie down-regulation of TNFSF cytokine production GOC:TermGenie down-regulation of tumor necrosis factor superfamily cytokine production GOC:TermGenie downregulation of TNFSF cytokine production GOC:TermGenie downregulation of tumor necrosis factor superfamily cytokine production GOC:TermGenie negative regulation of TNFSF cytokine production GOC:TermGenie inhibition of TNFSF cytokine production GOC:TermGenie inhibition of tumor necrosis factor superfamily cytokine production GOC:TermGenie down regulation of TNF superfamily production GOC:TermGenie down-regulation of TNF superfamily production GOC:TermGenie downregulation of TNF superfamily production GOC:TermGenie inhibition of TNF superfamily production GOC:TermGenie negative regulation of TNF superfamily production GOC:TermGenie Any process that activates or increases the frequency, rate or extent of tumor necrosis factor superfamily cytokine production. pga 2014-10-21T10:26:23Z 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 TNFSF cytokine production activation of tumor necrosis factor superfamily cytokine production biological_process 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 GO:1903557 positive 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. GOC:TermGenie GO_REF:0000058 PMID:24187568 positive regulation of TNFSF cytokine production GOC:TermGenie up regulation of TNFSF cytokine production GOC:TermGenie up regulation of tumor necrosis factor superfamily cytokine production GOC:TermGenie up-regulation of TNFSF cytokine production GOC:TermGenie up-regulation of tumor necrosis factor superfamily cytokine production GOC:TermGenie upregulation of TNFSF cytokine production GOC:TermGenie upregulation of tumor necrosis factor superfamily cytokine production GOC:TermGenie activation of TNFSF cytokine production GOC:TermGenie activation of tumor necrosis factor superfamily cytokine production GOC:TermGenie activation of TNF superfamily production GOC:TermGenie positive regulation of TNF superfamily production GOC:TermGenie up regulation of TNF superfamily production GOC:TermGenie up-regulation of TNF superfamily production GOC:TermGenie upregulation of TNF superfamily production GOC:TermGenie Any process that modulates the frequency, rate or extent of DNA catabolic process. sl 2014-11-19T22:36:35Z regulation of DNA breakdown regulation of DNA catabolism regulation of DNA degradation biological_process GO:1903624 regulation of DNA catabolic process Any process that modulates the frequency, rate or extent of DNA catabolic process. GOC:TermGenie GO_REF:0000058 PMID:2001740 regulation of DNA breakdown GOC:TermGenie regulation of DNA catabolism GOC:TermGenie regulation of DNA degradation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of DNA catabolic process. sl 2014-11-19T22:36:43Z down regulation of DNA breakdown down regulation of DNA catabolic process down regulation of DNA catabolism down regulation of DNA degradation down-regulation of DNA breakdown down-regulation of DNA catabolic process down-regulation of DNA catabolism down-regulation of DNA degradation downregulation of DNA breakdown downregulation of DNA catabolic process downregulation of DNA catabolism downregulation of DNA degradation negative regulation of DNA breakdown negative regulation of DNA catabolism negative regulation of DNA degradation inhibition of DNA breakdown inhibition of DNA catabolic process inhibition of DNA catabolism inhibition of DNA degradation biological_process GO:1903625 negative regulation of DNA catabolic process Any process that stops, prevents or reduces the frequency, rate or extent of DNA catabolic process. GOC:TermGenie GO_REF:0000058 PMID:2001740 down regulation of DNA breakdown GOC:TermGenie down regulation of DNA catabolic process GOC:TermGenie down regulation of DNA catabolism GOC:TermGenie down regulation of DNA degradation GOC:TermGenie down-regulation of DNA breakdown GOC:TermGenie down-regulation of DNA catabolic process GOC:TermGenie down-regulation of DNA catabolism GOC:TermGenie down-regulation of DNA degradation GOC:TermGenie downregulation of DNA breakdown GOC:TermGenie downregulation of DNA catabolic process GOC:TermGenie downregulation of DNA catabolism GOC:TermGenie downregulation of DNA degradation GOC:TermGenie negative regulation of DNA breakdown GOC:TermGenie negative regulation of DNA catabolism GOC:TermGenie negative regulation of DNA degradation GOC:TermGenie inhibition of DNA breakdown GOC:TermGenie inhibition of DNA catabolic process GOC:TermGenie inhibition of DNA catabolism GOC:TermGenie inhibition of DNA degradation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of DNA catabolic process. sl 2014-11-19T22:36:51Z positive regulation of DNA breakdown positive regulation of DNA catabolism positive regulation of DNA degradation up regulation of DNA breakdown up regulation of DNA catabolic process up regulation of DNA catabolism up regulation of DNA degradation up-regulation of DNA breakdown up-regulation of DNA catabolic process up-regulation of DNA catabolism up-regulation of DNA degradation upregulation of DNA breakdown upregulation of DNA catabolic process upregulation of DNA catabolism upregulation of DNA degradation activation of DNA breakdown activation of DNA catabolic process activation of DNA catabolism activation of DNA degradation biological_process GO:1903626 positive regulation of DNA catabolic process Any process that activates or increases the frequency, rate or extent of DNA catabolic process. GOC:TermGenie GO_REF:0000058 PMID:2001740 positive regulation of DNA breakdown GOC:TermGenie positive regulation of DNA catabolism GOC:TermGenie positive regulation of DNA degradation GOC:TermGenie up regulation of DNA breakdown GOC:TermGenie up regulation of DNA catabolic process GOC:TermGenie up regulation of DNA catabolism GOC:TermGenie up regulation of DNA degradation GOC:TermGenie up-regulation of DNA breakdown GOC:TermGenie up-regulation of DNA catabolic process GOC:TermGenie up-regulation of DNA catabolism GOC:TermGenie up-regulation of DNA degradation GOC:TermGenie upregulation of DNA breakdown GOC:TermGenie upregulation of DNA catabolic process GOC:TermGenie upregulation of DNA catabolism GOC:TermGenie upregulation of DNA degradation GOC:TermGenie activation of DNA breakdown GOC:TermGenie activation of DNA catabolic process GOC:TermGenie activation of DNA catabolism GOC:TermGenie activation of DNA degradation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of anion transport. sl 2015-01-12T21:50:20Z down regulation of anion transport down-regulation of anion transport downregulation of anion transport inhibition of anion transport biological_process GO:1903792 negative regulation of anion transport Any process that stops, prevents or reduces the frequency, rate or extent of anion transport. GOC:TermGenie GO_REF:0000058 PMID:11336802 down regulation of anion transport GOC:TermGenie down-regulation of anion transport GOC:TermGenie downregulation of anion transport GOC:TermGenie inhibition of anion transport GOC:TermGenie Any process that activates or increases the frequency, rate or extent of anion transport. sl 2015-01-12T21:50:30Z up regulation of anion transport up-regulation of anion transport upregulation of anion transport activation of anion transport biological_process GO:1903793 positive regulation of anion transport Any process that activates or increases the frequency, rate or extent of anion transport. GOC:TermGenie GO_REF:0000058 PMID:11336802 up regulation of anion transport GOC:TermGenie up-regulation of anion transport GOC:TermGenie upregulation of anion transport GOC:TermGenie activation of anion transport GOC:TermGenie 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. jl 2015-01-20T14:32:14Z regulation of cellular protein localisation regulation of channel localizer activity biological_process GO:1903827 regulation of cellular protein localization 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. GOC:TermGenie GOC:vw GO_REF:0000058 regulation of cellular protein localisation GOC:TermGenie regulation of channel localizer activity GOC:TermGenie 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. jl 2015-01-20T14:32:24Z 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 biological_process GO:1903828 negative 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. GOC:TermGenie GOC:vw GO_REF:0000058 down regulation of cellular protein localisation GOC:TermGenie down regulation of cellular protein localization GOC:TermGenie down-regulation of cellular protein localisation GOC:TermGenie down-regulation of cellular protein localization GOC:TermGenie downregulation of cellular protein localisation GOC:TermGenie downregulation of cellular protein localization GOC:TermGenie negative regulation of cellular protein localisation GOC:TermGenie down regulation of channel localizer activity GOC:TermGenie down-regulation of channel localizer activity GOC:TermGenie downregulation of channel localizer activity GOC:TermGenie inhibition of cellular protein localisation GOC:TermGenie inhibition of cellular protein localization GOC:TermGenie inhibition of channel localizer activity GOC:TermGenie negative regulation of channel localizer activity GOC:TermGenie 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. jl 2015-01-20T14:32:33Z 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 biological_process GO:1903829 positive 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. GOC:TermGenie GOC:vw GO_REF:0000058 positive regulation of cellular protein localisation GOC:TermGenie up regulation of cellular protein localisation GOC:TermGenie up regulation of cellular protein localization GOC:TermGenie up-regulation of cellular protein localisation GOC:TermGenie up-regulation of cellular protein localization GOC:TermGenie upregulation of cellular protein localisation GOC:TermGenie upregulation of cellular protein localization GOC:TermGenie activation of cellular protein localisation GOC:TermGenie activation of cellular protein localization GOC:TermGenie activation of channel localizer activity GOC:TermGenie positive regulation of channel localizer activity GOC:TermGenie up regulation of channel localizer activity GOC:TermGenie up-regulation of channel localizer activity GOC:TermGenie upregulation of channel localizer activity GOC:TermGenie The directed movement of an arachidonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. bhm 2015-02-25T16:06:14Z arachidonic acid transport biological_process GO:1903963 arachidonate transport The directed movement of an arachidonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:TermGenie GOC:bhm GO_REF:0000065 PMID:15642721 Any process that modulates the frequency, rate or extent of bleb assembly. als 2015-04-23T09:32:19Z regulation of cell blebbing biological_process GO:1904170 regulation of bleb assembly Any process that modulates the frequency, rate or extent of bleb assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:25651887 regulation of cell blebbing GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly. als 2015-04-23T09:32:25Z down regulation of bleb assembly down regulation of cell blebbing down-regulation of bleb assembly down-regulation of cell blebbing downregulation of bleb assembly downregulation of cell blebbing negative regulation of cell blebbing inhibition of bleb assembly inhibition of cell blebbing biological_process GO:1904171 negative regulation of bleb assembly Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:25651887 down regulation of bleb assembly GOC:TermGenie down regulation of cell blebbing GOC:TermGenie down-regulation of bleb assembly GOC:TermGenie down-regulation of cell blebbing GOC:TermGenie downregulation of bleb assembly GOC:TermGenie downregulation of cell blebbing GOC:TermGenie negative regulation of cell blebbing GOC:TermGenie inhibition of bleb assembly GOC:TermGenie inhibition of cell blebbing GOC:TermGenie Any process that activates or increases the frequency, rate or extent of bleb assembly. als 2015-04-23T09:32:31Z positive regulation of cell blebbing up regulation of bleb assembly up regulation of cell blebbing up-regulation of bleb assembly up-regulation of cell blebbing upregulation of bleb assembly upregulation of cell blebbing activation of bleb assembly activation of cell blebbing biological_process GO:1904172 positive regulation of bleb assembly Any process that activates or increases the frequency, rate or extent of bleb assembly. GOC:TermGenie GOC:als GO_REF:0000058 PMID:25651887 positive regulation of cell blebbing GOC:TermGenie up regulation of bleb assembly GOC:TermGenie up regulation of cell blebbing GOC:TermGenie up-regulation of bleb assembly GOC:TermGenie up-regulation of cell blebbing GOC:TermGenie upregulation of bleb assembly GOC:TermGenie upregulation of cell blebbing GOC:TermGenie activation of bleb assembly GOC:TermGenie activation of cell blebbing GOC:TermGenie Any process that modulates the frequency, rate or extent of tumor necrosis factor secretion. sl 2015-07-09T19:50:02Z regulation of TNF secretion regulation of TNF superfamily, member 2 secretion regulation of TNF-alpha secretion regulation of Tnfa secretion regulation of cachectin secretion regulation of tumor necrosis factor alpha secretion regulation of tumor necrosis factor ligand superfamily member 2 secretion biological_process GO:1904467 regulation of tumor necrosis factor secretion Any process that modulates the frequency, rate or extent of tumor necrosis factor secretion. GOC:TermGenie GO_REF:0000058 PMID:15560120 regulation of TNF secretion GOC:TermGenie regulation of TNF superfamily, member 2 secretion GOC:TermGenie regulation of TNF-alpha secretion GOC:TermGenie regulation of Tnfa secretion GOC:TermGenie regulation of cachectin secretion GOC:TermGenie regulation of tumor necrosis factor alpha secretion GOC:TermGenie regulation of tumor necrosis factor ligand superfamily member 2 secretion GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor secretion. sl 2015-07-09T19:50:08Z down regulation of TNF secretion down regulation of TNF superfamily, member 2 secretion down regulation of TNF-alpha secretion down regulation of Tnfa secretion down regulation of cachectin 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 secretion down-regulation of TNF superfamily, member 2 secretion down-regulation of TNF-alpha secretion down-regulation of Tnfa secretion down-regulation of cachectin 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 secretion downregulation of TNF superfamily, member 2 secretion downregulation of TNF-alpha secretion downregulation of Tnfa secretion downregulation of cachectin 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 secretion negative regulation of TNF superfamily, member 2 secretion negative regulation of TNF-alpha secretion negative regulation of Tnfa 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 secretion inhibition of TNF superfamily, member 2 secretion inhibition of TNF-alpha secretion inhibition of Tnfa secretion inhibition of cachectin secretion inhibition of tumor necrosis factor alpha secretion inhibition of tumor necrosis factor ligand superfamily member 2 secretion inhibition of tumor necrosis factor secretion biological_process GO:1904468 negative regulation of tumor necrosis factor secretion Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor secretion. GOC:TermGenie GO_REF:0000058 PMID:15560120 down regulation of TNF secretion GOC:TermGenie down regulation of TNF superfamily, member 2 secretion GOC:TermGenie down regulation of TNF-alpha secretion GOC:TermGenie down regulation of Tnfa secretion GOC:TermGenie down regulation of cachectin secretion GOC:TermGenie down regulation of tumor necrosis factor alpha secretion GOC:TermGenie down regulation of tumor necrosis factor ligand superfamily member 2 secretion GOC:TermGenie down regulation of tumor necrosis factor secretion GOC:TermGenie down-regulation of TNF secretion GOC:TermGenie down-regulation of TNF superfamily, member 2 secretion GOC:TermGenie down-regulation of TNF-alpha secretion GOC:TermGenie down-regulation of Tnfa secretion GOC:TermGenie down-regulation of cachectin secretion GOC:TermGenie down-regulation of tumor necrosis factor alpha secretion GOC:TermGenie down-regulation of tumor necrosis factor ligand superfamily member 2 secretion GOC:TermGenie down-regulation of tumor necrosis factor secretion GOC:TermGenie downregulation of TNF secretion GOC:TermGenie downregulation of TNF superfamily, member 2 secretion GOC:TermGenie downregulation of TNF-alpha secretion GOC:TermGenie downregulation of Tnfa secretion GOC:TermGenie downregulation of cachectin secretion GOC:TermGenie downregulation of tumor necrosis factor alpha secretion GOC:TermGenie downregulation of tumor necrosis factor ligand superfamily member 2 secretion GOC:TermGenie downregulation of tumor necrosis factor secretion GOC:TermGenie negative regulation of TNF secretion GOC:TermGenie negative regulation of TNF superfamily, member 2 secretion GOC:TermGenie negative regulation of TNF-alpha secretion GOC:TermGenie negative regulation of Tnfa secretion GOC:TermGenie negative regulation of cachectin secretion GOC:TermGenie negative regulation of tumor necrosis factor alpha secretion GOC:TermGenie negative regulation of tumor necrosis factor ligand superfamily member 2 secretion GOC:TermGenie inhibition of TNF secretion GOC:TermGenie inhibition of TNF superfamily, member 2 secretion GOC:TermGenie inhibition of TNF-alpha secretion GOC:TermGenie inhibition of Tnfa secretion GOC:TermGenie inhibition of cachectin secretion GOC:TermGenie inhibition of tumor necrosis factor alpha secretion GOC:TermGenie inhibition of tumor necrosis factor ligand superfamily member 2 secretion GOC:TermGenie inhibition of tumor necrosis factor secretion GOC:TermGenie Any process that activates or increases the frequency, rate or extent of tumor necrosis factor secretion. sl 2015-07-09T19:50:14Z positive regulation of TNF secretion positive regulation of TNF superfamily, member 2 secretion positive regulation of TNF-alpha secretion positive regulation of Tnfa 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 secretion up regulation of TNF superfamily, member 2 secretion up regulation of TNF-alpha secretion up regulation of Tnfa secretion up regulation of cachectin 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 secretion up-regulation of TNF superfamily, member 2 secretion up-regulation of TNF-alpha secretion up-regulation of Tnfa secretion up-regulation of cachectin 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 secretion upregulation of TNF superfamily, member 2 secretion upregulation of TNF-alpha secretion upregulation of Tnfa secretion upregulation of cachectin 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 secretion activation of TNF superfamily, member 2 secretion activation of TNF-alpha secretion activation of Tnfa secretion activation of cachectin secretion activation of tumor necrosis factor alpha secretion activation of tumor necrosis factor ligand superfamily member 2 secretion activation of tumor necrosis factor secretion biological_process GO:1904469 positive regulation of tumor necrosis factor secretion Any process that activates or increases the frequency, rate or extent of tumor necrosis factor secretion. GOC:TermGenie GO_REF:0000058 PMID:15560120 positive regulation of TNF secretion GOC:TermGenie positive regulation of TNF superfamily, member 2 secretion GOC:TermGenie positive regulation of TNF-alpha secretion GOC:TermGenie positive regulation of Tnfa secretion GOC:TermGenie positive regulation of cachectin secretion GOC:TermGenie positive regulation of tumor necrosis factor alpha secretion GOC:TermGenie positive regulation of tumor necrosis factor ligand superfamily member 2 secretion GOC:TermGenie up regulation of TNF secretion GOC:TermGenie up regulation of TNF superfamily, member 2 secretion GOC:TermGenie up regulation of TNF-alpha secretion GOC:TermGenie up regulation of Tnfa secretion GOC:TermGenie up regulation of cachectin secretion GOC:TermGenie up regulation of tumor necrosis factor alpha secretion GOC:TermGenie up regulation of tumor necrosis factor ligand superfamily member 2 secretion GOC:TermGenie up regulation of tumor necrosis factor secretion GOC:TermGenie up-regulation of TNF secretion GOC:TermGenie up-regulation of TNF superfamily, member 2 secretion GOC:TermGenie up-regulation of TNF-alpha secretion GOC:TermGenie up-regulation of Tnfa secretion GOC:TermGenie up-regulation of cachectin secretion GOC:TermGenie up-regulation of tumor necrosis factor alpha secretion GOC:TermGenie up-regulation of tumor necrosis factor ligand superfamily member 2 secretion GOC:TermGenie up-regulation of tumor necrosis factor secretion GOC:TermGenie upregulation of TNF secretion GOC:TermGenie upregulation of TNF superfamily, member 2 secretion GOC:TermGenie upregulation of TNF-alpha secretion GOC:TermGenie upregulation of Tnfa secretion GOC:TermGenie upregulation of cachectin secretion GOC:TermGenie upregulation of tumor necrosis factor alpha secretion GOC:TermGenie upregulation of tumor necrosis factor ligand superfamily member 2 secretion GOC:TermGenie upregulation of tumor necrosis factor secretion GOC:TermGenie activation of TNF secretion GOC:TermGenie activation of TNF superfamily, member 2 secretion GOC:TermGenie activation of TNF-alpha secretion GOC:TermGenie activation of Tnfa secretion GOC:TermGenie activation of cachectin secretion GOC:TermGenie activation of tumor necrosis factor alpha secretion GOC:TermGenie activation of tumor necrosis factor ligand superfamily member 2 secretion GOC:TermGenie activation of tumor necrosis factor secretion GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development. es 2015-10-19T14:12:27Z 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 biological_process 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 GO:1904746 U4PR86 in PMID:22801495 inferred from mutant phenotype negative regulation of apoptotic process involved in development Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development. GOC:TermGenie GO_REF:0000058 PMID:22801495 down regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie down regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie down regulation of apoptotic process involved in anatomical structure development GOC:TermGenie down regulation of apoptotic process involved in development GOC:TermGenie down regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie down regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie down regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie down regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie down regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic process involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic process involved in development GOC:TermGenie down-regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie down-regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie downregulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic process involved in anatomical structure development GOC:TermGenie downregulation of apoptotic process involved in development GOC:TermGenie downregulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie downregulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie downregulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie downregulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic process involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie negative regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie down regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of apoptosis involved in anatomical structure development GOC:TermGenie down regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie down regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie down regulation of apoptotic program involved in anatomical structure development GOC:TermGenie down regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie down regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie down regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie down-regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie down-regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptotic program involved in anatomical structure development GOC:TermGenie down-regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie down-regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie down-regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie downregulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie downregulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of apoptosis involved in anatomical structure development GOC:TermGenie downregulation of apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie downregulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie downregulation of apoptotic program involved in anatomical structure development GOC:TermGenie downregulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie downregulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie downregulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie inhibition of activation of apoptosis involved in anatomical structure development GOC:TermGenie inhibition of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of apoptosis involved in anatomical structure development GOC:TermGenie inhibition of apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of apoptosis signaling involved in anatomical structure development GOC:TermGenie inhibition of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic cell death involved in anatomical structure development GOC:TermGenie inhibition of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic process involved in anatomical structure development GOC:TermGenie inhibition of apoptotic process involved in development GOC:TermGenie inhibition of apoptotic process involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic program involved in anatomical structure development GOC:TermGenie inhibition of apoptotic program involved in development of an anatomical structure GOC:TermGenie inhibition of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie inhibition of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie inhibition of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie inhibition of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of type I programmed cell death involved in anatomical structure development GOC:TermGenie inhibition of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie negative regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie negative regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptotic program involved in anatomical structure development GOC:TermGenie negative regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie negative regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie negative regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie down regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie down regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie down regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie down regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie down regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie down regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie down regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie down regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie down regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie down-regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie down-regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie down-regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie down-regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie down-regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie down-regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie down-regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie down-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie downregulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie downregulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie downregulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie downregulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie downregulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie downregulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie downregulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie downregulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie downregulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie inhibition of apoptosis activator activity involved in anatomical structure development GOC:TermGenie inhibition of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie inhibition of commitment to apoptosis involved in anatomical structure development GOC:TermGenie inhibition of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie inhibition of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie inhibition of induction of apoptosis involved in anatomical structure development GOC:TermGenie inhibition of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie inhibition of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie inhibition of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie negative regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie negative regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie negative regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie negative regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie negative regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie negative regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie negative regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie negative regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development. es 2015-10-19T14:12:34Z 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 involved in anatomical structure development 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 biological_process 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 GO:1904747 U4PR86 in PMID:22801495 inferred from mutant phenotype positive regulation of apoptotic process involved in development Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development. GOC:TermGenie GO_REF:0000058 PMID:22801495 positive regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptotic process involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie positive regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie up regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic process involved in anatomical structure development GOC:TermGenie up regulation of apoptotic process involved in development GOC:TermGenie up regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie up regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie up regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie up regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic process involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic process involved in development GOC:TermGenie up-regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie up-regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie upregulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic process involved in anatomical structure development GOC:TermGenie upregulation of apoptotic process involved in development GOC:TermGenie upregulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie upregulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie upregulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie upregulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie activation of activation of apoptosis involved in anatomical structure development GOC:TermGenie activation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie activation of apoptosis involved in anatomical structure development GOC:TermGenie activation of apoptosis involved in development of an anatomical structure GOC:TermGenie activation of apoptosis signaling involved in anatomical structure development GOC:TermGenie activation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie activation of apoptotic cell death involved in anatomical structure development GOC:TermGenie activation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie activation of apoptotic process involved in anatomical structure development GOC:TermGenie activation of apoptotic process involved in development GOC:TermGenie activation of apoptotic process involved in development of an anatomical structure GOC:TermGenie activation of apoptotic program involved in anatomical structure development GOC:TermGenie activation of apoptotic program involved in development of an anatomical structure GOC:TermGenie activation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie activation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie activation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie activation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie activation of type I programmed cell death involved in anatomical structure development GOC:TermGenie activation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie positive regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie positive regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptotic program involved in anatomical structure development GOC:TermGenie positive regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie positive regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie positive regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie up regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie up regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of apoptosis involved in anatomical structure development GOC:TermGenie up regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie up regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie up regulation of apoptotic program involved in anatomical structure development GOC:TermGenie up regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie up regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie up regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie up-regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie up-regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptotic program involved in anatomical structure development GOC:TermGenie up-regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie up-regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie up-regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie upregulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie upregulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of apoptosis involved in anatomical structure development GOC:TermGenie upregulation of apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie upregulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie upregulation of apoptotic program involved in anatomical structure development GOC:TermGenie upregulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie upregulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie upregulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie activation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie activation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie activation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie activation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie activation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie activation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie activation of induction of apoptosis involved in anatomical structure development GOC:TermGenie activation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie activation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie activation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie positive regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie positive regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie positive regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie positive regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie positive regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie positive regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie positive regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie positive regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie up regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie up regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie up regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie up regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie up regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie up regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie up regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie up regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie up regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie up-regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie up-regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie up-regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie up-regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie up-regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie up-regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie up-regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie up-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie upregulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie upregulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie upregulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie upregulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie upregulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie upregulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie upregulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie upregulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie upregulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that modulates the frequency, rate or extent of apoptotic process involved in development. es 2015-10-19T15:02:28Z 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 biological_process 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 GO:1904748 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 apoptotic process involved in development. GOC:TermGenie GO_REF:0000058 PMID:22801495 regulation of apoptotic cell death involved in anatomical structure development GOC:TermGenie regulation of apoptotic cell death involved in development of an anatomical structure GOC:TermGenie regulation of apoptotic process involved in anatomical structure development GOC:TermGenie regulation of apoptotic process involved in development of an anatomical structure GOC:TermGenie regulation of apoptotic programmed cell death involved in anatomical structure development GOC:TermGenie regulation of apoptotic programmed cell death involved in development of an anatomical structure GOC:TermGenie regulation of programmed cell death by apoptosis involved in anatomical structure development GOC:TermGenie regulation of programmed cell death by apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of activation of apoptosis involved in anatomical structure development GOC:TermGenie regulation of activation of apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of apoptosis involved in anatomical structure development GOC:TermGenie regulation of apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of apoptosis signaling involved in anatomical structure development GOC:TermGenie regulation of apoptosis signaling involved in development of an anatomical structure GOC:TermGenie regulation of apoptotic program involved in anatomical structure development GOC:TermGenie regulation of apoptotic program involved in development of an anatomical structure GOC:TermGenie regulation of type I programmed cell death involved in anatomical structure development GOC:TermGenie regulation of type I programmed cell death involved in development of an anatomical structure GOC:TermGenie regulation of apoptosis activator activity involved in anatomical structure development GOC:TermGenie regulation of apoptosis activator activity involved in development of an anatomical structure GOC:TermGenie regulation of commitment to apoptosis involved in anatomical structure development GOC:TermGenie regulation of commitment to apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of induction of apoptosis by p53 involved in anatomical structure development GOC:TermGenie regulation of induction of apoptosis by p53 involved in development of an anatomical structure GOC:TermGenie regulation of induction of apoptosis involved in anatomical structure development GOC:TermGenie regulation of induction of apoptosis involved in development of an anatomical structure GOC:TermGenie regulation of signaling (initiator) caspase activity involved in anatomical structure development GOC:TermGenie regulation of signaling (initiator) caspase activity involved in development of an anatomical structure GOC:TermGenie Any process that modulates the frequency, rate or extent of core promoter binding. nc 2015-11-09T12:32:23Z biological_process GO:1904796 regulation of core promoter binding true Any process that modulates the frequency, rate or extent of core promoter binding. GOC:BHF GOC:BHF_telomere GOC:TermGenie GOC:nc GO_REF:0000059 PMID:22723415 Any process that stops, prevents or reduces the frequency, rate or extent of core promoter binding. nc 2015-11-09T12:32:31Z down regulation of core promoter binding down-regulation of core promoter binding downregulation of core promoter binding inhibition of core promoter binding biological_process GO:1904797 negative regulation of core promoter binding true Any process that stops, prevents or reduces the frequency, rate or extent of core promoter binding. GOC:BHF GOC:BHF_telomere GOC:TermGenie GOC:nc GO_REF:0000059 PMID:22723415 down regulation of core promoter binding GOC:TermGenie down-regulation of core promoter binding GOC:TermGenie downregulation of core promoter binding GOC:TermGenie inhibition of core promoter binding GOC:TermGenie Any process that activates or increases the frequency, rate or extent of core promoter binding. nc 2015-11-09T12:32:38Z up regulation of core promoter binding up-regulation of core promoter binding upregulation of core promoter binding activation of core promoter binding biological_process GO:1904798 positive regulation of core promoter binding true Any process that activates or increases the frequency, rate or extent of core promoter binding. GOC:BHF GOC:BHF_telomere GOC:TermGenie GOC:nc GO_REF:0000059 PMID:22723415 up regulation of core promoter binding GOC:TermGenie up-regulation of core promoter binding GOC:TermGenie upregulation of core promoter binding GOC:TermGenie activation of core promoter binding GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization. mec 2016-02-05T09:59:24Z down regulation of establishment of protein localisation down regulation of establishment of protein localization down regulation of protein positioning down regulation of protein recruitment down-regulation of establishment of protein localisation down-regulation of establishment of protein localization down-regulation of protein positioning down-regulation of protein recruitment downregulation of establishment of protein localisation downregulation of establishment of protein localization downregulation of protein positioning downregulation of protein recruitment 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 inhibition of protein positioning inhibition of protein recruitment biological_process GO:1904950 negative regulation of establishment of protein localization Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization. GOC:TermGenie GO_REF:0000058 PMID:22761445 down regulation of establishment of protein localisation GOC:TermGenie down regulation of establishment of protein localization GOC:TermGenie down regulation of protein positioning GOC:TermGenie down regulation of protein recruitment GOC:TermGenie down-regulation of establishment of protein localisation GOC:TermGenie down-regulation of establishment of protein localization GOC:TermGenie down-regulation of protein positioning GOC:TermGenie down-regulation of protein recruitment GOC:TermGenie downregulation of establishment of protein localisation GOC:TermGenie downregulation of establishment of protein localization GOC:TermGenie downregulation of protein positioning GOC:TermGenie downregulation of protein recruitment GOC:TermGenie negative regulation of establishment of protein localisation GOC:TermGenie negative regulation of protein positioning GOC:TermGenie negative regulation of protein recruitment GOC:TermGenie inhibition of establishment of protein localisation GOC:TermGenie inhibition of establishment of protein localization GOC:TermGenie inhibition of protein positioning GOC:TermGenie inhibition of protein recruitment GOC:TermGenie Any process that activates or increases the frequency, rate or extent of establishment of protein localization. mec 2016-02-05T09:59:32Z 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 protein positioning up regulation of protein recruitment up-regulation of establishment of protein localisation up-regulation of establishment of protein localization up-regulation of protein positioning up-regulation of protein recruitment upregulation of establishment of protein localisation upregulation of establishment of protein localization upregulation of protein positioning upregulation of protein recruitment activation of establishment of protein localisation activation of establishment of protein localization activation of protein positioning activation of protein recruitment biological_process GO:1904951 positive regulation of establishment of protein localization Any process that activates or increases the frequency, rate or extent of establishment of protein localization. GOC:TermGenie GO_REF:0000058 PMID:22761445 positive regulation of establishment of protein localisation GOC:TermGenie positive regulation of protein positioning GOC:TermGenie positive regulation of protein recruitment GOC:TermGenie up regulation of establishment of protein localisation GOC:TermGenie up regulation of establishment of protein localization GOC:TermGenie up regulation of protein positioning GOC:TermGenie up regulation of protein recruitment GOC:TermGenie up-regulation of establishment of protein localisation GOC:TermGenie up-regulation of establishment of protein localization GOC:TermGenie up-regulation of protein positioning GOC:TermGenie up-regulation of protein recruitment GOC:TermGenie upregulation of establishment of protein localisation GOC:TermGenie upregulation of establishment of protein localization GOC:TermGenie upregulation of protein positioning GOC:TermGenie upregulation of protein recruitment GOC:TermGenie activation of establishment of protein localisation GOC:TermGenie activation of establishment of protein localization GOC:TermGenie activation of protein positioning GOC:TermGenie activation of protein recruitment GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of DNA methylation. bc 2016-11-04T16:43:13Z down regulation of DNA methylation down-regulation of DNA methylation downregulation of DNA methylation inhibition of DNA methylation biological_process GO:1905642 negative regulation of DNA methylation Any process that stops, prevents or reduces the frequency, rate or extent of DNA methylation. GOC:PARL GOC:TermGenie GOC:bc GO_REF:0000058 PMID:27336847 down regulation of DNA methylation GOC:TermGenie down-regulation of DNA methylation GOC:TermGenie downregulation of DNA methylation GOC:TermGenie inhibition of DNA methylation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of DNA methylation. bc 2016-11-04T16:43:22Z up regulation of DNA methylation up-regulation of DNA methylation upregulation of DNA methylation activation of DNA methylation biological_process GO:1905643 positive regulation of DNA methylation Any process that activates or increases the frequency, rate or extent of DNA methylation. GOC:PARL GOC:TermGenie GOC:bc GO_REF:0000058 PMID:27336847 up regulation of DNA methylation GOC:TermGenie up-regulation of DNA methylation GOC:TermGenie upregulation of DNA methylation GOC:TermGenie activation of DNA methylation GOC:TermGenie Any process that modulates the frequency, rate or extent of lipid localization. rozaru 2017-02-21T12:12:22Z regulation of lipid localisation biological_process GO:1905952 regulation of lipid localization Any process that modulates the frequency, rate or extent of lipid localization. GOC:TermGenie GO_REF:0000058 PMID:17564681 regulation of lipid localisation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization. rozaru 2017-02-21T12:12:41Z down regulation of lipid localisation down regulation of lipid localization down-regulation of lipid localisation down-regulation of lipid localization downregulation of lipid localisation downregulation of lipid localization negative regulation of lipid localisation inhibition of lipid localisation inhibition of lipid localization biological_process GO:1905953 negative regulation of lipid localization Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization. GOC:TermGenie GO_REF:0000058 PMID:17564681 down regulation of lipid localisation GOC:TermGenie down regulation of lipid localization GOC:TermGenie down-regulation of lipid localisation GOC:TermGenie down-regulation of lipid localization GOC:TermGenie downregulation of lipid localisation GOC:TermGenie downregulation of lipid localization GOC:TermGenie negative regulation of lipid localisation GOC:TermGenie inhibition of lipid localisation GOC:TermGenie inhibition of lipid localization GOC:TermGenie Any process that activates or increases the frequency, rate or extent of lipid localization. rozaru 2017-02-21T12:12:49Z positive regulation of lipid localisation up regulation of lipid localisation up regulation of lipid localization up-regulation of lipid localisation up-regulation of lipid localization upregulation of lipid localisation upregulation of lipid localization activation of lipid localisation activation of lipid localization biological_process GO:1905954 positive regulation of lipid localization Any process that activates or increases the frequency, rate or extent of lipid localization. GOC:TermGenie GO_REF:0000058 PMID:17564681 positive regulation of lipid localisation GOC:TermGenie up regulation of lipid localisation GOC:TermGenie up regulation of lipid localization GOC:TermGenie up-regulation of lipid localisation GOC:TermGenie up-regulation of lipid localization GOC:TermGenie upregulation of lipid localisation GOC:TermGenie upregulation of lipid localization GOC:TermGenie activation of lipid localisation GOC:TermGenie activation of lipid localization GOC:TermGenie 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). bhm 2013-11-12T13:20:12Z cellular_component GO:1990234 transferase complex 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). GOC:bhm PMID:16540464 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. sl 2015-06-15T22:59:26Z TNF secretion TNF superfamily, member 2 secretion TNF-alpha secretion Tnfa secretion cachectin secretion tumor necrosis factor alpha secretion tumor necrosis factor ligand superfamily member 2 secretion biological_process GO:1990774 tumor necrosis factor secretion 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. PMID:15560120 Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process. tanyaberardini 2010-09-15T08:55:45Z 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 biological_process GO:2000112 regulation of cellular macromolecule biosynthetic process Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process. GOC:obol regulation of cellular biopolymer biosynthetic process GOC:obol regulation of cellular macromolecule anabolism GOC:obol regulation of cellular macromolecule biosynthesis GOC:obol regulation of cellular macromolecule formation GOC:obol regulation of cellular macromolecule synthesis GOC:obol Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process. tanyaberardini 2010-09-15T08:55:48Z 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 biological_process GO:2000113 negative regulation of cellular macromolecule biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process. GOC:obol negative regulation of cellular biopolymer biosynthetic process GOC:obol negative regulation of cellular macromolecule anabolism GOC:obol negative regulation of cellular macromolecule biosynthesis GOC:obol negative regulation of cellular macromolecule formation GOC:obol negative regulation of cellular macromolecule synthesis GOC:obol Any process that modulates the frequency, rate or extent of cell motility. midori 2010-10-01T09:41:21Z regulation of cell locomotion regulation of movement of a cell biological_process regulation of cell movement GO:2000145 regulation of cell motility Any process that modulates the frequency, rate or extent of cell motility. GOC:mah regulation of cell locomotion GOC:obol regulation of movement of a cell GOC:obol regulation of cell movement GOC:obol Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility. midori 2010-10-01T09:41:26Z negative regulation of cell locomotion negative regulation of movement of a cell biological_process negative regulation of cell movement GO:2000146 negative regulation of cell motility Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility. GOC:mah negative regulation of cell locomotion GOC:obol negative regulation of movement of a cell GOC:obol negative regulation of cell movement GOC:obol Any process that activates or increases the frequency, rate or extent of cell motility. midori 2010-10-01T09:41:30Z positive regulation of cell locomotion positive regulation of movement of a cell biological_process positive regulation of cell movement GO:2000147 positive regulation of cell motility Any process that activates or increases the frequency, rate or extent of cell motility. GOC:mah positive regulation of cell locomotion GOC:obol positive regulation of movement of a cell GOC:obol positive regulation of cell movement GOC:obol Any process that modulates the frequency, rate or extent of fatty acid transport. rl 2010-10-18T10:37:13Z biological_process GO:2000191 regulation of fatty acid transport Any process that modulates the frequency, rate or extent of fatty acid transport. GOC:BHF Any process that stops, prevents, or reduces the frequency, rate or extent of fatty acid transport. rl 2010-10-18T10:37:15Z biological_process GO:2000192 negative regulation of fatty acid transport Any process that stops, prevents, or reduces the frequency, rate or extent of fatty acid transport. GOC:BHF Any process that activates or increases the frequency, rate or extent of fatty acid transport. rl 2010-10-18T10:37:17Z biological_process GO:2000193 positive regulation of fatty acid transport Any process that activates or increases the frequency, rate or extent of fatty acid transport. GOC:BHF Any process that modulates the frequency, rate or extent of DNA biosynthetic process. yaf 2010-12-08T04:48:15Z regulation of DNA anabolism regulation of DNA biosynthesis regulation of DNA formation regulation of DNA synthesis biological_process GO:2000278 regulation of DNA biosynthetic process Any process that modulates the frequency, rate or extent of DNA biosynthetic process. GOC:obol regulation of DNA anabolism GOC:obol regulation of DNA biosynthesis GOC:obol regulation of DNA formation GOC:obol regulation of DNA synthesis GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of DNA biosynthetic process. yaf 2010-12-08T04:48:20Z negative regulation of DNA anabolism negative regulation of DNA biosynthesis negative regulation of DNA formation negative regulation of DNA synthesis biological_process GO:2000279 negative regulation of DNA biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of DNA biosynthetic process. GOC:obol negative regulation of DNA anabolism GOC:obol negative regulation of DNA biosynthesis GOC:obol negative regulation of DNA formation GOC:obol negative regulation of DNA synthesis GOC:obol Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process. yaf 2011-04-04T10:01:20Z positive regulation of DNA anabolism positive regulation of DNA biosynthesis positive regulation of DNA formation positive regulation of DNA synthesis biological_process GO:2000573 positive regulation of DNA biosynthetic process Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process. GOC:obol positive regulation of DNA anabolism GOC:obol positive regulation of DNA biosynthesis GOC:obol positive regulation of DNA formation GOC:obol positive regulation of DNA synthesis GOC:obol Any process that modulates the frequency, rate or extent of transcription regulatory region DNA binding. yaf 2011-05-09T03:28:11Z biological_process GO:2000677 regulation of transcription regulatory region DNA binding Any process that modulates the frequency, rate or extent of transcription regulatory region DNA binding. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of transcription regulatory region DNA binding. yaf 2011-05-09T03:28:14Z biological_process GO:2000678 negative 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. GOC:obol Any process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding. yaf 2011-05-09T03:28:17Z biological_process GO:2000679 positive regulation of transcription regulatory region DNA binding Any process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding. GOC:obol Any process that modulates the frequency, rate or extent of response to DNA damage stimulus. yaf 2011-08-19T10:20:25Z regulation of DNA damage response regulation of cellular DNA damage response regulation of cellular response to DNA damage stimulus regulation of response to genotoxic stress biological_process GO:2001020 regulation of response to DNA damage stimulus Any process that modulates the frequency, rate or extent of response to DNA damage stimulus. GOC:obol regulation of DNA damage response GOC:obol regulation of cellular DNA damage response GOC:obol regulation of cellular response to DNA damage stimulus GOC:obol regulation of response to genotoxic stress GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of response to DNA damage stimulus. yaf 2011-08-19T10:20:29Z 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 biological_process GO:2001021 negative 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. GOC:obol negative regulation of DNA damage response GOC:obol negative regulation of cellular DNA damage response GOC:obol negative regulation of cellular response to DNA damage stimulus GOC:obol negative regulation of response to genotoxic stress GOC:obol Any process that activates or increases the frequency, rate or extent of response to DNA damage stimulus. yaf 2011-08-19T10:20:33Z 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 biological_process GO:2001022 positive regulation of response to DNA damage stimulus Any process that activates or increases the frequency, rate or extent of response to DNA damage stimulus. GOC:obol positive regulation of DNA damage response GOC:obol positive regulation of cellular DNA damage response GOC:obol positive regulation of cellular response to DNA damage stimulus GOC:obol positive regulation of response to genotoxic stress GOC:obol Any process that modulates the frequency, rate or extent of response to drug. yaf 2011-08-19T01:47:20Z biological_process regulation of drug resistance regulation of drug susceptibility/resistance GO:2001023 regulation of response to drug Any process that modulates the frequency, rate or extent of response to drug. GOC:obol regulation of drug resistance GOC:obol regulation of drug susceptibility/resistance GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of response to drug. yaf 2011-08-19T01:47:24Z biological_process negative regulation of drug resistance negative regulation of drug susceptibility/resistance GO:2001024 negative regulation of response to drug Any process that stops, prevents or reduces the frequency, rate or extent of response to drug. GOC:obol negative regulation of drug resistance GOC:obol negative regulation of drug susceptibility/resistance GOC:obol Any process that activates or increases the frequency, rate or extent of response to drug. yaf 2011-08-19T01:47:27Z biological_process positive regulation of drug resistance positive regulation of drug susceptibility/resistance GO:2001025 positive regulation of response to drug Any process that activates or increases the frequency, rate or extent of response to drug. GOC:obol positive regulation of drug resistance GOC:obol positive regulation of drug susceptibility/resistance GOC:obol Any process that modulates the frequency, rate or extent of cellular response to drug. yaf 2011-08-27T04:12:19Z biological_process GO:2001038 regulation of cellular response to drug Any process that modulates the frequency, rate or extent of cellular response to drug. GOC:obol Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to drug. yaf 2011-08-27T04:12:23Z biological_process GO:2001039 negative regulation of cellular response to drug Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to drug. GOC:obol Any process that activates or increases the frequency, rate or extent of cellular response to drug. yaf 2011-08-27T04:12:25Z biological_process GO:2001040 positive regulation of cellular response to drug Any process that activates or increases the frequency, rate or extent of cellular response to drug. GOC:obol Any process that modulates the frequency, rate or extent of RNA biosynthetic process. dph 2011-10-17T11:36:25Z regulation of RNA anabolism regulation of RNA biosynthesis regulation of RNA formation regulation of RNA synthesis biological_process GO:2001141 regulation of RNA biosynthetic process Any process that modulates the frequency, rate or extent of RNA biosynthetic process. GOC:dph regulation of RNA anabolism GOC:obol regulation of RNA biosynthesis GOC:obol regulation of RNA formation GOC:obol regulation of RNA synthesis GOC:obol Any process that modulates the frequency, rate or extent of apoptotic signaling pathway. pr 2011-11-24T01:20:49Z regulation of apoptotic signalling pathway biological_process GO:2001233 regulation of apoptotic signaling pathway Any process that modulates the frequency, rate or extent of apoptotic signaling pathway. GOC:mtg_apoptosis regulation of apoptotic signalling pathway GOC:mah Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway. pr 2011-11-24T01:20:54Z negative regulation of apoptotic signalling pathway biological_process GO:2001234 negative regulation of apoptotic signaling pathway Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway. GOC:mtg_apoptosis negative regulation of apoptotic signalling pathway GOC:mah Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway. pr 2011-11-24T01:20:58Z positive regulation of apoptotic signalling pathway biological_process GO:2001235 positive regulation of apoptotic signaling pathway Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway. GOC:mtg_apoptosis positive regulation of apoptotic signalling pathway GOC:mah Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization. yaf 2011-12-02T02:01:20Z negative regulation of chromosome organisation biological_process negative regulation of chromosome organization and biogenesis negative regulation of maintenance of genome integrity negative regulation of nuclear genome maintenance GO:2001251 negative regulation of chromosome organization Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization. GOC:obol negative regulation of chromosome organisation GOC:obol negative regulation of chromosome organization and biogenesis GOC:obol negative regulation of maintenance of genome integrity GOC:obol negative regulation of nuclear genome maintenance GOC:obol Any process that activates or increases the frequency, rate or extent of chromosome organization. yaf 2011-12-02T02:01:26Z positive regulation of chromosome organisation biological_process positive regulation of chromosome organization and biogenesis positive regulation of maintenance of genome integrity positive regulation of nuclear genome maintenance GO:2001252 positive regulation of chromosome organization Any process that activates or increases the frequency, rate or extent of chromosome organization. GOC:obol positive regulation of chromosome organisation GOC:obol positive regulation of chromosome organization and biogenesis GOC:obol positive regulation of maintenance of genome integrity GOC:obol positive regulation of nuclear genome maintenance GOC:obol 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: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take Alan Ruttenberg 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 http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n 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. datum label 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: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software 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. PERSON: Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy information carrier 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: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity 1 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. PERSON: Alan Ruttenberg PERSON: Melanie Courtot 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 PERSON: Alan Ruttenberg PERSON: Bjoern Peters 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 OBI_0000123 group:OBI dot plot 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 person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph 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 OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm 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 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification 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" PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 data format specification 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. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set 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. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg 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 Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification 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? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum 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. GROUP: IAO material information bearer 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 GROUP:OBI histogram 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. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI heatmap 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. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram 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. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot scattergraph WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot 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. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification 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. PERSON: Lawrence Hunter figure 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 PERSON: Lawrence Hunter diagram 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 PERSON: Lawrence Hunter document 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. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg 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. PERSON:Chris Stoeckert PERSON:Melanie Courtot line chart GROUP:OBI WEB: http://en.wikipedia.org/wiki/Line_chart line graph 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. infection Viruses Viruses Euteleostomi bony vertebrates Euteleostomi Bacteria eubacteria Bacteria Archaea Archaea Eukaryota eucaryotes eukaryotes Eukaryota Euarchontoglires Euarchontoglires Tetrapoda tetrapods Tetrapoda Amniota amniotes Amniota Opisthokonta Opisthokonta Bilateria Bilateria Mammalia mammals Mammalia Vertebrata <Metazoa> Vertebrata vertebrates Vertebrata <Metazoa> Homo sapiens human human being man Homo sapiens planned process planned process Injecting mice with a vaccine in order to test its efficacy A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process regulator role 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 regulator 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 biological feature identification objective 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 regulatory role material supplier role 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 provider role supplier material supplier role classified data set 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. PERSON: James Malone PERSON: Monnie McGee data set with assigned class labels classified data set reference substance role 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. Person:Jennifer Fostel reference substance OBI 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 http://en.wikipedia.org/wiki/Column_chromatography open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 chromatography column xenotransplantation is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans PlanAndPlannedProcess Branch OBI branch derived xenotransplantation processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material 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. Frank Gibson chromatography instrument http://en.wikipedia.org/wiki/Chromatography open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 chromatography device 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 Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry mass spectrometer allotransplantation is the transplantation of organs between members of the same species. PlanAndPlannedProcess Branch OBI branch derived allotransplantation gamma counter A Geiger counter A processed material which measures gamma radiation Frank Gibson http://en.wikipedia.org/wiki/Gamma_counter gamma counter 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") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay culture medium 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 OBI culture medium reagent role 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 reagent 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 material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing 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 OBI 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 PlanAndPlannedProcess Branch OBI branch derived transplantation specimen role 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. GROUP: Role Branch OBI 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. Jennifer Fostel sequence feature identification objective intervention design PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. Philppe Rocca-Serra OBI branch derived intervention design 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. Jennifer Fostel molecular feature identification objective cell co-culturing Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one. PlanAndPlannedProcess Branch OBI branch derived cell co-culturing cDNA library PMID:6110205. collection of cDNA derived from mouse splenocytes. Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications. PERSON: Luisa Montecchi PERSON: Philippe Rocca-Serra GROUP: PSI PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction cDNA library imaging assay An imaging assay is an assay to produce a picture of an entity. definition_source: OBI. PlanAndPlannedProcess Branch OBI branch derived imaging assay microtiter plate A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA) A microtiter_plate is a flat plate with multiple wells used as small test tubes. Melanie Courtot microplate http://en.wikipedia.org/wiki/Microtiter_plate microtiter plate radioactivity detection 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. PlanAndPlannedProcess Branch, IEDB IEDB radioactivity detection 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. Jennifer Fostel cellular feature identification objective 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 PlanAndPlannedProcess Branch OBI branch derived enzymatic cleavage 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization artificially induced nucleic acid hybridization www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules. PlanAndPlannedProcess Branch OBI branch derived artificially induced nucleic acid hybridization DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. PlanAndPlannedProcess Branch OBI branch derived DNA extraction 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. Jennifer Fostel organism feature identification objective 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. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol adding a material entity into a target Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. BP branch derived adding a material entity into a target analyte role 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. GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. analyte role protein-protein interaction detection 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/ Philippe Rocca-Serra TF binding OBI 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 PERSON: Philippe Rocca-Serra eluted material OBI Bionaterial eluate material to be added role 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 Role Branch OBI 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 OBI branch derived histological sample preparation 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. Frank Gibson PERSON: Daniel Schober http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer mass analyzer 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))). Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source ion source 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. Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Detector ion detector metabolite profiling Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019 metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism Philippe Rocca-Serra metabolite assay OBI metabolite profiling light emission function A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. Bill Bug Daniel Schober Frank Gibson Melanie Courtot light emission function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot magnify function contain function A syringe, a beaker A contain function is a function to constrain a material entities location in space Bill Bug Daniel Schober Frank Gibson Melanie Courtot contain function heat function A heat function is a function that increases the internal kinetic energy of a material Bill Bug Daniel Schober Frank Gibson Melanie Courtot heat function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot material separation function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot excitation function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot synthesizing function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Perturbation_biology perturb 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 Frank Gibson filter function mechanical function A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Mechanical_work mechanical function 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. Daniel Schober Frank Gibson Melanie Courtot power supply electricity supply function ionization function The ion source in amass spectrometer 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Ionization ionization function 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. Daniel Schober Frank Gibson Melanie Courtot cool function 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 Frank Gibson energy supply function image acquisition function An image acquisition function is a function to acquire an image of a material Frank Gibson image acquisition function image acquisition device An image creation device is a device which captures a digitized image of an object Frank Gibson image acquisition device sep:00096 image creation device solid support function 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 Daniel Schober Frank Gibson Melanie Courtot 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot environment control function 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. Daniel Schober Frank Gibson Melanie Courtot sort function 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. GROUP: OBI BIomaterial Branch GROUP: OBI BIomaterial Branch PCR product nucleic acid template role 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 cloning vector 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/ PERSON: Helen Parkinson cloning vector role polymerase chain reaction 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. OBI Plan PCR adapted from wikipedai polymerase chain reaction cloning insert role 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" GROUP: Role branch OBII and Wikipedia cloning insert role reverse transcriptase enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) person:Melanie Courtot group:OBI reverse transcriptase extract Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 an extract is a material entity which results from an extraction process PERSON: Philippe Rocca-Serra extracted material GROUP: OBI Biomatrial Branch extract transcription profiling assay Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot Philippe Rocca-Serra gene expression profiling OBI transcription profiling transcription profiling assay 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. person: Melanie Courtot GROUP:OBI enzyme 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 PERSON: Jie Zheng PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch polyacrylamide gel adding material objective 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 BP adding material objective genotyping assay 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. Philippe Rocca-Serra genotype profiling, SNP genotyping OBI Biomaterial SNP analysis genotyping assay analyte measurement objective 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 PERSON: Bjoern Peters PPPB branch 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 PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch agarose gel assay objective 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) PPPB branch PPPB branch assay objective analyte assay example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. 2013-09-23: simplify equivalent axiom Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement. logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration')) PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch analyte assay target of material addition role 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. GROUP: Role Branch OBI 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 PERSON: Frank Gibson PERSON: Frank Gibson intra cellular electrophysiology recording regulatory agency The US Environmental Protection 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. GROUP: OBI Biomaterial Branch WEB: en.wikipedia.org/wiki/Regulator regulatory agency 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. PERSON: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson measure function 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 PERSON: Frank Gibson, Helen Parkinson PERSON: Frank Gibson extracellular electrophysiology recording material transformation objective 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. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective manufacturing 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. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing manufacturing objective is the objective to manufacture a material of a certain function (device) PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective mass spectrometry assay 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. Philippe Rocca-Serra Philippe Rocca-Serra mass spectrometry assay study design execution 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. branch derived 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. study design execution 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 GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094 affinity column 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104 gel filtration column 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 Philippe Rocca-Serra RT-PCR reverse transcription polymerase chain reaction reverse transcribed polymerase chain reaction manufacturer role 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. GROUP: Role Branch OBI manufacturer role scattered molecular aggregate 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 PERSON: Alan Ruttenberg 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115 chromatography device chromatography consumable 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100 size exclusion column NMR spectroscopy 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. Philippe Rocca-Serra Nuclear magnetic resonance spectroscopy adapted from Wikipedia NMR spectroscopy DNA sequencing 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. Philippe Rocca-Serra OBI Branch derived nucleotide sequencing DNA sequencing hematology 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 Philippe Rocca-Serra blood analysis, haematology OBI branch derived hematology DNA methylation profiling assay 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. Philippe Rocca-Serra OBI branch derived DNA methylation profiling DNA methylation profiling assay material separation objective 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. PPPB branch PPPB branch material separation objective clustered data set 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. PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels AR thinks could be a data item instead 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 Melanie Courtot Monnie McGee WEB: differential expression analysis data transformation urine specimen 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? urine specimen material combination Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. is a material processing with the objective to combine two or more material entities as input into a single material entity as output. created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. bp bp material combination device setting 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 PERSON: Frank Gibson device setting specimen collection process 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. 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. 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/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process class prediction data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. James Malone supervised classification data transformation PERSON: James Malone class prediction data transformation BrdU incorporation assay The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of 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. IEDB IEDB BrdU incorporation assay tritiated thymidine incorporation assay The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity. A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. IEDB IEDB tritiated thymidine incorporation assay sample from organism a material obtained from an organism in order to be a representative of the whole 5/29: This is a helper class for now 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. sample from organism portioning objective 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. portioning objective 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 separation into different composition objective specimen collection objective 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. Bjoern Peters Bjoern Peters specimen collection objective creating a mixture of molecules in solution The production of PBS is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations. Bjoern Peters PERSON: Helen Parkinson creating a mixture of molecules in solution material combination objective is an objective to obtain an output material that contains several input materials. PPPB branch bp material combination objective immunoprecipitation 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 Philippe Rocca-Serra OBI plan and planned process branch immunoprecipitation survival assessment Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time Need to point out more specifically that survival / death is measured. survival assessment support vector machine 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. James Malone Ryan Brinkman SVM PERSON: Ryan Brinkman support vector machine decision tree induction objective 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. James Malone decision tree induction objective decision tree building data transformation A decision tree building data transformation is a data transformation that has objective decision tree induction. James Malone PERSON: James Malone decision tree building data transformation library preparation 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. Philippe Rocca-Serra library construction library preparation GenePattern software a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. James Malone Person:Helen Parkinson WEB: http://www.broadinstitute.org/cancer/software/genepattern/ GenePattern software ChIP-seq assay 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. Philippe Rocca-Serra chromatin immunoprecipitation sequencing assay adapted from Wikipedia 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 ChIP-seq assay paired-end library 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 Philippe Rocca-Serra mate-paired library paired-end tag (PET) library adapted from information provided by Solid web site paired-end library peak matching 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 James Malone Ryan Brinkman PERSON: Ryan Brinkman peak matching 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. James Malone k-NN PERSON: James Malone k-nearest neighbors recombinant vector A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. recombinant vector single fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs Philippe Rocca-Serra fragment library single fragment library cloning vector 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. cloning vector material sample role 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. material sample role material sampling process A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity material sampling process material sample 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 OBI: workshop sample population sample material sample CART A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. James Malone classification and regression trees BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. CART independent variable specification 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 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert experimental factor independent variable 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 factor study design independent variable survival rate 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. Oliver He adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate survival rate statistical model validation 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. Helen Parkinson http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation transcription factor binding site SO:0000235 PLace_holder for sequence ontology term transcription factor binding site purification objective 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 PERSON:Bjoern Peters isolation objective BP 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality purification objective cross linking 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 PERSON: Chris Stoeckert http://en.wikipedia.org/wiki/Cross-link cross linking material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective presentation of stimulus The presentation of a flashing light to a monkey during reward training a planned process in which an organism is exposed to some stimulus with the intent to invoke an action Helen Parkinson, Jessica Turner, Dirk Derom stimulation of organism Helen Parkinson, Jessica Turner, Dirk Derom presentation of stimulus amplified DNA Amplied DNA created by PCR DNA that has been produced in an enzymatic amplification process PERSON: Alan Ruttenberg Alan Ruttenberg amplified DNA primary structure of DNA macromolecule a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. placeholder for SO BP et al primary structure of DNA macromolecule micro electrode 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. Helen Parkinson, Jessica Turner, Dirk Derom micro electrode measuring device Jessica Turner, Dirk Derom micro electrode measurement device A ruler, a microarray scanner, a Geiger counter. A device in which a measure function inheres. GROUP:OBI Philly workshop OBI measurement device high molecular weight DNA extract 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. PERSON:Chris Stoeckert OBI high molecular weight DNA extract manufacturer A person or organization that has a manufacturer role manufacturer material maintenance a process with that achieves the objective to maintain some or all of the characteristics of an input material over time material maintenance primary structure of RNA molecule 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 Person:Bjoern Peters primary structure of RNA molecule polyA RNA extraction A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. Person: Chris Stoeckert Person: Jie Zheng UPenn Group polyA RNA extraction complementary nucleotide probe role 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 PERSON:Bjoern Peters complementary nucleotide probe role northern blot analysis PMID: 18428227. Analysis of RNA by northern blot hybridization. Brown T, Mackey K. Curr Protoc Hum Genet. 2001 Nov;Appendix 3:Appendix 3K. a northern blot analysis is an assay allowing monitoring presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing agarose gel, transfered by blotting procedure to a nitrocellulose or nylon membrane and immobilized by cross linking or baking to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager 2010-01-31: Philippe Rocca-Serra: Need to add a restriction taking into account probe and transcript information Person: Philippe Rocca-Serra northern blot northern blot analysis polyA RNA extract 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. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group polyA RNA extract single-nucleotide-resolution nucleic acid structure mapping assay is an assay which aims to provide information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity. 2010-01-31: Philippe Rocca-Serra: OBI needs to review 'structure assay' as currently defined. Need to get feedback from Kevin Clancy. Person: Philippe Rocca-Serra RNAO single-nucleotide-resolution nucleic acid structure mapping assay pre-mortem specimen material obtained through a liver biopsy from a human patient a specimen that was taken from a live organism Bjoern Peters MO_705 premortem pre-mortem specimen 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. IEDB IEDB detection of specific nucleic acid polymers with complementary probes RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng Group: UPenn Group RNA extract cell-cell killing assay Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. A cytometry assay that monitors a cell population to track how many are killed by other cells. IEDB IEDB cell-cell killing assay in vivo cell killing assay 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. IEDB IEDB in vivo cell killing assay secondary structure of sequence macromolecule A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford. 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO Person: Philippe Rocca-Serra Wikipedia secondary structure of sequence macromolecule cell proliferation assay Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation. A cytometry assay which measures the degreee to which input cells are replicating. IEDB IEDB cell proliferation assay Southern blot analysis PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. Li C, Weber G, Ekman P, Lagercrantz J, Norlen BJ, Akerström G, Nordenskjöld M, Bergerheim US. Hum Mutat. 1998;Suppl 1:S31-3. Southern blot analysis is a an assay used in molecular biology to assert the presence/absence status of a specific DNA sequence in DNA samples. DNA samples to be assayed are first digested by restriction enzymes, fragments are then resolved by gel electrophoresis following by a blotting ensuring transfer to nitrocellulose or nylon membrane. Immobilization of DNA fragments to the membrane is achieved by UV crosslinking and/or baking. Probes raised against the specific sequences are then hybridized to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager. 2010-01-31: Philippe Rocca-Serra: need extra work on 'labeled probe' 2010-01-31: Philippe Rocca-Serra: departure from naming convention as the assay is named after Edwin Southern. Person: Philippe Rocca-Serra Southern blot OBI & Wikipedia Southern blot analysis real time polymerase chain reaction assay A laboratory technique based on the PCR, which is used to amplify and simultaneously quantify a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. person: Bjoern Peters person: Melanie Courtot Q-PCR kinetic polymerase chain reaction qPCR quantitative real time polymerase chain reaction WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction real time PCR real time polymerase chain reaction assay post mortem specimen the spleen taken from a dead mouse a specimen that was taken from a dead organism Bjoern Peters MO_416 postmortem post mortem specimen in vitro cell killing assay Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. IEDB IEDB in vitro cell killing assay sequence feature annotation Information about a sequence region Bjoern Peters Bjoern Peters place holder for sequence ontology term sequence feature annotation 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) PERSON: Bjoern Peters PERSON: Melanie Courtot RRT-PCR RT-rt PCR qRT-PCR real time reverse-transcription polymerase chain reaction assay X-ray crystallography assay 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. IEDB IEDB X-ray crystallography assay 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. IEDB IEDB promoter activity detection by reporter gene assay flow cytometry assay 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. IEDB IEDB flow cytometry assay labeled RNA extract 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 Group: OBI group Group: OBI group labeled RNA extract labeled specimen A specimen that has been modified in order to be able to detect it in future experiments added during call 3/1/2010 OBI group labeled specimen infectious agent is a material entity bearing the disposition to infect an organism IEDB IEDB infectious agent calorimeter A measurement device that is used to calculate the heat flow of a chemical reaction or physical change. PERSON:Bjoern Peters calorimetry instrument? http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm calorimeter study intervention the part of the execution of an intervention design study which is varied between two or more subjects in the study PERSON: Bjoern Peters GROUP: OBI study intervention material separation device flow cytometer A device with a separation function realized in a planed process material separation device handedness assay 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. Helen Parkinson handedness test http://en.wikipedia.org/wiki/Handedness handedness assay service provider role 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 PERSON:Helen Parkinson service provider role processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen categorical label 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. Bjoern Peters Bjoern Peters categorical label in live cell assay An assay in which a measurement is made by observing entities located in a live cell. in live cell assay in live organism assay Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells. An assay in which a measurement is made by observing entities located in an organism. PERSON:Bjoern Peters in vivo assay in live organism assay container A device that can be used to restrict the location of material entities over time 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) PERSON: Bjoern Peters container device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device sequence data 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. Person:Chris Stoeckert GROUP: OBI 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. IEDB IEDB cell-cell binding detection by flow cytometry assay in container assay an assay in which a measurement is made by observing entities located in a container. in container assay growth condition intervention design A study design in which the independent variable is the environmental condition in which the specimen is growing PERSON: Bjoern Peters MO_588 growth_condition_design growth condition intervention design PCR instrument 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. PCR instrument electron microscope A microscope that produces an image of an object by targeting it with an electron beam electron microscope growth environment 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 OBI group growth environment questionnaire 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 questionnaire image acquisition 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. PERSON: Jie Zheng image acquisition image creation nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. PERSON: Jie Zheng UPenn Group nucleic acid extract single-nucleotide-resolution nucleic acid structure mapping assay using 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. Person: Philippe Rocca-Serra RNAO and OBI single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing a single-nucleotide-resolution nucleic acid structure mapping assay which relies on small chemical compounds acting as chemical probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study. Person: Philippe Rocca-Serra RNAO and OBI single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing 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 binding constant determination assay light emission device 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. Person:Helen Parkinson OBI light emission device perturbation device A homogenizer is a perturbation device. A perturbation device is a device which is designed to perform a perturb function Helen Parkinson OBI Vancouver workshop 2010 PERSON: Helen Parkinson perturbation device environmental control device 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. Helen Parkinson OBI environmental control device DNA extract The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Person: Jie Zheng Group: UPenn group DNA extract electrophoresis system A device that moves charged particles through a medium by using an electric field induced by electrodes. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Category:Electrophoresis electrophoresis system 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. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/High_performance_liquid_chromatography high performance liquid chromatography instrument confocal microscope 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. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Confocal_microscopy confocal microscope patch clamp device A device used in electrophysiology that allows the study of single or multiple ion channels in cells. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Patch_clamp patch clamp device gel electrophoresis system A device that moves charged particles through a medium by using an electric field induced by electrodes. PERSON: Erik Segerdell electrophoresis system http://en.wikipedia.org/wiki/Category:Electrophoresis gel electrophoresis system voltage clamp device 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. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Voltage_clamp voltage clamp device X-ray source A device that is used to generate X-rays. PERSON: Erik Segerdell x-ray generator http://en.wikipedia.org/wiki/X-ray_generator X-ray source liquid chromatography instrument 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 PERSON: Matthew Brush PERSON: Matthew Brush liquid chromatography instrument labeled nucleic acid extract 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. Person: Jie Zheng labeled extract MO_221 labeledExtract labeled extract labeled nucleic acid extract 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. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum binding constant 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. IEDB IEDB 3D structure determination of bound complex assay binding assay 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 PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum binding assay cell culture expansion a processual entity that results in the increase of cell numbers including grow of yeast and bacteria PERSON: Chris Stoeckert, Jie Zheng MO_758 grow BP: add it as subclass of 'cell culturing' JZ: No 'cell culturing' in OBI Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process. cell culture expansion 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. PERSON: Chris Stoeckert, Jie Zheng MO_771 gene_knock_out 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. PERSON: Chris Stoeckert, Jie Zheng MO_437 gene_knock_in WEB: http://en.wikipedia.org/wiki/Gene_Knock-in gene knock in genetically modified material a material entity, organism or cell, that is the output of a genetic transformation process. PERSON: Jie Zheng GROUP: OBI term is proposed by BP on Oct 25, 2010 dev call genetically modified material transfection a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell PERSON: Chris Stoeckert, Jie Zheng MO_366 transfection transfection genetic transformation objective a material transformation objective aims to create genetically modified organism or cell Person: Jie Zheng Person: Jie Zheng suggested to be added by BP and AR during Oct 25, 2010 dev call genetic transformation objective induced mutation a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation. PERSON: Chris Stoeckert, Jie Zheng MO_564 induced_mutation induced mutation 3D structural organization datum 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 3D structural organization datum half life datum (t 1/2) The time it takes for 50% of a class of stochastic processes to occur. Bjoern Peters t 1/2 Bjoern Peters half life datum (t 1/2) dose response curve 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. Bjoern Peters; Randi Vita dose response curve RNA sequencing 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 Bjoern Peters Bjoern Peters RNA sequencing 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. Bjoern Peters; Randi Vita wikipedia half maximal effective concentration (EC50) binding datum 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. Bjoern Peters; Randi Vita binding datum 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. Bjoern Peters; Randi Vita wikipedia half maximal inhibitory concentration (IC50) in vivo design A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. Person: Chris Stoeckert, Jie Zheng MO_454 in_vivo_design in vivo design 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. Person: Chris Stoeckert, Jie Zheng MO_560 genotyping_design genotyping by high throughput sequencing design 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. Person: Chris Stoeckert, Jie Zheng MO_808 ex_vivo_design 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 Group: OBI group genetic population background information 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 epigenetic modification identification objective transcription profiling by high thoughput sequencing design A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team transcription profiling by high throughput sequencing design genotyping by high throughput sequencing assay An assay in which high througput sequencer is used to detect polymorphisms in DNA samples Person: James Malone EFO_0002771: genotyping by high throughput sequencing genotyping by high throughput sequencing assay 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. Person: James Malone ChIP-on-chip assay WEB: http://en.wikipedia.org/wiki/ChIP-on-chip Philippe Rocca-Serra ChIP-chip assay 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 http://en.wikipedia.org/wiki/Chip-Sequencing ChIP-seq design 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 Philippe Rocca-Serra DNA methylation profiling by high throughput sequencing assay RNA-seq assay An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance PERSON: James Malone transcription profiling by high throughput sequencing EFO_0002770 transcription profiling by high throughput sequencing JZ: should be inferred as 'DNA sequencing'. Will check in the future. an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. WEB: http://en.wikipedia.org/wiki/RNA-Seq RNA-seq assay 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. Person: Chris Stoeckert, Jie Zheng GROUP: ArrayExpress production team DNA methylation profiling by array design in vitro design A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. Person: Chris Stoeckert, Jie Zheng MO_347 in_vitro_design in vitro design transcription profiling by array design A study design that identifies forms and abundance of transcripts in the genome using microarray technology. Person: Chris Stoeckert, Jie Zheng MO_533 transcript_identification_design transcription profiling by array design 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 Group: OBI group Group: OBI group genotype information transcription profiling by RT-PCR design A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team transcription profiling by RT-PCR design 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 Person: James Malone EFO_0002765 proteomic profiling by array proteomic profiling by array assay transcription profiling identification objective A molecular feature identification objective that aims to characterize the abundance of transcripts Person: Chris Stoeckert, Jie Zheng Group: Penn Group transcription profiling identification objective 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 Person: James Malone EFO_0002759 methylation profiling by array Philippe Rocca-Serra DNA methylation profiling by array assay post-transcriptional modification design A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. Person: Chris Stoeckert, Jie Zheng MO_392 cellular_modification_design post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases post-transcriptional modification design transcription profiling by RT-PCR assay An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR) Person: Anna Farne EFO_0002943: transcription profiling by RT-PCR transcription profiling by RT-PCR assay 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. proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic alteration information cellular process design A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. Person: Chris Stoeckert, Jie Zheng MO_810 cellular_process_design cellular process design stimulus or stress design A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. Person: Chris Stoeckert, Jie Zheng MO_568 stimulus_or_stress_design stimulus or stress design 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. Person: Chris Stoeckert, Jie Zheng MO_933 binding_site_identification_design protein and DNA interaction identification objective 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. Person: Chris Stoeckert, Jie Zheng ChIP-on-chip design MO_933 binding_site_identification_design ChIP-chip design genetic characteristics information a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. Person: Chris Stoeckert, Jie Zheng 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) genetic characteristics information protein binding site identification design A study design that investigates protein binding sites on nucleic acids. Person: Chris Stoeckert, Jie Zheng MO_933 binding_site_identification_design protein binding site identification design transcription profiling design A study design that identifies forms and abundance of transcripts in the genome. Person: Chris Stoeckert, Jie Zheng MO_533 transcript_identification_design transcription profiling design 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 Group: ArrayExpress production team https://github.com/obi-ontology/obi/issues/854 proteomic profiling by array design genotyping design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. Person: Chris Stoeckert, Jie Zheng MO_560 genotyping_design 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. Person: Chris Stoeckert, Jie Zheng MO_447 genetic_modification_design 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/ Person: James Malone RNA profiling by array assay EFO_0002768: transcription profiling by array transcription profiling by array assay 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). PERSON: Chris Stoeckert, Jie Zheng tissue specimen MO_954 organism_part specimen from organism radioactivity detection binding assay binding assay that uses radioactivity detection as an indicator of binding PERSON:Bjoern Peters, Randi Vita IEDB radioactivity detection binding assay fluorescence detection binding assay binding assay that uses fluorescence detection as an indicator of binding PERSON:Bjoern Peters, Randi Vita IEDB fluorescence detection binding assay fluorescence detection assay 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. IEDB IEDB fluorescence detection assay 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 PERSON: Chris Stoeckert, Jie Zheng MO_406 purify purification 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 PERSON: Chris Stoeckert, Jie Zheng MO_84 OrganismStatus specimen with pre- or post-mortem status equilibrium dissociation constant (KD) 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) PERSON: Bjoern Peters, Randi Vita IEDB equilibrium dissociation constant (KD) equilibrium association constant (KA) 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) PERSON: Bjoern Peters, Randi Vita IEDB equilibrium association constant (KA) rate measurement datum 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 PERSON: Bjoern Peters, Randi Vita IEDB rate measurement datum 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. PERSON: Bjoern Peters, Randi Vita http://dx.doi.org/10.1016/0006-2952(73)90196-2 equilibrium dissociation constant (KD) approximated by IC50 DNA sequence data The part of a FASTA file that contains the letters ACTGGGAA A sequence data item that is about the primary structure of DNA OBI call; Bjoern Peters OBI call; Melanie Courtout 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. DNA sequence data 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. PERSON: Bjoern Peters, Randi Vita Assay Development: Fundamentals and Practices, By Ge Wu, page 74 equilibrium dissociation constant (KD) approximated by EC50 half life of binding datum 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. PERSON: Bjoern Peters, Randi Vita IEDB half life of binding datum binding 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. PERSON: Bjoern Peters, Randi Vita IEDB binding binding off rate measurement datum (koff) A rate measurement datum of how quickly bound complexes disassociate PERSON: Bjoern Peters, Randi Vita IEDB binding off rate measurement datum (koff) binding on rate measurement datum (kon) A rate measurement datum of how quickly bound complexes form PERSON: Bjoern Peters, Randi Vita IEDB binding on rate measurement datum (kon) analytical chromatography 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. IEDB IEDB analytical chromatography electron microscopy imaging assay 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. IEDB IEDB electron microscopy imaging assay immuno staining assay 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. IEDB IEDB immuno staining assay purified material 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 GROUP: OBI call OBI conference call purified material calorimetric binding assay 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. IEDB IEDB calorimetric binding assay 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). IEDB IEDB antibody binding detection by fluorescence quenching 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 RNA protection assay 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. PERSON:Philippe Rocca-Serra; Marcus Chibucos EMSA,gel shift assay, gel mobility shift assay, band shift assay, gel retardation assay PMID:6269071 electrophoretic mobility shift 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. PERSON:Philippe Rocca-Serra; Marcus Chibucos PMID:17430206 gene knock-down assay nano-cap analysis of gene expression Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. PMID:20543846 nano-CAGE is a type of CAGE developed to work from very low amount (nanogram scale) of mRNA samples PERSON:Philippe Rocca-Serra; Marcus Chibucos nano-CAGE PMID: 20543846 nano-cap analysis of gene expression cap analysis of gene expression 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Takahashi H, Lassmann T, Murata M, Carninci P. Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005. PMID: 22362160 An assay which aims at monitoring RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome PERSON:Philippe Rocca-Serra; Marcus Chibucos CAGE PMID:14663149 cap analysis of gene expression 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. PERSON:Philippe Rocca-Serra; Marcus Chibucos Y1H PMID: 22218861 add regulatory region DNA binding;obo:GO:0000975; yeast one-hybrid 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 PERSON:Philippe Rocca-Serra; Marcus Chibucos B1H http://en.wikipedia.org/wiki/Bacterial_one-hybrid_system add regulatory region DNA binding;obo:GO:0000975; bacterial one-hybrid 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 PERSON:Philippe Rocca-Serra; Marcus Chibucos FISH chromosome organization assay by fluorescence in situ hybridization 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/ PERSON:Philippe Rocca-Serra; Marcus Chibucos MSP PMID:8790415 methylation-specific polymerase chain reaction 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. PERSON:Philippe Rocca-Serra; Marcus Chibucos AIMS assay,intermethylated site amplification PMID: 18987810 amplification of intermethylated sites (AIMS) assay 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 PERSON:Philippe Rocca-Serra; Marcus Chibucos ISH PMID:9021518 in situ hybridization 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). PERSON:Philippe Rocca-Serra; Marcus Chibucos add ;actin filament polymerization obo:GO:0070358; cytochalasin-induced inhibition of actin polymerization assay cellular structure feature identification objective is an objective specification which aims to discover cellular structure properties PERSON:Philippe Rocca-Serra OBI group cellular structure feature identification objective immunoprecipitation assay 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. IEDB IEDB immunoprecipitation assay 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. Person: Venkat Malladi, Jie Zheng Venkat Malladi, Jie Zheng ENCODE project paired-end library preparation 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 MRE-seq MRE-seq assay Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] ENCODE project methylation-sensitive restriction enzyme sequencing assay 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 Penn Group assay array 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. PERSON:Matthew Brush PERSON:Matthew Brush (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). reagent cell freezing medium 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. PERSON: Matthew Brush 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. Chris Stoeckert, Jie Zheng LMA MLPA 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/ multiplex ligation-mediated amplification chromosome conformation identification objective A molecular feature identification objective that aims to determine spatial organization of chromatin. Chris Stoeckert, Jie Zheng Group: Penn Group chromosome conformation identification objective 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 5C 5C assay "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]" ENCODE project Carbon-copy chromosome conformation capture assay 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. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng ChIP-exo assay Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] ENCODE project chromatin immunoprecipitation with exonuclease sequencing assay categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification 1 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification value specification 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. PERSON:Bjoern Peters value specification molecular-labeled material 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 PERSON:Matthew Brush OBI developer call, 3-12-12 molecular-labeled material ChIP 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 Philippe Rocca-Serra chromatin immunoprecipitation assay 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 http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html an assay which uses immunoprecipitation and which produces data about protein-DNA interaction or DNA epigenetic modification as per user (pployd) request and proposal by Alan Ruttenberg http://sourceforge.net/p/obi/obi-terms/707/ PERSON: Philippe Rocca-Serra assay using chromatin immunoprecipitation cytometry assay An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. An assay that measures properties of cells. IEDB IEDB cytometry assay fluorescence quenching binding assay 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. IEDB IEDB fluorescence quenching binding assay microarray assay 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. IEDB IEDB microarray assay immunohistochemistry 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. IEDB IEDB immunohistochemistry epigenetic modification assay An assay that identifies epigenetic modification including histone modifications, open chromatin, and DNA methylation. Person: Chris Stoeckert, Jie Zheng Penn group Beta Cell Biology Consoritum epigenetic modification assay peptide mass fingerprinting 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/ Janos Demeter, Chris Stoeckert PMF protein fingerprinting ERO:0001668 (http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting) Saccharomyces Genome Database (SGD) 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/ Person: Chris Stoeckert, Jie Zheng OBIB, OBI Biobank collection of specimens 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 reporter gene assay 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 physical store rapid amplification of cDNA ends 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 RACE http://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/RACE_Rapid_Amplification_of_cDNA_Ends/5_Prime_RACE_and_3_Prime_RACE 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. ImmPort HPLC http://www.ncbi.nlm.nih.gov/pubmed/9491555 high performance liquid chromotography assay microscopy assay 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. ImmPort http://www.ncbi.nlm.nih.gov/pubmed/21685355 microscopy assay protein localization assay 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. Rebecca Tauber OBI development call protein localization assay subcellular protein localization assay A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy. Rebecca Tauber ECO subcellular protein localization assay ChIP-qPCR assay A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples. Chris Stoeckert PMID:18388953 ChIP-qPCR assay dot blot assay An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies. Bjoern Peters dot blot analysis PMID:10473518 dot blot assay ATP bioluminescence assay An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen. Rebecca Tauber ATP quantitation assay cell viability ATP quantitation assay ECO ATP bioluminescence assay electrophysiology assay 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. Gully Burns https://en.wikipedia.org/wiki/Electrophysiology electrophysiology assay patch clamp assay 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. Gully Burns ECO:0006012 http://www.annualreviews.org/doi/pdf/10.1146/annurev.ph.46.030184.002323 https://en.wikipedia.org/wiki/Patch_clamp patch clamp assay whole-cell patch clamp assay 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. Gully Burns ECO:0006015 https://en.wikipedia.org/wiki/Patch_clamp#Whole-cell_recording_or_whole-cell_patch whole-cell patch clamp assay cell-attached patch clamp assay 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. Gully Burns https://en.wikipedia.org/wiki/Patch_clamp#Cell-attached_patch cell-attached patch clamp assay inside-out patch clamp assay 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. Gully Burns http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ https://en.wikipedia.org/wiki/Patch_clamp#Inside-out_patch inside-out patch clamp assay outside-out patch clamp assay 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. Gully Burns http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ https://en.wikipedia.org/wiki/Patch_clamp#Outside-out_patch outside-out patch clamp assay electroencephalography 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. Gully Burns EEG electroencephalography single-unit recording 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. Gully Burns http://www.thieme.com/media/samples/pubid-80418214.pdf single-unit recording local field potential recording 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. Gully Burns doi:10.1007/978-1-4614-7320-6_723-1 local field potential recording histologic grade according to AJCC 7th edition G4: Undifferentiated G1:Well differentiated 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. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis Histologic Grade (Fuhrman Nuclear Grading System) NCI BBRB, OBI NCI BBRB histologic grade according to the Fuhrman Nuclear Grading System histologic grade for ovarian tumor A categorical value specification that is a histologic grade assigned to a ovarian tumor. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for 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. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to a two-tier grading system 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). Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to the World Health Organization 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. Chris Stoeckert, Helena Ellis pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for colon and rectum according to 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. Chris Stoeckert, Helena Ellis pT: Pathologic spread lung primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for lung according to 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. Chris Stoeckert, Helena Ellis pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for kidney according to 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. Chris Stoeckert, Helena Ellis pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for ovary according to 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. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for colon and rectum according to 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. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for lung according to AJCC 7th edition 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. Chris Stoeckert, Helena Ellis pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for kidney according to 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. Chris Stoeckert, Helena Ellis pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for ovary according to 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. Chris Stoeckert, Helena Ellis M: colon distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for colon according to 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. Chris Stoeckert, Helena Ellis M: lung distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for lung according to 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. Chris Stoeckert, Helena Ellis M: kidney distant Metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for kidney according to 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. Chris Stoeckert, Helena Ellis M: ovarian distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for ovary according to 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. Chris Stoeckert, Helena Ellis Clinical tumor stage group (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB clinical tumor stage group according to 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. Chris Stoeckert, Helena Ellis Clinical FIGO stage NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics cervical cancer stage value specification 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. Chris Stoeckert, Helena Ellis Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics ovarian cancer stage value specification performance status value specification A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). Chris Stoeckert, Helena Ellis Performance Status Scale https://en.wikipedia.org/wiki/Performance_status NCI BBRB performance status value specification 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. Chris Stoeckert, Helena Ellis ECOG score NCI BBRB, OBI NCI BBRB Eastern Cooperative Oncology Group score value specification Karnofsky score vaue specification A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Chris Stoeckert, Helena Ellis Karnofsky Score NCI BBRB, OBI NCI BBRB Karnofsky score vaue specification nuclear ligation assay An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei. Chris S PMID: 8327891 nuclear ligation assay chromosome conformation capture assay 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. Chris S 3C assay PMID:11847345 http://www.nature.com/nprot/journal/v2/n7/full/nprot.2007.243.html chromosome conformation capture assay Hi-C assay 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. Chris S PMID:20461051 Hi-C assay 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. Person: Alan Ruttenberg, Jie Zheng https://en.wiktionary.org/wiki/measurand https://github.com/obi-ontology/obi/issues/778 measurand role suppression subtractive hybridization An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library. Rebecca Tauber SSH subtractive hybridization PMID:14970460 suppression subtractive hybridization differential screening hybridization An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes. Rebecca Tauber DSH differential screening PMID:25472628 differential screening hybridization brain specimen A specimen that is derived from brain. Chris Stoeckert Chris Stoeckert, NCI BBRB brain specimen 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 PERSON: Susanna Sansone GROUP: OBI Biomaterial Branch Epstein Barr virus transformed B cell organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen cultured cell population 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. PERSON:Matthew Brush cell culture sample PERSON:Matthew Brush 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. cultured cell population 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 PERSON: Philippe Rocca-Serra GROUP: CEBS GROUP: OBI Biomaterial Branch organ section 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 James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation differential expression analysis objective Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. Elisabetta Manduchi PERSON: Elisabetta Manduchi differential expression analysis objective 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 Person:Helen Parkinson leave one out cross validation method 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). Elisabetta Manduchi James Malone Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/K-means k-means clustering 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). James Malone WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_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. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra data projection PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot dimensionality reduction 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. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra pca data reduction PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot principal components analysis dimensionality reduction mass spectrometry analysis A data transformation which has the objective of spectrum analysis. mass spectrometry analysis data visualization Generation of a heatmap from a microarray dataset An planned process that creates images, diagrams or animations from the input data. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard data encoding as image visualization PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot 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 James Malone PERSON: James Malone data transformation objective partitioning data transformation A partitioning data transformation is a data transformation that has objective partitioning. James Malone PERSON: James Malone partitioning data transformation 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. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi partitioning objective class discovery data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. James Malone clustering data transformation unsupervised classification data transformation PERSON: James Malone class discovery 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. James Malone clustering objective discriminant analysis objective unsupervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class discovery 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. James Malone classification objective supervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class prediction 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. James Malone rotation estimation objective WEB: http://en.wikipedia.org/wiki/Cross_validation cross validation objective clustered data visualization 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. James Malone clustered data visualization spectrum analysis objective 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. PERSON: Tina Boussard Person:Helen Parkinson spectrum analysis objective 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 PERSON: Jennifer Fostel GROUP: CEBS pool of specimens 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. PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra liquid chemical solution GROUP: OBI Biomaterial Branch chemical solution solvent role 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 Philippe Rocca-Serra adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) solvent role solute 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 Philippe Rocca-Serra 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. Philippe Rocca-Serra 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. comet assay genetically modified organism 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 PERSON: Philippe Rocca-Serra OBI Biomaterial genetically modified organism dissolved material entity Salt molecules that have been mixed into water A material entity that has been going through a process of being put into solution Person:Bjoern Peters Philippe Rocca-Serra dissolved material entity extraction 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. Person:Bjoern Peters Philippe Rocca-Serra extraction staining PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8. Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. Philippe Rocca-Serra adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining staining polymerization 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 Philippe Rocca-Serra OBI-Branch polymerization enzymatic ligation 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 Philippe Rocca-Serra OBI-Branch enzymatic ligation nucleic acid hybridization 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. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] hybridization assay nucleic acid hybridization elution 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) Philippe Rocca-Serra wordnet.princeton.edu/perl/webwn 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 http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm flow cytometer analyzer flow cell Biofilm Flow Cell Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. Person:John Quinn flow_cell http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm flow cell 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. John Quinn http://en.wikipedia.org/wiki/Flow_cytometer flow cytometer 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 John Quinn Olga Tchuvatkina Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 light source 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 John Quinn obscuration bar 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. John Quinn http://en.wikipedia.org/wiki/Optical_filter optical filter 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. John Quinn http://einstein.stanford.edu/content/glossary/glossary.html photodetector 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 MO DNA sequencer 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 Trish Whetzel GROUP: MGED Ontology array scanner 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. Trish Whetzel MO_563 hybridization_chamber 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. Trish Whetzel MO_497 hybridization station 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. Trish Whetzel MO sonicator 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. Melanie Courtot Trish Whetzel MO spectrophotometer 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. Melanie Courtot Trish Whetzel DNA_amplifier PCR_machine Polymerase_Chain_Reaction_ machine thermocycler MO thermal cycler cytometer A cytometer is an instrument for counting and measuring cells. Melanie Courtot http://medical.merriam-webster.com/medical/cytometer cytometer 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:Frank Gibson Person:Kevin Clancy electrophoresis box electrophoresis unit sep:00095 gel tank power supply 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. Daniel Schober Frank Gibson PSU electrical power supply power pack power supply unit PERSON: Daniel Schober sep:00093 was power_pack, maps to SEP electrical_power_supply 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. Daniel Schober PERSON: Chris Stoeckert microarray 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. PERSON: Daniel Schober PERSON: Frank Gibson DNA Chip DNA-array Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03 DNA microarray 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. Daniel Schober PERSON: Daniel Schober protein microarray 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. OBI Instrument branch OBI Instrument branch droplet sorter 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. PERSON: Phillippe Rocca-Serra PERSON: Daniel Schober microtome 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) PERSON: Phillippe Rocca-Serra wikipedia 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. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design 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 PlanAndPlannedProcess Branch Clinical Research Glossary Version 4.0 CDICS glossary group clinical study design 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 reference design adding substance to cell culture adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient is process in which a material substance is added to a cell culture renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms Bjoern Peters IEDB adding substance to cell culture 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 PERSON:Bjoern Peters IEDB collecting specimen from organism 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. Bjoern Peters Person:Bjoern Peters IEDB administering substance in vivo 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 Bjoern Peters IEDB material component separation 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 PERSON:Matthew Brush OBI developer call, 3-12-12 detection of molecular label 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 histopathology OBI branch derived 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 PlanAndPlannedProcess Branch OBI branch derived maintaining cell culture 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 OBI branch derived substance detection 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 PERSON:Kevin Clancy OBI branch derived artificially induced reverse transcription 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 PERSON:Bjoern Peters OBI branch derived definition blessed by Jay, Alan, Randi cell permeabilization 'establishing cell culture' 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). PERSON:Matthew Brush PERSON:Matthew Brush 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. establishing cell culture 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 PERSON:Matthew Brush labeling OBI developer call, 3-12-12 addition of molecular label genetic transformation The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 the introduction. alteration or integration of genetic material into a cell or organism PERSON:Kevin Clancy genetic modification OBI branch derived genetic transformation 3D structure determination assay 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. IEDB IEDB 3D structure determination assay 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 OBI branch derived preparative chromatography sequencing assay The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template the use of a chemical or biochemical means to infer the sequence of a biomaterial has_output should be sequence of input; we don't have sequence well defined yet PlanAndPlannedProcess Branch OBI branch derived sequencing assay 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 PERSON:Kevin Clancy OBI branch derived specific enzymatic cleavage 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 PERSON:Kevin Clancy OBI branch derived gradient separation 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 PERSON:Kevin Clancy OBI branch derived 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. electrophoresis 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 PERSON:Kevin Clancy OBI branch derived selection by survival 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 PERSON:Kevin Clancy restriction enzyme assay the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components DNA cleavage, restriction analysis 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 PERSON:Kevin Clancy OBI branch derived enzymatic amplification 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) molecular cloning OBI branch derived recombinant vector cloning RNA extraction A RNA extraction is a nucleic acid extraction where the desired output material is RNA PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO RNA extraction 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 PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO. Could be defined class nucleic acid extraction 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. PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra display library WEB: http://www.immuneepitope.org/home.do PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction phage display library 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 PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra GROUP:IEDB transgenic organism infection process the detrimental process in which an infectious agent colonizes or replicates in a host environment IEDB IEDB infection process adaptive immune receptor is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. IEDB IEDB adaptive immune receptor experimental infection of cell culture is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture IEDB IEDB experimental infection of cell culture antigen is a material entity that has the antigen role IEDB IEDB antigen disposition to infect an organism 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 IEDB IEDB disposition to infect an organism material to be added 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 IEDB material to be added target of material addition 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. IEDB target of material addition assay antigen role 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 IEDB IEDB assay antigen role pathologic process abnormal, harmful processes caused by or associated with a disease IEDB IEDB pathologic process chromium release assay Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1. After a 4-h incubation of the effector cells with the target cells, supernatants were collected following brief centrifugation and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac). Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died. PlanAndPlannedProcess Branch, IEDB IEDB chromium release assay fluorescence 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. fluorescence behavioral quality 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. behavioral quality quality of a single physical entity A physical object quality which inheres in a single-bearer. quality of a single physical entity alive A viability quality inhering in a bearer by virtue of the bearer's condition before death. alive dead A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. dead radioactive A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity. radioactive handedness 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 left handedness 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. left handedness right handedness 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. right handedness ambidextrous handedness 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. ambidextrous handedness protein antithrombin III is a protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA. protein DNA ligase 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 ligase DNA ligase nuclease S1 A protein that is a translation product of the Aspergillus oryzae nucS gene or a 1:1 ortholog thereof. nuclease S1 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) molecular tracer role OBI developer call, 3-12-12 molecular label role molecular label 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 molecular tracer OBI developer call, 3-12-12 molecular label region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule sequence region blood A fluid that is composed of blood plasma and erythrocytes. blood organism substance 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. organism substance material anatomical entity Anatomical entity that has mass. material anatomical entity anatomical cluster Anatomical group that has its parts adjacent to one another. anatomical cluster tissue 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. tissue brain 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]. brain urine Excretion that is the output of a kidney urine length unit A unit which is a standard measure of the distance between two points. length unit mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit temperature unit A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. temperature unit substance unit A unit which is a standardised quantity of an element or compound with uniform composition. substance unit concentration unit A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. concentration unit volume unit A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. volume unit frequency unit A unit which is a standard measure of the number of repetitive actions in a particular time. frequency unit volumetric flow rate unit A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time . volumetric flow rate unit rate unit A unit which represents a standard measurement occurrence of a process per unit time. rate unit A type of quantitative reverse transcription polymerase chain reaction evidence used in automatic assertion. jbmunro 2018-07-07T12:00:00Z eco ECO:000156 quantitative reverse transcription polymerase chain reaction evidence used in automatic assertion. true 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. jbmunro 2018-07-07T12:00:00Z RRT-PCR evidence RT-qPCR evidence qRT-PCR evidence quantitative RT-PCR evidence quantitative real-time RT-PCR evidence rRT-PCR evidence real-time RT-PCR evidence real-time qRT-PCR evidence real-time quantitative reverse transcription PCR evidence real-time reverse transcription polymerase chain reaction evidence eco ECO:0001566 quantitative reverse transcription polymerase chain reaction evidence A type of quantitative reverse transcription polymerase chain reaction evidence used in manual assertion. jbmunro 2018-07-07T12:00:00Z eco ECO:0001567 quantitative reverse transcription polymerase chain reaction evidence used in manual assertion true 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 Person:Alan Ruttenberg 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 PERSON:Alan Ruttenberg 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. PERSON: Alan Ruttenberg PERSON: Melanie Courtot 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 true 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. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal 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. Alan Ruttenberg defined class 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 Alan Ruttenberg named class expression Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI 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. Alan Ruttenberg group:OBI 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 web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf Transformation-ML 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/) person:Jennifer Fostel web-page:http://www.isac-net.org/content/view/607/150/ ACS 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/) person:Jennifer Fostel web-page:http://www.w3.org/XML/ 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/) person:Jennifer Fostel web-page:http://www.w3.org/RDF/ 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/) person:Jennifer Fostel web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ zip 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/) person:Jennifer Fostel web-page:http://www.gnu.org/software/tar/manual/ tar 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/) person:Jennifer Fostel web-page:http://www.fcspress.com/ FCS 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) person:Jennifer Fostel web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf Compensation-ML 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/) person:Jennifer Fostel web-page:http://www.flowcyt.org/gating/ Gating-ML 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/) person:Jennifer Fostel web-page:http://www.w3.org/2004/OWL/ OWL Affymetrix Affymetrix supplied microarray An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix Thermo Philippe Rocca-Serra Thermo Waters Philippe Rocca-Serra Waters BIO-RAD Philippe Rocca-Serra BIO-RAD GenePattern hierarchical clustering James Malone GenePattern hierarchical clustering Ambion Philippe Rocca-Serra Ambion Helicos Philippe Rocca-Serra Helicos Roche Philippe Rocca-Serra Roche Illumina Philippe Rocca-Serra Illumina GenePattern PCA GenePattern PCA GenePattern module SVM GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. James Malone Ryan Brinkman GenePattern module SVM GenePattern k-nearest neighbors James Malone GenePattern k-nearest neighbors GenePattern LOOCV GenePattern LOOCV GenePattern k-means clustering James Malone GenePattern k-means clustering Agilent Philippe Rocca-Serra Agilent GenePattern module KMeansClustering GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. James Malone PERSON: James Malone GenePattern module KMeansClustering GenePattern CART James Malone GenePattern CART GenePattern module CARTXValidation 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 CARTXValidation Li-Cor Philippe Rocca-Serra Li-Cor Bruker Corporation Philippe Rocca-Serra Bruker Corporation GenePattern module KNNXValidation GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. James Malone PERSON: James Malone GenePattern module KNNXValidation GenePattern module PeakMatch GenePattern module PeakMatch GenePattern module KNN GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. James Malone GenePattern module KNN GenePattern module HierarchicalClustering GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. James Malone PERSON: James Malone GenePattern module HierarchicalClustering GenePattern SVM James Malone GenePattern SVM Applied Biosystems Philippe Rocca-Serra Applied Biosystems GenePattern module PCA GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. James Malone PERSON: James Malone GenePattern module PCA GenePattern peak matching James Malone Ryan Brinkman GenePattern peak matching Bruker Daltonics Philippe Rocca-Serra Bruker Daltonics GenePattern HeatMapViewer data visualization The GenePattern process of generating Heat Maps from clustered data. James Malone GenePattern HeatMapViewer data visualization GenePattern HierarchicalClusteringViewer data visualization The GenePattern process of generating hierarchical clustering visualization from clustered data. James Malone GenePattern HierarchicalClusteringViewer data visualization GenePattern module HeatMapViewer A GenePattern software module which is used to generate a heatmap view of data. James Malone GenePattern module HeatMapViewer GenePattern module HierarchicalClusteringViewer A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. James Malone GenePattern module HierarchicalClusteringViewer Sysmex Corporation, Kobe, Japan WEB:http://www.sysmex.com/@2009/08/06 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Sysmex Corporation, Kobe, Japan U.S. Food and Drug Administration FDA U.S. Food and Drug Administration right handed right handed ambidexterous ambidexterous left handed left handed Edingburgh handedness inventory 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. PERSON:Alan Ruttenberg PERSON:Jessica Turner PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html Edingburgh handedness inventory eBioscience A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.ebioscience.com/@2011/04/11 eBioscience Cytopeia A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.cytopeia.com/@2011/04/11 Cytopeia Exalpha Biological A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.exalpha.com/@2011/04/11 Exalpha Biological Apogee Flow Systems A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.apogeeflow.com/@2011/04/11 Apogee Flow Systems Exbio Antibodies A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.exbio.cz/@2011/04/11 Exbio Antibodies Becton Dickinson (BD Biosciences) A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.bdbiosciences.com/@2011/04/11 Becton Dickinson (BD Biosciences) Dako Cytomation A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.dakousa.com/@2011/04/11 Dako Cytomation Millipore A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.guavatechnologies.com/@2011/04/11 Millipore Antigenix A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.antigenix.com/@2011/04/11 Antigenix Partec A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.partec.de/@2011/04/11 Partec Beckman Coulter A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.beckmancoulter.com/@2011/04/11 Beckman Coulter Advanced Instruments Inc. (AI Companies) A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.aicompanies.com/@2011/04/11 Advanced Instruments Inc. (AI Companies) Miltenyi Biotec A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.miltenyibiotec.com/@2011/04/11 Miltenyi Biotec AES Chemunex A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.aeschemunex.com/@2011/04/11 AES Chemunex Bentley Instruments A supplier of flow cytometry analyzers Karin Breuer WEB:http://bentleyinstruments.com/@2011/04/11 Bentley Instruments Invitrogen A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.invitrogen.com/@2011/04/11 Invitrogen Luminex A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.luminexcorp.com/@2011/04/11 Luminex CytoBuoy A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.cytobuoy.com/@2011/04/11 CytoBuoy Nimblegen An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Person: Jie Zheng Nimblegen 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. Person: Jie Zheng Pacific Biosciences 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. NanoString Technologies Thermo Fisher Scientific An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific NCI BBRB Thermo Fisher Scientific G1: Well differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. Chris Stoeckert, Helena Ellis G1 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G1: Well differentiated G2: Moderately differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. Chris Stoeckert, Helena Ellis G2 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G2: Moderately differentiated G3: Poorly differentiated 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. Chris Stoeckert, Helena Ellis G3 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G3: Poorly differentiated G4: Undifferentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G4 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G4: Undifferentiated G1 (Fuhrman) 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. Chris Stoeckert, Helena Ellis Grade 1 NCI BBRB, OBI NCI BBRB G1 (Fuhrman) G2 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. Chris Stoeckert, Helena Ellis Grade 2 NCI BBRB, OBI NCI BBRB G2 (Fuhrman) G3 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. Chris Stoeckert, Helena Ellis Grade 3 NCI BBRB, OBI NCI BBRB G3 (Fuhrman) G4 (Fuhrman) 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. Chris Stoeckert, Helena Ellis Grade 4 NCI BBRB, OBI NCI BBRB G4 (Fuhrman) Low grade ovarian tumor A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. Chris Stoeckert, Helena Ellis Low grade NCI BBRB, OBI NCI BBRB Low grade ovarian tumor High grade ovarian tumor A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. Chris Stoeckert, Helena Ellis High grade NCI BBRB, OBI NCI BBRB High grade ovarian tumor G1 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. Chris Stoeckert, Helena Ellis G1 NCI BBRB, OBI NCI BBRB G1 (WHO) G2 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. Chris Stoeckert, Helena Ellis G2 NCI BBRB, OBI NCI BBRB G2 (WHO) G3 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. Chris Stoeckert, Helena Ellis G3 NCI BBRB, OBI NCI BBRB G3 (WHO) G4 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. Chris Stoeckert, Helena Ellis G4 NCI BBRB, OBI NCI BBRB G4 (WHO) pT0 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT0 (colon) pTis (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pTis (colon) pT1 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT1 (colon) pT2 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT2 (colon) pT3 (colon) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT3 (colon) pT4a (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT4a (colon) pT4b (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT4b (colon) pT0 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT0 (lung) pTis (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pTis (lung) pT1 (lung) 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). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1 (lung) pT1a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1a (lung) pT1b (lung) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1b (lung) pT2 (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 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2 (lung) pT2a (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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2a (lung) pT2b (lung) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2b (lung) pT3 (lung) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT3 (lung) pT4 (lung) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT4 (lung) pT0 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT0 (kidney) pT1 (kidney) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1 (kidney) pT1a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1a (kidney) pT1b (kidney) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1b (kidney) pT2 (kidney) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2 (kidney) pT2a (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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2a (kidney) pT2b (kidney) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2b (kidney) pT3 (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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3 (kidney) pT3a (kidney) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3a (kidney) pT3b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3b (kidney) pT3c (kidney) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3c (kidney) pT4 (kidney) 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). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT4 (kidney) pT0 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT0 (ovary) pT1 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1 (ovary) pT1a (ovary) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1a (ovary) pT1b (ovary) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1b (ovary) pT1c (ovary) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1c (ovary) pT2 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2 (ovary) pT2a (ovary) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2a (ovary) pT2b (ovary) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2b (ovary) pT2c (ovary) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2c (ovary) pT3 (ovary) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3 (ovary) pT3a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3a (ovary) pT3b (ovary) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3b (ovary) pT3c (ovary) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3c (ovary) pN0 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN0 (colon) pN1 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1 (colon) pN1a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1a (colon) pN1b (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1b (colon) pN1c (colon) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1c (colon) pN2 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2 (colon) pN2a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2a (colon) pN2b (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2b (colon) pN0 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN0 (lung) pN1 (lung) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN1 (lung) pN2 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN2 (lung) pN3 (lung) 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). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN3 (lung) pN0 (kidney) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB pN0 (kidney) pN1 (kidney) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB pN1 (kidney) pN0 (ovary) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB pN0 (ovary) pN1 (ovary) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB pN1 (ovary) cM0 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB cM0 (colon) cM1 (colon) 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. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB cM1 (colon) cM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB cM1a (colon) cM1b (colon) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB cM1b (colon) pM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1 (colon) pM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1a (colon) pM1b (colon) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1b (colon) cM0 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM0 (lung) cM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1 (lung) cM1a (lung) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1a (lung) cM1b (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1b (lung) pM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1 (lung) pM1a (lung) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1a (lung) pM1b (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1b (lung) cM0 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB cM0 (kidney) cM1 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB cM1 (kidney) pM1 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB pM1 (kidney) cM0 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB cM0 (ovary) cM1 (ovary) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB cM1 (ovary) pM1 (ovary) 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. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB pM1 (ovary) Occult Carcinoma (AJCC 7th) 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. Chris Stoeckert, Helena Ellis Occult Carcinoma http://www.medilexicon.com/dictionary/14371 NCI BBRB Occult Carcinoma (AJCC 7th) Stage 0 (AJCC 7th) 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. Chris Stoeckert, Helena Ellis Stage 0 https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage 0 (AJCC 7th) Stage I (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. Chris Stoeckert, Helena Ellis Stage I https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage I (AJCC 7th) Stage IIA (AJCC 7th) 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. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIA (AJCC 7th) Stage IIB (AJCC 7th) 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. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIB (AJCC 7th) Stage IIC (AJCC 7th) 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. Chris Stoeckert, Helena Ellis Stage IIC https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIC (AJCC 7th) Stage IIIA (AJCC 7th) 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. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIA (AJCC 7th) Stage IIIB (AJCC 7th) 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. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIB (AJCC 7th) Stage IIIC (AJCC 7th) 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. Chris Stoeckert, Helena Ellis Stage IIIC https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIC (AJCC 7th) Stage IVA (AJCC 7th) 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. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IVA (AJCC 7th) Stage IVB (AJCC 7th) 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. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IVB (AJCC 7th) Stage IA (FIGO) 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. Chris Stoeckert, Helena Ellis Stage IA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA (FIGO) Stage IA1 (FIGO) 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. Chris Stoeckert, Helena Ellis Stage IA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA1 (FIGO) Stage IA2 (FIGO) 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. Chris Stoeckert, Helena Ellis Stage IA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA2 (FIGO) Stage IB (FIGO) 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 Chris Stoeckert, Helena Ellis Stage IB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB (FIGO) Stage IB1 (FIGO) 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. Chris Stoeckert, Helena Ellis Stage IB1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB1 (FIGO) Stage IB2 (FIGO) 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. Chris Stoeckert, Helena Ellis Stage IB2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB2 (FIGO) Stage IIA (FIGO) 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. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA (FIGO) Stage IIA1 (FIGO) 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. Chris Stoeckert, Helena Ellis Stage IIA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA1 (FIGO) Stage IIA2 (FIGO) 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. Chris Stoeckert, Helena Ellis Stage IIA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA2 (FIGO) Stage IIB (FIGO) 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. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIB (FIGO) Stage IIIA (FIGO) 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. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIIA (FIGO) Stage IIIB (FIGO) 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. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIIB (FIGO) Stage IVA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IVA (FIGO) Stage IVB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IVB (FIGO) Stage 1 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1 (FIGO) Stage 1A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1A (FIGO) Stage 1B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1B (FIGO) Stage 1C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1C (FIGO) Stage 2 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2 (FIGO) Stage 2A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2A (FIGO) Stage 2B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2B (FIGO) Stage 2C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2C (FIGO) Stage 3 (FIGO) 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). Chris Stoeckert, Helena Ellis Stage 3 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3 (FIGO) Stage 3A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3A (FIGO) Stage 3B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3B (FIGO) Stage 3C (FIGO) 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). Chris Stoeckert, Helena Ellis Stage 3C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3C (FIGO) Stage 4 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. Chris Stoeckert, Helena Ellis Stage 4 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 4 (FIGO) Stage Unknown (FIGO) 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). Chris Stoeckert, Helena Ellis Stage Unknown https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage Unknown (FIGO) 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. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 3: symptomatic in bed more than 50% of the day but 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. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 2: symptomatic but in bed less than 50% of the day 4: bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 4: bed ridden 0: asymptomatic An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 0: asymptomatic 1: symptomatic but fully ambulatory An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 1: symptomatic but fully ambulatory 100: asymptomatic A Karnofsky score vaue specification indicating that a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 100: asymptomatic 80-90: symptomatic but fully ambulatory A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 80-90: 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. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 60-70: 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. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden meter 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. m meter kilogram A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. kg kilogram second 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. s sec second centimeter A length unit which is equal to one hundredth of a meter or 10^[-2] m. cm centimeter millimeter A length unit which is equal to one thousandth of a meter or 10^[-3] m. mm millimeter micrometer A length unit which is equal to one millionth of a meter or 10^[-6] m. um micrometer nanometer A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. nm nanometer angstrom A length unit which is equal to 10 [-10] m. angstrom gram A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. g gram milligram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. mg milligram microgram A mass unit which is equal to one millionth of a gram or 10^[-6] g. ug microgram nanogram A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. ng nanogram picogram A mass unit which is equal to 10^[-12] g. pg picogram degree Celsius 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. C degree C degree Celsius minute A time unit which is equal to 60 seconds. min minute hour A time unit which is equal to 3600 seconds or 60 minutes. h hr hour day A time unit which is equal to 24 hours. day week A time unit which is equal to 7 days. week month 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. month year A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. year micromole A substance unit equal to a millionth of a mol or 10^[-6] mol. umol micromole nanomole A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. nmol nanomole picomole A substance unit equal to 10^[-12] mol. pmol picomole molar A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). M molar millimolar A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. mM millimolar micromolar A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. uM micromolar nanomolar A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. nM nanomolar picomolar A unit of molarity which is equal to 10^[-12] M. pM picomolar cubic centimeter A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. cc cubic centimeter milliliter A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. ml milliliter liter A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. L liter cubic decimeter A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. cubic decimeter microliter A volume unit which is equal to one millionth of a liter or 10^[-6] L. ul microliter nanoliter A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. nl nanoliter picoliter A volume unit which is equal to 10^[-12] L. pl picoliter hertz A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. hertz mass percentage A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. % w/w percent weight pr weight mass percentage mass volume percentage A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. % w/v percent vol per vol mass volume percentage volume percentage A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. % v/v percent vol per vol volume percentage gram per liter A mass unit density which is equal to mass of an object in grams divided by the volume in liters. g per L g/L gram per liter milligram per milliliter A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. mg per ml mg/ml milligram per milliliter degree Fahrenheit A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. degree Fahrenheit pH A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). pH milliliter per liter A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. ml per L ml/l milliliter per liter gram per deciliter A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. g/dl gram per deciliter colony forming unit per volume A concentration unit which a measure of viable bacterial numbers in a given volume. colony forming unit per volume microliters per minute A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. microliters per minute count per nanomolar second A rate unit which is equal to one over one nanomolar second. count per nanomolar second count per molar second A rate unit which is equal to one over one molar second. count per molar second count per nanomolar A rate unit which is equal to one over one nanomolar. count per nanomolar count per molar A rate unit which is equal to one over one molar. count per molar microgram per liter A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. ng/ml ug/L microgram per liter