Evidence & Conclusion Ontology (ECO)
type: Ontology
version IRI: eco.owl
description: 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.
license: https://creativecommons.org/publicdomain/zero/1.0/
date: 20:10:2021 16:01
default-namespace: eco
comment: 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.

has GO evidence code
type: AnnotationProperty

example of usage
type: AnnotationProperty
definition: 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.

definition
type: AnnotationProperty
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.

term editor
type: AnnotationProperty
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

definition source
type: AnnotationProperty
definition: 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

ontology term requester
type: AnnotationProperty
definition: The 'term requester' can credit the person, organization or project who request the ontology term.,The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.

go_groupings
type: AnnotationProperty
comment: Grouping classes used by GO
sub property of: subset_property

valid_with_biological_process
type: AnnotationProperty
comment: GO biological process terms should be used in the GO with/from field
sub property of: subset_property

valid_with_cellular_component
type: AnnotationProperty
comment: GO cellular component terms should be used in the GO with/from field
sub property of: subset_property

valid_with_chemical_entity
type: AnnotationProperty
comment: Chemical entity IDs should be used in the GO with/from field
sub property of: subset_property

valid_with_gene
type: AnnotationProperty
comment: Gene IDs should be used in the GO with/from field
sub property of: subset_property

valid_with_molecular_function
type: AnnotationProperty
comment: GO molecular function terms should be used in the GO with/from field
sub property of: subset_property

valid_with_protein
type: AnnotationProperty
comment: Protein IDs should be used in the GO with/from field
sub property of: subset_property

valid_with_protein_complex
type: AnnotationProperty
comment: Protein complex IDs should be used in the GO with/from field
sub property of: subset_property

valid_with_transcript
type: AnnotationProperty
comment: Transcript IDs should be used in the GO with/from field
sub property of: subset_property

description
type: AnnotationProperty

title
type: AnnotationProperty

license
type: AnnotationProperty

subset_property
type: AnnotationProperty

auto-generated-by
type: AnnotationProperty

created_by
type: AnnotationProperty

creation_date
type: AnnotationProperty

date
type: AnnotationProperty

default-namespace
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

id
type: AnnotationProperty

in_subset
type: AnnotationProperty

is_inferred
type: AnnotationProperty

saved-by
type: AnnotationProperty

shorthand
type: AnnotationProperty

part of
type: ObjectProperty
equivalent property:
  inverse of: has part
inverse of: has part
type: TransitiveProperty
definition: a core relation that holds between a part and its whole
id: part_of

has part
type: ObjectProperty
equivalent property:
  inverse of: part of
type: TransitiveProperty
definition: a core relation that holds between a whole and its part
id: has_part

realized in
type: ObjectProperty
equivalent property:
  inverse of: realizes
inverse of: realizes
domain: realizable entity
range: process

realizes
type: ObjectProperty
equivalent property:
  inverse of: realized in
domain: process
range: realizable entity

preceded by
type: ObjectProperty
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent

precedes
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
domain: occurrent
range: occurrent

used_in
type: ObjectProperty
inverse of: uses
domain: evidence
range: assertion method
definition: A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence.
created_by: mchibucos
creation_date: 2010-12-09T05:00:20Z
database_cross_reference: ECO:9000000
has_obo_namespace: eco
id: used_in
shorthand: used_in
comment: In the future we may use a more generic relation with weaker domain and range constraints taken from IAO, RO or OBI.

Axiom
annotated source: used_in
annotated property: definition
annotated target: A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence.
database_cross_reference: GOC:cjm

uses
type: ObjectProperty
database_cross_reference: ECO:9000001
has_obo_namespace: eco
id: uses
shorthand: uses

has measurement unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
range: IAO_0000003

is about
type: ObjectProperty
domain: IAO_0000030
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.

is quality measurement of
type: ObjectProperty
equivalent property:
  inverse of: is quality measured as
sub property of: is about
inverse of: is quality measured as
domain: IAO_0000109
range: quality
definition: m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q

is duration of
type: ObjectProperty
sub property of: is about
domain: IAO_0000416
range: process
definition: relates a process to a time-measurement-datum that represents the duration of the process

is quality measured as
type: ObjectProperty
equivalent property:
  inverse of: is quality measurement of
definition: inverse of the relation of is quality measurement of

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has participant
inverse of: is_specified_input_of
domain: OBI_0000011
definition: 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.

is_specified_input_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_input
sub property of: participates in
range: OBI_0000011
definition: 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.

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has participant
inverse of: is_specified_output_of
domain: OBI_0000011
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.

is_manufactured_by
type: ObjectProperty
domain: material entity
range: Class
  union of: NCBITaxon 9606
  union of: OBI_0000245
definition: 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.

is_specified_output_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_output
sub property of: participates in
range: OBI_0000011
definition: 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.

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: OBI_0000011
range: IAO_0000005
definition: 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.

has grain
type: ObjectProperty
sub property of: has part
definition: 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.

supplies
type: ObjectProperty
inverse of: has_supplier
definition: 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.

has_supplier
type: ObjectProperty
domain: material entity
range: Class
  union of: NCBITaxon 9606
  union of: OBI_0000245
definition: 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.

objective_achieved_by
type: ObjectProperty
domain: IAO_0000005
range: OBI_0000011
definition: This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.

has value specification
type: ObjectProperty
sub property of: has part
domain: IAO_0000030
range: OBI_0001933
definition: A relation between an information content entity and a value specification that specifies its value.

bound_to
type: ObjectProperty
domain: material entity
range: material entity
definition: A relationship between two material entities that form a complex based on a selective, non-covalent interaction.

inheres in
type: ObjectProperty
equivalent property:
  inverse of: bearer of
inverse of: bearer of
definition: 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

bearer of
type: ObjectProperty
equivalent property:
  inverse of: inheres in
range: specifically dependent continuant
definition: 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

participates in
type: ObjectProperty
equivalent property:
  inverse of: has participant
inverse of: has participant
domain: continuant
range: occurrent
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process

has participant
type: ObjectProperty
equivalent property:
  inverse of: participates in
domain: occurrent
range: continuant
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process

is concretized as
type: ObjectProperty
equivalent property:
  inverse of: concretizes
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
definition: 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.

concretizes
type: ObjectProperty
equivalent property:
  inverse of: is concretized as
domain: specifically dependent continuant
range: generically dependent continuant
definition: 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.

function of
type: ObjectProperty
equivalent property:
  inverse of: has function
sub property of: inheres in
inverse of: has function
domain: function
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence

quality of
type: ObjectProperty
equivalent property:
  inverse of: has quality
sub property of: inheres in
inverse of: has quality
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence

role of
type: ObjectProperty
equivalent property:
  inverse of: has role
sub property of: inheres in
inverse of: has role
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence

has function
type: ObjectProperty
equivalent property:
  inverse of: function of
sub property of: bearer of
domain: independent continuant
range: function
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence

has quality
type: ObjectProperty
equivalent property:
  inverse of: quality of
sub property of: bearer of
range: quality
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence

has role
type: ObjectProperty
equivalent property:
  inverse of: role of
sub property of: bearer of
domain: independent continuant
range: role
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence

has disposition
type: ObjectProperty
definition: A relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

derives from
type: ObjectProperty
equivalent property:
  inverse of: derives into
sub property of: topObjectProperty
inverse of: derives into
domain: independent continuant
range: independent continuant
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity

derives into
type: ObjectProperty
equivalent property:
  inverse of: derives from
definition: 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

location of
type: ObjectProperty
equivalent property:
  inverse of: located in
inverse of: located in
type: TransitiveProperty
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location

located in
type: ObjectProperty
equivalent property:
  inverse of: location of
type: TransitiveProperty
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes

immediately precedes
type: ObjectProperty
sub property of: precedes

regulates
type: ObjectProperty
type: TransitiveProperty
id: regulates

negatively regulates
type: ObjectProperty
sub property of: regulates
id: negatively_regulates

positively regulates
type: ObjectProperty
sub property of: regulates
property chain axiom: negatively regulates
id: positively_regulates

temporal relation
type: ObjectProperty
range: occurrent

member of
type: ObjectProperty
equivalent property:
  inverse of: has member
sub property of: part of
inverse of: has member
definition: is member of is a mereological relation between a item and a collection.

has member
type: ObjectProperty
equivalent property:
  inverse of: member of
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.

has measurement value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: IAO_0000032
range: double

has specified numeric value
type: DatatypeProperty
sub property of: has specified value
domain: OBI_0001933
range: real
definition: A relation between a value specification and a number that quantifies it.

has specified value
type: DatatypeProperty
domain: OBI_0001933
definition: A relation between a value specification and a literal.

entity
type: Class

continuant
type: Class
subclass of: entity
disjoint with: occurrent
definition: 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.

occurrent
type: Class
subclass of: entity
definition: An entity that has temporal parts and that happens, unfolds or develops through time.

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.

process
type: Class
subclass of: occurrent
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.

disposition
type: Class
subclass of: realizable entity
disjoint with: role

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
definition: 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.

quality
type: Class
subclass of: specifically dependent continuant

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
definition: 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.

role
type: Class
subclass of: realizable entity
definition: 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.

site
type: Class
subclass of: immaterial entity

generically dependent continuant
type: Class
subclass of: continuant
definition: 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.

function
type: Class
subclass of: disposition

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

immaterial entity
type: Class
subclass of: independent continuant

ATP
type: Class
subclass of: molecular entity
definition: 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.

peptide
type: Class
subclass of: macromolecule
definition: 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.

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.

molecular entity
type: Class
subclass of: material entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.

cytochalasin
type: Class
subclass of: molecular entity

acrylamide
type: Class
subclass of: molecular entity
definition: A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia.

atom
type: Class
subclass of: material entity
definition: A chemical entity constituting the smallest component of an element having the chemical properties of the element.

nucleic acid
type: Class
subclass of: macromolecule
definition: 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.

ribonucleic acid
type: Class
subclass of: nucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.

macromolecule
type: Class
subclass of: molecular entity
definition: 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.

double-stranded DNA
type: Class
subclass of: deoxyribonucleic acid

5-bromo-2'-deoxyuridine
type: Class
subclass of: molecular entity
definition: A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase.

chromium-51
type: Class
subclass of: molecular entity
definition: 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.

tritiated thymidine
type: Class
subclass of: molecular entity
definition: Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis.

fluorescence microscopy
type: Class
subclass of: OBI_0002119
definition: 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.

light microscopy
type: Class
subclass of: OBI_0002119
definition: Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image.

cell
type: Class
subclass of: material entity
definition: 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.

cultured cell
type: Class
subclass of: experimentally modified cell in vitro
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: OBI_0600036
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: OBI_0600036
definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.

B cell
type: Class
subclass of: lymphocyte
definition: A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.

lymphocyte
type: Class
subclass of: mononuclear cell
definition: 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.

experimentally modified cell in vitro
type: Class
subclass of: cell
subclass of: OBI_0000047
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000094
definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.

mononuclear cell
type: Class
subclass of: cell
definition: A leukocyte with a single non-segmented nucleus in the mature form.

evidence
type: Class
disjoint with: assertion method
definition: A type of information that is used to support an assertion.
has_obo_namespace: eco
has_related_synonym: evidence code
has_related_synonym: evidence_code
id: ECO:0000000

Axiom
annotated source: evidence
annotated property: definition
annotated target: A type of information that is used to support an assertion.
database_cross_reference: ECO:MCC

inference from background scientific knowledge
type: Class
subclass of: curator inference
definition: A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator.
has_obo_namespace: eco
id: ECO:0000001

Axiom
annotated source: inference from background scientific knowledge
annotated property: definition
annotated target: A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator.
database_cross_reference: ECO:SN

direct assay evidence
type: Class
subclass of: experimental evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0008150
definition: A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature.
has_alternative_id: ECO:0005006
has_obo_namespace: eco
id: ECO:0000002

Axiom
annotated source: direct assay evidence
annotated property: definition
annotated target: A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature.
database_cross_reference: ECO:SN

reconstitution assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
has_obo_namespace: eco
id: ECO:0000003

Axiom
annotated source: reconstitution assay evidence
annotated property: definition
annotated target: A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
database_cross_reference: ECO:KAV
database_cross_reference: PMID:26029343

cell fractionation evidence
type: Class
subclass of: fractionation evidence
definition: A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
has_obo_namespace: eco
has_related_synonym: cell fractionation
id: ECO:0000004
comment: If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology.

Axiom
annotated source: cell fractionation evidence
annotated property: definition
annotated target: A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
database_cross_reference: ECO:KIM
database_cross_reference: TAIR:TED

enzymatic activity assay evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0003824
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0000427
definition: A type of protein assay evidence where the catalytic activity of an enzyme is determined.
has_alternative_id: ECO:0005001
database_cross_reference: MI:0415
has_exact_synonym: enzyme assay evidence
has_obo_namespace: eco
has_related_synonym: enzyme assays
id: ECO:0000005

Axiom
annotated source: enzymatic activity assay evidence
annotated property: definition
annotated target: A type of protein assay evidence where the catalytic activity of an enzyme is determined.
database_cross_reference: url:http://www.sciencedirect.com/science/article/pii/S2213020914000068

enzymatic study
type: Axiom
annotated source: enzymatic activity assay evidence
annotated property: database_cross_reference
annotated target: MI:0415

experimental evidence
type: Class
subclass of: evidence
subclass of: IAO_0000030
subclass of: Restriction
  on property: is about
  some values from: process
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0500000
definition: A type of evidence resulting from manipulation of variables in order to discover cause and effect.
has_alternative_id: ECO:0005023
has_obo_namespace: eco
id: ECO:0000006
in_subset: go_groupings

Axiom
annotated source: experimental evidence
annotated property: definition
annotated target: A type of evidence resulting from manipulation of variables in order to discover cause and effect.
database_cross_reference: url:http://holah.co.uk/page/experimental/

Axiom
annotated source: experimental evidence
annotated property: subClassOf
annotated target: IAO_0000030
is_inferred: true

immunofluorescence evidence
type: Class
subclass of: protein detection assay evidence
definition: 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.
has_obo_namespace: eco
has_related_synonym: immunofluorescence
id: ECO:0000007

Axiom
annotated source: immunofluorescence evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: TAIR:TED

expression pattern evidence
type: Class
subclass of: experimental evidence
example of usage: The 10 previously identified GlnR-regulated genes were all confirmed to be under GlnR control during nitrogen stress (i.e. differential expression in the wild type compared to the DeltaglnR mutant), but in addition a total of 392 genes were significantly up-regulated and 291 significantly down regulated (Additional file 1: Table S1). This indicates that GlnR mediates (directly or indirectly) the expression of over 680 genes.
definition: A type of experimental evidence that is based on characterization of gene expression.
has_obo_namespace: eco
id: ECO:0000008
comment: 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.

Axiom
annotated source: expression pattern evidence
annotated property: example of usage
annotated target: The 10 previously identified GlnR-regulated genes were all confirmed to be under GlnR control during nitrogen stress (i.e. differential expression in the wild type compared to the DeltaglnR mutant), but in addition a total of 392 genes were significantly up-regulated and 291 significantly down regulated (Additional file 1: Table S1). This indicates that GlnR mediates (directly or indirectly) the expression of over 680 genes.
database_cross_reference: PMID:23642041

Axiom
annotated source: expression pattern evidence
annotated property: definition
annotated target: A type of experimental evidence that is based on characterization of gene expression.
database_cross_reference: ECO:MCC
database_cross_reference: GO:IEP

transcript expression evidence
type: Class
subclass of: expression pattern evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0010467
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000424
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001430
definition: A type of expression pattern evidence where abundance of a transcript is analyzed.
has_alternative_id: ECO:0000048
has_exact_synonym: transcript expression level evidence
has_exact_synonym: transcriptomics evidence
has_obo_namespace: eco
id: ECO:0000009

Axiom
annotated source: transcript expression evidence
annotated property: definition
annotated target: A type of expression pattern evidence where abundance of a transcript is analyzed.
database_cross_reference: ECO:RCT

protein expression evidence
type: Class
subclass of: expression pattern evidence
example of usage: In the BL21(DE3)(pJS429) cells, the levels of ClpP2s and VapC10 remained unchanged over a 2-hour period of translation arrest, but the VapB10 level showed to be decreased with a half-life (Figure 7C) similar to that observed in the strain BL21(DE3)(pJS883) (Figure 7B). These indicate that ClpXP2s could degrade VapB10 regardless of the presence or absence of VapC10.
definition: A type of expression pattern evidence resulting from protein abundance quantification techniques.
has_alternative_id: ECO:0000046
has_exact_synonym: protein expression level evidence
has_obo_namespace: eco
id: ECO:0000010

Axiom
annotated source: protein expression evidence
annotated property: example of usage
annotated target: In the BL21(DE3)(pJS429) cells, the levels of ClpP2s and VapC10 remained unchanged over a 2-hour period of translation arrest, but the VapB10 level showed to be decreased with a half-life (Figure 7C) similar to that observed in the strain BL21(DE3)(pJS883) (Figure 7B). These indicate that ClpXP2s could degrade VapB10 regardless of the presence or absence of VapC10.
database_cross_reference: PMID:24260461

Axiom
annotated source: protein expression evidence
annotated property: definition
annotated target: A type of expression pattern evidence resulting from protein abundance quantification techniques.
database_cross_reference: NBK:22011
database_cross_reference: PMC:4029002
database_cross_reference: url:http://www.informatics.jax.org/glossary/gain-of-function
database_cross_reference: 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

genetic interaction evidence
type: Class
subclass of: experimental phenotypic evidence
definition: A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products.
database_cross_reference: TAIR:TED
has_obo_namespace: eco
id: ECO:0000011

Axiom
annotated source: genetic interaction evidence
annotated property: definition
annotated target: A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products.
database_cross_reference: ECO:RCT
database_cross_reference: PMID:11822023

functional complementation evidence
type: Class
subclass of: genetic interaction evidence
example of usage: In addition, complementation of the ompR mutation in strain AR6 with plasmid pBR3 resulted in an increase in beta-galactosidase activity (1303 +- 80 Miller units), indicating that the His-tagged OmpR protein, expressed from the gene introduced in trans, was able to positively regulate flhDC expression.
example of usage: Trans-complementation of fimR on pDL276 (pHR6) in strain DeltafimR harboring pfim(445 b)-cat restored wild-type pfim expression (Figure S1). Taken together, pfim is negatively regulated by FimR.
definition: 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.
has_obo_namespace: eco
has_related_synonym: functional complementation
id: ECO:0000012

Axiom
annotated source: functional complementation evidence
annotated property: example of usage
annotated target: In addition, complementation of the ompR mutation in strain AR6 with plasmid pBR3 resulted in an increase in beta-galactosidase activity (1303 +- 80 Miller units), indicating that the His-tagged OmpR protein, expressed from the gene introduced in trans, was able to positively regulate flhDC expression.
database_cross_reference: PMID:20830609

Axiom
annotated source: functional complementation evidence
annotated property: example of usage
annotated target: Trans-complementation of fimR on pDL276 (pHR6) in strain DeltafimR harboring pfim(445 b)-cat restored wild-type pfim expression (Figure S1). Taken together, pfim is negatively regulated by FimR.
database_cross_reference: PMID:23823757

Axiom
annotated source: functional complementation evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:27403640

transgenic rescue experiment evidence
type: Class
subclass of: functional complementation evidence
definition: A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
has_obo_namespace: eco
id: ECO:0000013

Axiom
annotated source: transgenic rescue experiment evidence
annotated property: definition
annotated target: A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
database_cross_reference: url:http://www.mdpi.com/1420-3049/19/9/13932/pdf
database_cross_reference: url:http://www.nature.com/gt/journal/v11/n15/full/3302282a.html

mutant phenotype evidence
type: Class
subclass of: experimental phenotypic evidence
example of usage: Indeed, the GroEL protein appears to be more abundant in the LM3 wild type strain compared to the LM3-2 mutant strain, suggesting the involvement of the CcpA protein in the positive regulation of its expression.
definition: A type of experimental phenotypic evidence in which an observable phenotypic difference results from a change or mutation in DNA.
has_obo_namespace: eco
id: ECO:0000015
comment: Note that mutations need not be negative. Changes to DNA sequence (mutations) may be detrimental, have no impact, or be beneficial.
comment: The allele that encodes the phenotype most common in a particular natural population is referred to as the wild type allele, while any other form of that allele is known as the mutant form.

Axiom
annotated source: mutant phenotype evidence
annotated property: example of usage
annotated target: Indeed, the GroEL protein appears to be more abundant in the LM3 wild type strain compared to the LM3-2 mutant strain, suggesting the involvement of the CcpA protein in the positive regulation of its expression.
database_cross_reference: PMID:17129387

Axiom
annotated source: mutant phenotype evidence
annotated property: definition
annotated target: A type of experimental phenotypic evidence in which an observable phenotypic difference results from a change or mutation in DNA.
database_cross_reference: GO:IMP

loss-of-function mutant phenotype evidence
type: Class
subclass of: mutant phenotype evidence
definition: 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.
has_obo_namespace: eco
id: ECO:0000016

Axiom
annotated source: loss-of-function mutant phenotype evidence
annotated property: definition
annotated target: 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.
database_cross_reference: SO:0002054

ectopic expression evidence
type: Class
subclass of: experimental phenotypic evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600043
definition: 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.
has_obo_namespace: eco
has_related_synonym: analysis of overexpression/ectopic expression phenotype
id: ECO:0000017

Axiom
annotated source: ectopic expression evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:10948520
database_cross_reference: PMID:19301619

anti-sense experiment evidence
type: Class
subclass of: mutant phenotype evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0009300
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001672
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001358
definition: 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.
has_obo_namespace: eco
has_related_synonym: anti-sense experiments
id: ECO:0000018

Axiom
annotated source: anti-sense experiment evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN

RNAi evidence
type: Class
subclass of: mutant phenotype evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0070549
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001672
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001358
definition: 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.
has_obo_namespace: eco
has_related_synonym: RNAi experiment
id: ECO:0000019

Axiom
annotated source: RNAi evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

protein inhibition evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0048519
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0002590
definition: A type of direct assay evidence based on the inhibition of the molecular function of a protein.
has_narrow_synonym: specific protein inhibition evidence
has_obo_namespace: eco
id: ECO:0000020

Axiom
annotated source: protein inhibition evidence
annotated property: definition
annotated target: A type of direct assay evidence based on the inhibition of the molecular function of a protein.
database_cross_reference: ECO:MCC

physical interaction evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0005488
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001146
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0002590
definition: A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
has_alternative_id: ECO:0005025
database_cross_reference: MI:0045
has_obo_namespace: eco
id: ECO:0000021
comment: Molecules interacted with might include protein, nucleic acid, ion, or complex.

Axiom
annotated source: physical interaction evidence
annotated property: definition
annotated target: A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
database_cross_reference: ECO:SN

experimental interaction detection
type: Axiom
annotated source: physical interaction evidence
annotated property: database_cross_reference
annotated target: MI:0045

co-purification evidence
type: Class
subclass of: physical interaction evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0001505
definition: A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
database_cross_reference: MI:0025
has_obo_namespace: eco
has_related_synonym: co-purification
id: ECO:0000022

Axiom
annotated source: co-purification evidence
annotated property: definition
annotated target: A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
database_cross_reference: TAIR:TED

copurification
type: Axiom
annotated source: co-purification evidence
annotated property: database_cross_reference
annotated target: MI:0025

affinity evidence
type: Class
subclass of: physical interaction evidence
definition: A type of physical interaction evidence that depends on the strength of the interaction between two entities.
database_cross_reference: MI:0400
has_narrow_synonym: ligand binding evidence
has_obo_namespace: eco
id: ECO:0000023

Axiom
annotated source: affinity evidence
annotated property: definition
annotated target: A type of physical interaction evidence that depends on the strength of the interaction between two entities.
database_cross_reference: ECO:MCC
database_cross_reference: PSI-MI:MI:0400

affinity technology
type: Axiom
annotated source: affinity evidence
annotated property: database_cross_reference
annotated target: MI:0400

protein binding evidence
type: Class
subclass of: affinity evidence
definition: A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex.
has_obo_namespace: eco
id: ECO:0000024

Axiom
annotated source: protein binding evidence
annotated property: definition
annotated target: A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex.
database_cross_reference: GO:0005515
database_cross_reference: url:https://en.wikipedia.org/wiki/Mutation

bait-prey hybrid interaction evidence
type: Class
subclass of: protein binding evidence
definition: A type of protein binding 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.
ontology term requester: DisProt:FedericaQuaglia
database_cross_reference: MI:0090
has_exact_synonym: bait-prey protein pull-down evidence
has_obo_namespace: eco
id: ECO:0000025
comment: 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.

Axiom
annotated source: bait-prey hybrid interaction evidence
annotated property: definition
annotated target: A type of protein binding 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.
database_cross_reference: ECO:MCC
database_cross_reference: PSI-MI:MI:0090

protein complementation assay
type: Axiom
annotated source: bait-prey hybrid interaction evidence
annotated property: database_cross_reference
annotated target: MI:0090

nucleic acid hybridization evidence
type: Class
definition: 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.
has_obo_namespace: eco
id: ECO:0000026
comment: This term has been made obsolete with the clean up of experimental genomic evidence branch.
deprecated: true

Axiom
annotated source: nucleic acid hybridization evidence
annotated property: definition
annotated target: 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.
database_cross_reference: OBI:0302903

structural similarity evidence
type: Class
subclass of: phenotypic similarity evidence
example of usage: The secondary structure of VapC10 (Figure S2), predicted with the 3DJIGSAW prediction tool [36] and the DALI server [37], exhibited homology with several well studied VapC toxins, such as the first PIN domain structure for the protein PAE2754 from the archae bacterium Pyrobaculum aerophilum (30).
definition: A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
has_obo_namespace: eco
id: ECO:0000027
comment: 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.

Axiom
annotated source: structural similarity evidence
annotated property: example of usage
annotated target: The secondary structure of VapC10 (Figure S2), predicted with the 3DJIGSAW prediction tool [36] and the DALI server [37], exhibited homology with several well studied VapC toxins, such as the first PIN domain structure for the protein PAE2754 from the archae bacterium Pyrobaculum aerophilum (30).
database_cross_reference: PMID:24260461

Axiom
annotated source: structural similarity evidence
annotated property: definition
annotated target: A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
database_cross_reference: ECO:MCC
database_cross_reference: TAIR:TED

motif similarity evidence
type: Class
subclass of: match to sequence model evidence
example of usage: A CRP box-like sequence was found in the promoter-proximate region of sycO-ypkA-yopJ [4], indicating the direct association of CRP with the sycO-ypkA-yopJ promoter region.
example of usage: To identify further CopR target genes, the binding motif TGAAGATTTnnTGAAGATTT was used to search for similar sequences in the whole C. glutamicum genome using the ERGO (TM) bioinformatics suite (Integrated Genomics, Illinois, USA) allowing four mutations, no deletions and no insertions. 46 hits were found, but only in six cases the putative CopR binding site was located in intergenic regions up to 200 bp upstream of the start codon of the neighbouring gene (cg1336, cg2976, cg3187, cg3337, cg3357 and cg0414).
definition: 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.
has_obo_namespace: eco
has_related_synonym: recognized domains
id: ECO:0000028

Axiom
annotated source: motif similarity evidence
annotated property: example of usage
annotated target: A CRP box-like sequence was found in the promoter-proximate region of sycO-ypkA-yopJ [4], indicating the direct association of CRP with the sycO-ypkA-yopJ promoter region.
database_cross_reference: PMID:19703315

Axiom
annotated source: motif similarity evidence
annotated property: example of usage
annotated target: To identify further CopR target genes, the binding motif TGAAGATTTnnTGAAGATTT was used to search for similar sequences in the whole C. glutamicum genome using the ERGO (TM) bioinformatics suite (Integrated Genomics, Illinois, USA) allowing four mutations, no deletions and no insertions. 46 hits were found, but only in six cases the putative CopR binding site was located in intergenic regions up to 200 bp upstream of the start codon of the neighbouring gene (cg1336, cg2976, cg3187, cg3337, cg3357 and cg0414).
database_cross_reference: PMID:21799779

Axiom
annotated source: motif similarity evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN

match to InterPro member signature evidence
type: Class
subclass of: match to sequence model evidence
definition: 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.
has_obo_namespace: eco
id: ECO:0000029

Axiom
annotated source: match to InterPro member signature evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMC:2686546
database_cross_reference: url:http://www.ncbi.nlm.nih.gov/mesh?term=Nucleic+Acid+Hybridization

BLAST evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: BLAST evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: BLAST evidence
subclass of: pairwise sequence alignment evidence used in manual assertion
has GO evidence code: ISA
definition: A type of BLAST evidence that is used in a manual assertion.
has_obo_namespace: eco
has_related_synonym: curated BLAST analysis
id: ECO:0000030

Axiom
annotated source: BLAST evidence used in manual assertion
annotated property: subClassOf
annotated target: pairwise sequence alignment evidence used in manual assertion
is_inferred: true

Axiom
annotated source: BLAST evidence used in manual assertion
annotated property: definition
annotated target: A type of BLAST evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

protein BLAST evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein BLAST evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: BLAST evidence used in manual assertion
subclass of: protein BLAST evidence
has GO evidence code: ISA
definition: A type of protein BLAST evidence that is used in a manual assertion.
database_cross_reference: GO_REF:0000012
database_cross_reference: GO_REF:0000027
has_obo_namespace: eco
has_related_synonym: curated protein BLAST analysis
id: ECO:0000031

Axiom
annotated source: protein BLAST evidence used in manual assertion
annotated property: subClassOf
annotated target: BLAST evidence used in manual assertion
is_inferred: true

Axiom
annotated source: protein BLAST evidence used in manual assertion
annotated property: definition
annotated target: A type of protein BLAST evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

Pairwise alignment (TIGR)
type: Axiom
annotated source: protein BLAST evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000012

BLAST search criteria for ISS assignment in PAMGO_GAT
type: Axiom
annotated source: protein BLAST evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000027

nucleotide BLAST evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: nucleotide BLAST evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: BLAST evidence used in manual assertion
subclass of: nucleotide BLAST evidence
has GO evidence code: ISA
definition: A type of nucleotide BLAST evidence that is used in a manual assertion.
has_obo_namespace: eco
has_related_synonym: curated nucleic acid BLAST analysis
id: ECO:0000032

Axiom
annotated source: nucleotide BLAST evidence used in manual assertion
annotated property: subClassOf
annotated target: BLAST evidence used in manual assertion
is_inferred: true

Axiom
annotated source: nucleotide BLAST evidence used in manual assertion
annotated property: definition
annotated target: A type of nucleotide BLAST evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

author statement supported by traceable reference
type: Class
subclass of: author statement
disjoint with: author statement without traceable support
definition: 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.
has_obo_namespace: eco
has_related_synonym: traceable author statement
id: ECO:0000033

Axiom
annotated source: author statement supported by traceable reference
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT
database_cross_reference: GO:TAS

author statement without traceable support
type: Class
subclass of: author statement
definition: A type of author statement that is not associated with results presented or a cited reference.
has_obo_namespace: eco
has_related_synonym: non-traceable author statement
id: ECO:0000034

Axiom
annotated source: author statement without traceable support
annotated property: definition
annotated target: A type of author statement that is not associated with results presented or a cited reference.
database_cross_reference: ECO:SN

no evidence data found
type: Class
subclass of: curator inference
definition: A type of curator inference that results when research finds no evidence information in the scientific literature, at reference databases, or from other resources.
has_obo_namespace: eco
id: ECO:0000035
comment: An assertion of "no evidence data found" carries the assumption that a more-or-less exhaustive search has been conducted.

Axiom
annotated source: no evidence data found
annotated property: definition
annotated target: A type of curator inference that results when research finds no evidence information in the scientific literature, at reference databases, or from other resources.
database_cross_reference: ECO:SN

not_recorded
type: Class
has_obo_namespace: eco
id: ECO:0000037
comment: The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations.
deprecated: true

transient rescue experiment evidence
type: Class
subclass of: functional complementation evidence
definition: A type of functional complementation evidence resulting from the introduction of nucleic acids, which are not permanently incorporated into the genome, to temporarily prevent, or "rescue" an organism from a condition.
has_obo_namespace: eco
id: ECO:0000038

protein assay evidence
type: Class
definition: A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins.
has_alternative_id: ECO:0005022
has_obo_namespace: eco
id: ECO:0000039
deprecated: true

Axiom
annotated source: protein assay evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins.
database_cross_reference: PMID:18429326

immunological assay evidence
type: Class
subclass of: affinity evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0003823
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000443
definition: A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
has_alternative_id: ECO:0005018
has_obo_namespace: eco
id: ECO:0000040

Axiom
annotated source: immunological assay evidence
annotated property: definition
annotated target: A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
database_cross_reference: ERO:0001362
database_cross_reference: url:http://www.ncbi.nlm.nih.gov/books/NBK21589/,http://cores.ucsf.edu/protein-assay.html

similarity evidence
type: Class
subclass of: evidence
definition: A type of evidence resulting from comparing likeness of distinct biological entities.
has_exact_synonym: IS
has_obo_namespace: eco
has_related_synonym: inferred from similarity
id: ECO:0000041

Axiom
annotated source: similarity evidence
annotated property: definition
annotated target: A type of evidence resulting from comparing likeness of distinct biological entities.
database_cross_reference: ECO:SN

gain-of-function mutant phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
definition: A type of mutant phenotype evidence resulting from an altered gene product which possesses a new molecular function or a new pattern of gene expression.
has_exact_synonym: gain-of-function mutant phenotype evidence
has_obo_namespace: eco
id: ECO:0000042

Axiom
annotated source: gain-of-function mutant phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from an altered gene product which possesses a new molecular function or a new pattern of gene expression.
database_cross_reference: SO:0002053
database_cross_reference: url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614608/

sequence similarity evidence
type: Class
subclass of: similarity evidence
subclass of: ECO_0007672
definition: A type of similarity based on biomolecular sequence.
has_obo_namespace: eco
id: ECO:0000044
comment: 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.

Axiom
annotated source: sequence similarity evidence
annotated property: definition
annotated target: A type of similarity based on biomolecular sequence.
database_cross_reference: ECO:MCC
database_cross_reference: TAIR:TED

spatial pattern of protein expression evidence
type: Class
subclass of: protein expression evidence
definition: A type of protein expression evidence that accounts for the position of RNA translation to a protein product ranging in scale from differing tissues to regions of an anatomical structure.
has_obo_namespace: eco
id: ECO:0000045

spatial pattern of transcript expression evidence
type: Class
subclass of: transcript expression evidence
definition: A type of transcript expression evidence that accounts for the position of transcription ranging in scale from the position of genes on the chromosome to differing tissues to regions of an anatomical structure.
has_obo_namespace: eco
id: ECO:0000047

reporter gene assay evidence
type: Class
subclass of: expression pattern evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0010467
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002082
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
definition: A type of expression pattern evidence that is based on the expression pattern of a reporter gene.
has_obo_namespace: eco
has_related_synonym: expression of a reporter gene
id: ECO:0000049

Axiom
annotated source: reporter gene assay evidence
annotated property: definition
annotated target: A type of expression pattern evidence that is based on the expression pattern of a reporter gene.
database_cross_reference: TAIR:TED

voucher specimen phenotypic analysis evidence
type: Class
subclass of: experimental phenotypic evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0500010
definition: A type of experimental phenotypic evidence based on an authors phenotypic description of a species (or higher-level group), which explicitly references an observation made of a voucher specimen (a specimen with a permanent museum catalog).
has_exact_synonym: IVS
has_exact_synonym: voucher specimen analysis evidence
has_obo_namespace: eco
id: ECO:0000050

Axiom
annotated source: voucher specimen phenotypic analysis evidence
annotated property: definition
annotated target: A type of experimental phenotypic evidence based on an authors phenotypic description of a species (or higher-level group), which explicitly references an observation made of a voucher specimen (a specimen with a permanent museum catalog).
database_cross_reference: TAIR:TED

genetic similarity evidence
type: Class
subclass of: similarity evidence
definition: A type of similarity based on genotype without respect to expression.
has_exact_synonym: IGTS
has_obo_namespace: eco
has_related_synonym: inferred from genetic similarity
id: ECO:0000051
comment: 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.

Axiom
annotated source: genetic similarity evidence
annotated property: definition
annotated target: A type of similarity based on genotype without respect to expression.
database_cross_reference: ECO:MCC
database_cross_reference: PhenoScape:IGTS

suppressor/enhancer interaction phenotypic evidence
type: Class
subclass of: genetic interaction evidence
definition: A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
database_cross_reference: TAIR:TED
has_exact_synonym: suppressor/enhancer interaction evidence
has_obo_namespace: eco
has_related_synonym: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)
id: ECO:0000052

Axiom
annotated source: suppressor/enhancer interaction phenotypic evidence
annotated property: definition
annotated target: A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
database_cross_reference: url:http://biorxiv.org/content/early/2015/10/03/021592
database_cross_reference: url:http://www.wormbook.org/chapters/www:geneticsuppression/geneticsuppression.html

automatically integrated combinatorial evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: ECO_0007673
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: combinatorial evidence used in automatic assertion
subclass of: ECO_0007673
has GO evidence code: IEA
definition: A type of automatically integrated combinatorial evidence that is used in an automatic assertion.
has_alternative_id: ECO:0000246
database_cross_reference: TAIR:TED
has_obo_namespace: eco
id: ECO:0000053
comment: 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.

Axiom
annotated source: automatically integrated combinatorial evidence used in automatic assertion
annotated property: subClassOf
annotated target: combinatorial evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: automatically integrated combinatorial evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007673
is_inferred: true

Axiom
annotated source: automatically integrated combinatorial evidence used in automatic assertion
annotated property: definition
annotated target: A type of automatically integrated combinatorial evidence that is used in an automatic assertion.
database_cross_reference: ECO:MCC
database_cross_reference: ECO:RCT

double mutant phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
example of usage: In the hns slyA double mutant, hlyE expression was twofold greater than in the parent, and slightly higher than the hns single mutant, suggesting that slyA has a small negative effect on hlyE expressionin the absence of H-NS.
definition: A type of mutant phenotype evidence resulting from an experiment typically constructed to determine if two different genes have an observable genetic interaction (functional connection) as the result of a mutation occurring in the alleles of the two genes of interest.
has_exact_synonym: double mutant phenotype evidence
has_obo_namespace: eco
has_related_synonym: double mutant analysis
id: ECO:0000054

Axiom
annotated source: double mutant phenotypic evidence
annotated property: example of usage
annotated target: In the hns slyA double mutant, hlyE expression was twofold greater than in the parent, and slightly higher than the hns single mutant, suggesting that slyA has a small negative effect on hlyE expressionin the absence of H-NS.
database_cross_reference: PMID:17892462

Axiom
annotated source: double mutant phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from an experiment typically constructed to determine if two different genes have an observable genetic interaction (functional connection) as the result of a mutation occurring in the alleles of the two genes of interest.
database_cross_reference: ECO:RCT
database_cross_reference: PMID:18305163

array experiment evidence
type: Class
has_obo_namespace: eco
id: ECO:0000055
comment: 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.)
deprecated: true

epistatic interaction phenotypic evidence
type: Class
subclass of: genetic interaction evidence
definition: A type of genetic interaction evidence resulting from the suppression of one allelic effect by an allele at another genetic locus.
has_exact_synonym: epistatic interaction evidence
has_obo_namespace: eco
has_related_synonym: epistatic interactions
id: ECO:0000056
comment: 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.

Axiom
annotated source: epistatic interaction phenotypic evidence
annotated property: definition
annotated target: A type of genetic interaction evidence resulting from the suppression of one allelic effect by an allele at another genetic locus.
database_cross_reference: PMID:18852697

phenotypic similarity evidence
type: Class
subclass of: similarity evidence
definition: A type of similarity based on the expression of a genotype in an environment.
has_exact_synonym: IPTS
has_exact_synonym: phenotype similarity evidence
has_obo_namespace: eco
has_related_synonym: inferred from phenotypic similarity
id: ECO:0000057
comment: 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.

Axiom
annotated source: phenotypic similarity evidence
annotated property: definition
annotated target: A type of similarity based on the expression of a genotype in an environment.
database_cross_reference: ECO:MCC
database_cross_reference: PhenoScape:IPTS

expression microarray evidence
type: Class
subclass of: transcript expression evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001463
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001290
example of usage: S. lividans AdpA directly regulates at least the six AdpA-dependent genes listed above and identified by microarrays and qRT-PCR analysis.
example of usage: To identify the regulon of the response regulator CopR, the transcriptome of the DeltacopRS deletion mutant was compared to that of the wild type using DNA microarrays. For cells grown in standard CGXII medium (1.25 microM CuSO4), no significant gene expression differences were observed, indicating that the CopRS two-component system is not active under this condition (data not shown).
definition: 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.
has_alternative_id: ECO:0000356
has_narrow_synonym: differential gene expression evidence from microarray experiment
has_obo_namespace: eco
id: ECO:0000058

Axiom
annotated source: expression microarray evidence
annotated property: example of usage
annotated target: S. lividans AdpA directly regulates at least the six AdpA-dependent genes listed above and identified by microarrays and qRT-PCR analysis.
database_cross_reference: PMID:24694298

Axiom
annotated source: expression microarray evidence
annotated property: example of usage
annotated target: To identify the regulon of the response regulator CopR, the transcriptome of the DeltacopRS deletion mutant was compared to that of the wild type using DNA microarrays. For cells grown in standard CGXII medium (1.25 microM CuSO4), no significant gene expression differences were observed, indicating that the CopRS two-component system is not active under this condition (data not shown).
database_cross_reference: PMID:21799779

Axiom
annotated source: expression microarray evidence
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://www.illumina.com/techniques/microarrays/gene-expression-arrays.html
database_cross_reference: url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435252/

experimental phenotypic evidence
type: Class
subclass of: experimental evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0010467
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000966
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001199
definition: A type of experimental evidence that is based on an observable characteristic trait, which is the result of the expression of an organisms genotype in an environment.
has_alternative_id: ECO:0000014
has_alternative_id: ECO:0005017
has_obo_namespace: eco
has_related_synonym: inferred from phenotype
id: ECO:0000059
comment: Observable characteristic traits can be morphology, development, behavior, biochemical or physiological properties, etc.

Axiom
annotated source: experimental phenotypic evidence
annotated property: definition
annotated target: A type of experimental evidence that is based on an observable characteristic trait, which is the result of the expression of an organisms genotype in an environment.
database_cross_reference: ECO:SN

positional similarity evidence
type: Class
subclass of: phenotypic similarity evidence
definition: A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements.
has_exact_synonym: IPS
has_obo_namespace: eco
id: ECO:0000060

Axiom
annotated source: positional similarity evidence
annotated property: definition
annotated target: A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements.
database_cross_reference: TAIR:TED

quantitative trait analysis evidence
type: Class
subclass of: experimental phenotypic evidence
definition: 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.
has_exact_synonym: QTL analysis evidence
has_obo_namespace: eco
has_related_synonym: quantitative trait analysis
id: ECO:0000061

Axiom
annotated source: quantitative trait analysis evidence
annotated property: definition
annotated target: 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.
database_cross_reference: TAIR:TED

cRNA to DNA expression microarray evidence
type: Class
subclass of: expression microarray evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001463
    intersection of: Restriction
      on property: has_specified_input
      some values from: OBI_0000880
definition: 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.
has_exact_synonym: genomic microarray evidence
has_obo_namespace: eco
id: ECO:0000062

Axiom
annotated source: cRNA to DNA expression microarray evidence
annotated property: definition
annotated target: 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.
database_cross_reference: url:https://link.springer.com/chapter/10.1007/978-94-017-9716-0_30

compositional similarity evidence
type: Class
subclass of: phenotypic similarity evidence
definition: A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures.
has_exact_synonym: ICS
has_obo_namespace: eco
id: ECO:0000063

Axiom
annotated source: compositional similarity evidence
annotated property: definition
annotated target: A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures.
database_cross_reference: TAIR:TED

functional complementation in heterologous system evidence
type: Class
subclass of: functional complementation evidence
definition: 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.
has_obo_namespace: eco
has_related_synonym: functional complementation in heterologous system
id: ECO:0000064

Axiom
annotated source: functional complementation in heterologous system evidence
annotated property: definition
annotated target: 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.
database_cross_reference: TAIR:TED

yeast one-hybrid evidence
type: Class
subclass of: bait-prey hybrid interaction evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0043565
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001681
definition: A type of bait-prey 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.
database_cross_reference: MI:0432
has_obo_namespace: eco
has_related_synonym: yeast one-hybrid assay
id: ECO:0000066
comment: 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).

Axiom
annotated source: yeast one-hybrid evidence
annotated property: definition
annotated target: A type of bait-prey 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.
database_cross_reference: ECO:MCC
database_cross_reference: PSI-MI:MI:0432
database_cross_reference: TAIR:TED

one hybrid
type: Axiom
annotated source: yeast one-hybrid evidence
annotated property: database_cross_reference
annotated target: MI:0432

developmental similarity evidence
type: Class
subclass of: phenotypic similarity evidence
definition: A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures.
has_exact_synonym: IDS
has_obo_namespace: eco
id: ECO:0000067

Axiom
annotated source: developmental similarity evidence
annotated property: definition
annotated target: A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures.
database_cross_reference: TAIR:TED

yeast 2-hybrid evidence
type: Class
subclass of: bait-prey hybrid interaction evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0019904
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001679
definition: A type of bait-prey 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.
has_obo_namespace: eco
has_related_synonym: yeast two-hybrid assay
id: ECO:0000068

Axiom
annotated source: yeast 2-hybrid evidence
annotated property: definition
annotated target: A type of bait-prey 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.
database_cross_reference: PMID:12734586

differential methylation hybridization evidence
type: Class
subclass of: in vitro methylation assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0044030
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001861
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001278
definition: 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.
has_alternative_id: ECO:0000065
has_exact_synonym: CpG island microarray evidence
has_obo_namespace: eco
id: ECO:0000069
comment: Color is indicative of methylation status - be it hypo- (pseudo-green), hyper- (pseudo-red), or equal methylation (pseudo-yellow).

Axiom
annotated source: differential methylation hybridization evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18987809

co-immunoprecipitation evidence
type: Class
subclass of: immunoprecipitation evidence
definition: 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.
database_cross_reference: MI:0019
has_obo_namespace: eco
has_related_synonym: co-immunoprecipitation
id: ECO:0000070
comment: If performing GO annotation, the interacting protein is referenced in the evidence_with column.

Axiom
annotated source: co-immunoprecipitation evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

coimmunoprecipitation
type: Axiom
annotated source: co-immunoprecipitation evidence
annotated property: database_cross_reference
annotated target: MI:0019

morphological similarity evidence
type: Class
subclass of: phenotypic similarity evidence
definition: A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures.
has_exact_synonym: IMS
has_obo_namespace: eco
id: ECO:0000071

Axiom
annotated source: morphological similarity evidence
annotated property: definition
annotated target: A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures.
database_cross_reference: TAIR:TED

Sos-recruitment assay evidence
type: Class
has_obo_namespace: eco
id: ECO:0000072
deprecated: true

experimental genomic evidence
type: Class
definition: A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product.
has_exact_synonym: inferred from genomic analysis
has_obo_namespace: eco
id: ECO:0000073
comment: This term has been made obsolete with the clean up of experimental genomic evidence branch.
deprecated: true

Axiom
annotated source: experimental genomic evidence
annotated property: definition
annotated target: A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product.
database_cross_reference: ECO:MCC

split-ubiquitin functional complementation evidence
type: Class
subclass of: protein fragment functional complementation evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0019904
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001668
definition: A type of protein fragment functional complementation 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.
database_cross_reference: MI:0112
has_obo_namespace: eco
has_related_synonym: split-ubiquitin assay
id: ECO:0000074
comment: 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

Axiom
annotated source: split-ubiquitin functional complementation evidence
annotated property: definition
annotated target: A type of protein fragment functional complementation 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.
database_cross_reference: PMID:15064465

ubiquitin reconstruction
type: Axiom
annotated source: split-ubiquitin functional complementation evidence
annotated property: database_cross_reference
annotated target: MI:0112

gene expression similarity evidence
type: Class
subclass of: phenotypic similarity evidence
definition: A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles.
has_exact_synonym: IGES
has_obo_namespace: eco
id: ECO:0000075

Axiom
annotated source: gene expression similarity evidence
annotated property: definition
annotated target: A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles.
database_cross_reference: PMID:19958477

far-Western blotting evidence
type: Class
subclass of: physical interaction evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001669
definition: 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.
database_cross_reference: MI:0047
has_obo_namespace: eco
has_related_synonym: far-Western analysis
id: ECO:0000076
comment: The interacting protein is referenced in the evidence_with column.

Axiom
annotated source: far-Western blotting evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18079728

methylation-specific polymerase chain reaction evidence
type: Class
subclass of: in vitro methylation assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0006306
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001684
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
definition: 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.
has_exact_synonym: MS-PCR
has_exact_synonym: MSP
has_exact_synonym: methylation-specific PCR evidence
has_obo_namespace: eco
id: ECO:0000077
comment: The product is the amplification of existing sequences - i.e. more DNA that can be further processed e.g. sequenced, DNA fingerprinting.

Axiom
annotated source: methylation-specific polymerase chain reaction evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMC:38513
database_cross_reference: PMID:8790415

southern hybridization evidence
type: Class
subclass of: DNA detection assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000892
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001444
definition: 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.
has_exact_synonym: Southern blot
has_obo_namespace: eco
has_related_synonym: Southern blotting
id: ECO:0000078
comment: The DNA fragments are prepared through gel electrophoresis then transferred to a filter membrane.

Axiom
annotated source: southern hybridization evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18432697

affinity chromatography evidence
type: Class
subclass of: affinity evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001630
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: Class
        intersection of: OBI_0600046
        intersection of: Restriction
definition: 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 bound compound.
database_cross_reference: MI:0004
has_obo_namespace: eco
has_related_synonym: affinity chromatography
id: ECO:0000079
comment: "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.

Axiom
annotated source: affinity chromatography evidence
annotated property: definition
annotated target: 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 bound compound.
database_cross_reference: ECO:MCC
database_cross_reference: TAIR:TED

affinity chromatography technology
type: Axiom
annotated source: affinity chromatography evidence
annotated property: database_cross_reference
annotated target: MI:0004

phylogenetic evidence
type: Class
subclass of: similarity evidence
example of usage: Comparative phylogenomics along with MLST (multilocus sequence typing) and whole genome sequecing has shown that ribotype 078 lineage is different than other C. difficile lineages [22].
definition: A type of similarity that indicates common ancestry.
has_exact_synonym: IP
has_obo_namespace: eco
id: ECO:0000080

Axiom
annotated source: phylogenetic evidence
annotated property: example of usage
annotated target: Comparative phylogenomics along with MLST (multilocus sequence typing) and whole genome sequecing has shown that ribotype 078 lineage is different than other C. difficile lineages [22].
database_cross_reference: PMID:24713082

Axiom
annotated source: phylogenetic evidence
annotated property: definition
annotated target: A type of similarity that indicates common ancestry.
database_cross_reference: ECO:MCC
database_cross_reference: PhenoScape:IP

Axiom
annotated source: phylogenetic evidence
annotated property: has_exact_synonym
annotated target: IP
database_cross_reference: PhenoScape:IP

targeting sequence prediction evidence
type: Class
subclass of: motif similarity evidence
definition: 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.
has_obo_namespace: eco
has_related_synonym: targeting sequence prediction
id: ECO:0000081

Axiom
annotated source: targeting sequence prediction evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT
database_cross_reference: TAIR:TED

polymerase chain reaction evidence
type: Class
definition: A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand.
has_exact_synonym: PCR evidence
has_obo_namespace: eco
id: ECO:0000082
comment: This term has been made obsolete because PCR is not evidence. The children have been appropriately placed under other parents.
deprecated: true

Axiom
annotated source: polymerase chain reaction evidence
annotated property: definition
annotated target: A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand.
database_cross_reference: OBI:0000415

transmembrane domain prediction evidence
type: Class
subclass of: motif similarity evidence
definition: 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.
has_obo_namespace: eco
has_related_synonym: transmembrane domain prediction
id: ECO:0000083

Axiom
annotated source: transmembrane domain prediction evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT
database_cross_reference: TAIR:TED

gene neighbors evidence
type: Class
subclass of: genomic context evidence
definition: A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes.
created_by: mgiglio
creation_date: 2009-03-20T11:55:18Z
database_cross_reference: GO_REF:0000025
has_exact_synonym: inferred from genome cluster
has_obo_namespace: eco
has_related_synonym: ICL
id: ECO:0000084
comment: Genomic cluster analyses include synteny and operon structure.

Axiom
annotated source: gene neighbors evidence
annotated property: definition
annotated target: A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes.
database_cross_reference: ECO:MCC
database_cross_reference: GOC:MG

Operon structure as IGC evidence
type: Axiom
annotated source: gene neighbors evidence
annotated property: database_cross_reference
annotated target: GO_REF:0000025

immunoprecipitation evidence
type: Class
subclass of: protein binding evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0003823
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001700
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000690
definition: A type of protein binding evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
ontology term requester: CollecTF
has_obo_namespace: eco
has_related_synonym: immunoprecipitation
id: ECO:0000085
comment: Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding.

Axiom
annotated source: immunoprecipitation evidence
annotated property: definition
annotated target: A type of protein binding evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation.
database_cross_reference: ECO:MCC
database_cross_reference: ECO:SW
database_cross_reference: TAIR:TED

amplification of intermethylated sites evidence
type: Class
subclass of: in vitro methylation assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0006306
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001685
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
definition: 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.
has_exact_synonym: AIMS
has_obo_namespace: eco
id: ECO:0000086
comment: The bands can be individually isolated and characterized which leads to the identification of hypo- and hypermethylation events.

Axiom
annotated source: amplification of intermethylated sites evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18987810
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/probe/docs/techpcr/

immunolocalization evidence
type: Class
subclass of: microscopy evidence
subclass of: immunodetection assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0033036
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000185
    intersection of: OBI_0001632
definition: A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues.
has_obo_namespace: eco
has_related_synonym: immunolocalization
id: ECO:0000087

Axiom
annotated source: immunolocalization evidence
annotated property: definition
annotated target: A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues.
database_cross_reference: ECO:MCC
database_cross_reference: ECO:SN

biological system reconstruction evidence
type: Class
subclass of: evidence
definition: 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.
created_by: mgiglio
creation_date: 2009-03-20T12:00:17Z
has_obo_namespace: eco
has_related_synonym: ISR
has_related_synonym: inferred from system reconstruction
id: ECO:0000088
comment: 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.

Axiom
annotated source: biological system reconstruction evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: GOC:mg

restriction landmark genomic scanning evidence
type: Class
subclass of: DNA detection assay evidence
definition: 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.
ontology term requester: SIB:PG
has_alternative_id: ECO:0001125
has_exact_synonym: RLGS evidence
has_exact_synonym: restriction landmark genome scanning evidence
has_obo_namespace: eco
id: ECO:0000089

Axiom
annotated source: restriction landmark genomic scanning evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:8388788

immunogold labelling evidence
type: Class
subclass of: immunolocalization evidence
definition: A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy.
has_obo_namespace: eco
has_related_synonym: immunogold labelling
id: ECO:0000090

Axiom
annotated source: immunogold labelling evidence
annotated property: definition
annotated target: A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy.
database_cross_reference: ECO:MCC

epitope-tagged protein immunolocalization evidence
type: Class
subclass of: immunolocalization evidence
definition: A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies.
has_obo_namespace: eco
has_related_synonym: immunolocalization of epitope-tagged protein
id: ECO:0000092

Axiom
annotated source: epitope-tagged protein immunolocalization evidence
annotated property: definition
annotated target: A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies.
database_cross_reference: TAIR:TED

array-based sequence capture evidence
type: Class
subclass of: DNA detection assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001985
    intersection of: Restriction
      on property: has_specified_output
      some values from: OBI_0000973
definition: 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.
has_broad_synonym: DNA microarray
has_broad_synonym: oligonucleotide microarray evidence
has_narrow_synonym: SNP array evidence
has_narrow_synonym: single nucleotide polymorphism array evidence
has_obo_namespace: eco
id: ECO:0000093

Axiom
annotated source: array-based sequence capture evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:21049075

biological assay evidence
type: Class
has_obo_namespace: eco
id: ECO:0000094
comment: The children of 'biological assay evidence' have been moved under 'direct assay evidence', and this term has been deprecated with no children left.
deprecated: true

cell growth regulation assay evidence
type: Class
subclass of: cell growth assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000964
definition: 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.
created_by: mchibucos
creation_date: 2014-10-15T00:58:50Z
has_obo_namespace: eco
has_related_synonym: growth curve analysis
id: ECO:0000095
comment: Cell growth aspects can include growth rate and extent of growth. A cell growth curve acts as a natural reporter.

Axiom
annotated source: cell growth regulation assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PomBase:MAH

electrophoretic mobility shift assay evidence
type: Class
subclass of: physical interaction evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001671
example of usage: Each of the promoter-proximal regions of qrr2 - 4 was subjected to EMSA with the purified His-OpaR protein (Fig. 6b). The results showed that His-OpaR was able to bind to each of the three DNA fragments tested in a dose-dependent manner in vitro.
definition: A type of affinity evidence based on an electrophoretic mobility shift of macromolecules, where proteins, nucleic acids, or both, are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect interactions/complexes between proteins and/or nucleic acid.
ontology term requester: CollecTF
database_cross_reference: MI:0413
has_exact_synonym: EMSA: electrophoretic mobility shift assay
has_obo_namespace: eco
has_related_synonym: Gel retardation assay
has_related_synonym: electrophoretic mobility shift assay
id: ECO:0000096
comment: 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.

Axiom
annotated source: electrophoretic mobility shift assay evidence
annotated property: example of usage
annotated target: Each of the promoter-proximal regions of qrr2 - 4 was subjected to EMSA with the purified His-OpaR protein (Fig. 6b). The results showed that His-OpaR was able to bind to each of the three DNA fragments tested in a dose-dependent manner in vitro.
database_cross_reference: PMID:22506036

Axiom
annotated source: electrophoretic mobility shift assay evidence
annotated property: definition
annotated target: A type of affinity evidence based on an electrophoretic mobility shift of macromolecules, where proteins, nucleic acids, or both, are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect interactions/complexes between proteins and/or nucleic acid.
database_cross_reference: ECO:KIM
database_cross_reference: ECO:SW
database_cross_reference: PMID:17703195
database_cross_reference: TAIR:TED

electrophoretic mobility shift assay
type: Axiom
annotated source: electrophoretic mobility shift assay evidence
annotated property: database_cross_reference
annotated target: MI:0413

Axiom
annotated source: electrophoretic mobility shift assay evidence
annotated property: has_related_synonym
annotated target: Gel retardation assay
database_cross_reference: PMID:17703195

cDNA to DNA expression microarray evidence
type: Class
subclass of: expression microarray evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001463
    intersection of: Restriction
      on property: has_specified_input
      some values from: OBI_0000164
definition: 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.
ontology term requester: CollecTF
has_alternative_id: ECO:0001041
has_alternative_id: ECO:0005524
has_obo_namespace: eco
has_related_synonym: DNA microarray
has_related_synonym: RNA microarray
id: ECO:0000097

Axiom
annotated source: cDNA to DNA expression microarray evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT

obsolete in situ hybridization evidence
type: Class
definition: 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.
has_obo_namespace: eco
has_related_synonym: in situ hybridization
id: ECO:0000098
comment: This term has been made obsolete with the clean up of experimental genomic evidence branch.
deprecated: true

Axiom
annotated source: obsolete in situ hybridization evidence
annotated property: definition
annotated target: 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.
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/probe/docs/techish/

fractionation evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions.
has_obo_namespace: eco
id: ECO:0000100

Axiom
annotated source: fractionation evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions.
database_cross_reference: NBK:26936
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/books/NBK26936/

Affymetrix GeneChip evidence
type: Class
subclass of: cRNA to DNA expression microarray evidence
definition: A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information.
has_exact_synonym: Affymetrix array experiment evidence
has_obo_namespace: eco
id: ECO:0000101

Axiom
annotated source: Affymetrix GeneChip evidence
annotated property: definition
annotated target: A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information.
database_cross_reference: ERO:0001265

co-fractionation evidence
type: Class
subclass of: fractionation evidence
definition: A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules.
has_obo_namespace: eco
has_related_synonym: co-fractionation
id: ECO:0000102

Axiom
annotated source: co-fractionation evidence
annotated property: definition
annotated target: A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules.
database_cross_reference: TAIR:TED

DNA to cDNA expression microarray evidence
type: Class
subclass of: expression microarray evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001463
    intersection of: Restriction
      on property: has_specified_input
      some values from: OBI_0000164
definition: 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.
has_exact_synonym: REM evidence
has_exact_synonym: RNA expression microarray evidence
has_exact_synonym: microarray RNA expression level evidence
has_obo_namespace: eco
has_related_synonym: transcript levels (e.g. microarray data)
id: ECO:0000104
comment: REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that.

Axiom
annotated source: DNA to cDNA expression microarray evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT
database_cross_reference: PMID:15329382

Axiom
annotated source: DNA to cDNA expression microarray evidence
annotated property: comment
annotated target: REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that.
database_cross_reference: PMID:15329382

Nimblegen array evidence
type: Class
subclass of: cDNA to DNA expression microarray evidence
definition: A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels.
has_obo_namespace: eco
id: ECO:0000105

Axiom
annotated source: Nimblegen array evidence
annotated property: definition
annotated target: A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels.
database_cross_reference: PMID:15607417
database_cross_reference: url:https://roche-biochem.jp/pdf/products/microarray/user_guide/SeqCap/SeqCap_UserGuide_Delivery_ver3.0.pdf

northern blot evidence
type: Class
subclass of: transcript expression evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000860
example of usage: Northern blot analysis indicated that there was one major band of 1.5-kb (which was used for the stability determination) and two other minor bands of approximately 3.0- and 6.0-kb, which constituted less than 5% of the total signal (Fig. 1C), suggesting that other genes may be cotranscribed along with SMU.1882.
definition: 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.
ontology term requester: CollecTF
has_exact_synonym: RNA blot evidence
has_exact_synonym: northern assay evidence
has_obo_namespace: eco
has_related_synonym: transcript levels (e.g. Northerns)
id: ECO:0000106

Axiom
annotated source: northern blot evidence
annotated property: example of usage
annotated target: Northern blot analysis indicated that there was one major band of 1.5-kb (which was used for the stability determination) and two other minor bands of approximately 3.0- and 6.0-kb, which constituted less than 5% of the total signal (Fig. 1C), suggesting that other genes may be cotranscribed along with SMU.1882.
database_cross_reference: PMID:21124877

Axiom
annotated source: northern blot evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: TAIR:TED

reverse transcription polymerase chain reaction evidence
type: Class
subclass of: RNA detection assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001361
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001313
example of usage: Taken together, the results of the RT-PCR analyses and the reporter fusion assays indicate that expression of SMU.1882 is up regulated in the presence of CovR.
example of usage: The RT-PCR assay indicated that the sycO, ypkA and yopJ genes (designated as pCD12, pCD13 and pCD14 in Y. pestis 91001 [19], respectively) were transcribed as a single primary RNA (Fig. 1), and thereby these three genes constituted a single operon in Y. pestis Microtus strain 201.
example of usage: Using reverse transcription-PCR, we found that primers designed to span the intergenic regions between zur and the znuC homolog, as well as znuC and znuB homolog each generated a PCR product (Figure 2A). This indicated that these genes were transcribed on the same mRNA.
definition: A type of RNA detection assay evidence where an RNA transcript is reverse transcribed into cDNA and amplified to qualitatively detect gene expression.
ontology term requester: CollecTF
has_alternative_id: ECO:0000108
has_broad_synonym: reverse transcription polymerase chain reaction transcription evidence
has_exact_synonym: RT-PCR
has_obo_namespace: eco
has_related_synonym: transcript levels (e.g. RT-PCR)
id: ECO:0000109
comment: The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate.

Axiom
annotated source: reverse transcription polymerase chain reaction evidence
annotated property: example of usage
annotated target: Taken together, the results of the RT-PCR analyses and the reporter fusion assays indicate that expression of SMU.1882 is up regulated in the presence of CovR.
database_cross_reference: PMID:21124877

Axiom
annotated source: reverse transcription polymerase chain reaction evidence
annotated property: example of usage
annotated target: The RT-PCR assay indicated that the sycO, ypkA and yopJ genes (designated as pCD12, pCD13 and pCD14 in Y. pestis 91001 [19], respectively) were transcribed as a single primary RNA (Fig. 1), and thereby these three genes constituted a single operon in Y. pestis Microtus strain 201.
database_cross_reference: PMID:19703315

Axiom
annotated source: reverse transcription polymerase chain reaction evidence
annotated property: example of usage
annotated target: Using reverse transcription-PCR, we found that primers designed to span the intergenic regions between zur and the znuC homolog, as well as znuC and znuB homolog each generated a PCR product (Figure 2A). This indicated that these genes were transcribed on the same mRNA.
database_cross_reference: PMID:24086521

Axiom
annotated source: reverse transcription polymerase chain reaction evidence
annotated property: definition
annotated target: A type of RNA detection assay evidence where an RNA transcript is reverse transcribed into cDNA and amplified to qualitatively detect gene expression.
database_cross_reference: ECO:SW
database_cross_reference: PMID:11013345
database_cross_reference: PMID:12901609

RNA protection assay evidence
type: Class
subclass of: nuclease protection assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: Class
        intersection of: OBI_0302903
        intersection of: Restriction
example of usage: fur RPAs were performed on RNA isolated from each strain, and an increase in fur expression was seen for G27, 26695, and the Fur swap strain under iron-depletion shock conditions while little to no increase was seen under iron-limited growth conditions (Fig. 4D and data not shown). This data shows that Fur autoregulation is consistent in each strain and further supports the notion that the AA difference in Fur is not responsible for the difference in sodB regulation between G27 and 26695.
definition: 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.
ontology term requester: CollecTF
has_exact_synonym: ribonuclease protection assay
has_narrow_synonym: RPA
has_obo_namespace: eco
has_related_synonym: RNA protection assay
has_related_synonym: RNAse protection assay
id: ECO:0000110

Axiom
annotated source: RNA protection assay evidence
annotated property: example of usage
annotated target: fur RPAs were performed on RNA isolated from each strain, and an increase in fur expression was seen for G27, 26695, and the Fur swap strain under iron-depletion shock conditions while little to no increase was seen under iron-limited growth conditions (Fig. 4D and data not shown). This data shows that Fur autoregulation is consistent in each strain and further supports the notion that the AA difference in Fur is not responsible for the difference in sodB regulation between G27 and 26695.
database_cross_reference: PMID:19399190

Axiom
annotated source: RNA protection assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:23457339
database_cross_reference: TAIR:TED

qualitative western immunoblotting evidence
type: Class
subclass of: protein expression evidence
subclass of: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence
subclass of: immunodetection assay evidence
example of usage: When we determined the proteolysis role of Lons in VapBC10 proteins by Western blot analysis using the strains BL21(DE3)(pJS882) and BL21(DE3)(pJS427), the levels of VapB10 and VapC10 remained stable over the course of translation inhibition (Figure 7D and E). Thus, Lon could not degrade VapBC10 proteins, consistent with our drop growth evidence (Figure 6B).
definition: A type of protein expression evidence where proteins are separated using gel electrophoresis, blotted onto a membrane, and probed with an antibody that can be detected via light or radioactive emission.
ontology term requester: CollecTF
has_alternative_id: ECO:0005602
has_exact_synonym: protein expression level evidence based on western blot
has_obo_namespace: eco
has_related_synonym: Western blot expression analysis
has_related_synonym: protein immunoblot
has_related_synonym: protein levels (e.g. Western blots)
id: ECO:0000112
comment: 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.

Axiom
annotated source: qualitative western immunoblotting evidence
annotated property: example of usage
annotated target: When we determined the proteolysis role of Lons in VapBC10 proteins by Western blot analysis using the strains BL21(DE3)(pJS882) and BL21(DE3)(pJS427), the levels of VapB10 and VapC10 remained stable over the course of translation inhibition (Figure 7D and E). Thus, Lon could not degrade VapBC10 proteins, consistent with our drop growth evidence (Figure 6B).
database_cross_reference: PMID:24260461

Axiom
annotated source: qualitative western immunoblotting evidence
annotated property: definition
annotated target: A type of protein expression evidence where proteins are separated using gel electrophoresis, blotted onto a membrane, and probed with an antibody that can be detected via light or radioactive emission.
database_cross_reference: ECO:SW
database_cross_reference: PMID:23050259
database_cross_reference: TAIR:TED

expression library screen evidence
type: Class
subclass of: protein expression evidence
definition: 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.
has_obo_namespace: eco
has_related_synonym: expression library screening
id: ECO:0000114

Axiom
annotated source: expression library screen evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: TAIR:TED

differential hybridization evidence
type: Class
subclass of: transcript expression evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0002448
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
definition: 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.
has_obo_namespace: eco
has_related_synonym: differential hybridization
id: ECO:0000116
comment: Differential hybridization identifies differentially expressed cloned genes. Two different mRNA-derived probes are used to demonstrate RNA expression under a specific condition.

Axiom
annotated source: differential hybridization evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:14668817

subtractive hybridization evidence
type: Class
subclass of: transcript expression evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0002447
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
definition: 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'.
has_obo_namespace: eco
has_related_synonym: subtractive hybridization
id: ECO:0000118
comment: 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.

Axiom
annotated source: subtractive hybridization evidence
annotated property: definition
annotated target: 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'.
database_cross_reference: PMID:11298187

over expression analysis evidence
type: Class
subclass of: genetic transformation evidence
example of usage: In contrast, when RpoQ was overexpressed in either the wild type or the DeltalitR mutant, both were essentially nonmotile (Fig. 7), suggesting that quorum signaling regulates motility, at least in part, through an RpoQ mechanism downstream of LitR.
definition: 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.
has_obo_namespace: eco
has_related_synonym: analysis of overexpression/ectopic expression phenotype
id: ECO:0000120

Axiom
annotated source: over expression analysis evidence
annotated property: example of usage
annotated target: In contrast, when RpoQ was overexpressed in either the wild type or the DeltalitR mutant, both were essentially nonmotile (Fig. 7), suggesting that quorum signaling regulates motility, at least in part, through an RpoQ mechanism downstream of LitR.
database_cross_reference: PMID:22233679

Axiom
annotated source: over expression analysis evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:22419077

protein localization evidence
type: Class
subclass of: localization evidence
definition: A type of localization evidence where sub-cellular localization of a protein is determined.
has_obo_namespace: eco
id: ECO:0000122

Axiom
annotated source: protein localization evidence
annotated property: definition
annotated target: A type of localization evidence where sub-cellular localization of a protein is determined.
database_cross_reference: GO:0008104
database_cross_reference: url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019937

fusion protein localization evidence
type: Class
subclass of: protein localization evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0033036
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002167
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: 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.
has_obo_namespace: eco
id: ECO:0000124

Axiom
annotated source: fusion protein localization evidence
annotated property: definition
annotated target: 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.
database_cross_reference: MI:0240

green fluorescent protein fusion protein localization evidence
type: Class
subclass of: fusion protein localization evidence
definition: 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.
has_exact_synonym: GFP fusion protein localization evidence
has_obo_namespace: eco
has_related_synonym: localization of GFP/YFP fusion protein
id: ECO:0000126

Axiom
annotated source: green fluorescent protein fusion protein localization evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:9759496

yellow fluorescent protein fusion protein localization evidence
type: Class
subclass of: fusion protein localization evidence
definition: 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.
has_exact_synonym: YFP fusion protein localization evidence
has_obo_namespace: eco
has_related_synonym: localization of GFP/YFP fusion protein
id: ECO:0000128

Axiom
annotated source: yellow fluorescent protein fusion protein localization evidence
annotated property: definition
annotated target: 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.
database_cross_reference: MI:0368
database_cross_reference: url:http://www.jbc.org/content/276/31/29188.long

beta-glucuronidase fusion protein localization evidence
type: Class
subclass of: fusion protein localization evidence
definition: 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.
has_exact_synonym: GUS fusion protein localization evidence
has_narrow_synonym: GUS staining evidence
has_obo_namespace: eco
has_related_synonym: localization of GUS fusion protein
id: ECO:0000130

Axiom
annotated source: beta-glucuronidase fusion protein localization evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT

beta-galactosidase fusion protein localization evidence
type: Class
subclass of: fusion protein localization evidence
definition: 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.
has_exact_synonym: LacZ fusion protein localization evidence
has_obo_namespace: eco
id: ECO:0000132

Axiom
annotated source: beta-galactosidase fusion protein localization evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:23681629

transport assay evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0015031
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000964
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: A type of direct assay evidence resulting from the activity assessment of transport proteins.
has_obo_namespace: eco
has_related_synonym: transport assay
id: ECO:0000134

Axiom
annotated source: transport assay evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from the activity assessment of transport proteins.
database_cross_reference: PMID:18401524

nucleic acid binding evidence
type: Class
subclass of: affinity evidence
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: GO_0005488
    intersection of: Restriction
      on property: has participant
      some values from: nucleic acid
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001591
definition: A type of affinity evidence resulting from the binding of a molecule to a nucleic acid.
has_obo_namespace: eco
id: ECO:0000136

Axiom
annotated source: nucleic acid binding evidence
annotated property: definition
annotated target: A type of affinity evidence resulting from the binding of a molecule to a nucleic acid.
database_cross_reference: GO:0003676

ribohomopolymer binding assay evidence
type: Class
subclass of: nucleic acid binding evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0032549
definition: A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer.
has_obo_namespace: eco
has_related_synonym: ribohomopolymer binding assay
id: ECO:0000138

Axiom
annotated source: ribohomopolymer binding assay evidence
annotated property: definition
annotated target: A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer.
database_cross_reference: PMC:102612

thin layer chromatography evidence
type: Class
subclass of: chromatography evidence
definition: A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
has_exact_synonym: TLC evidence
has_obo_namespace: eco
has_related_synonym: thin layer chromatography
id: ECO:0000140

Axiom
annotated source: thin layer chromatography evidence
annotated property: definition
annotated target: A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
database_cross_reference: ECO:MCC

protein:ion binding evidence
type: Class
subclass of: protein binding evidence
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: GO_0005488
    intersection of: Restriction
      on property: has participant
      some values from: PR_000000001
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001591
definition: A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site.
has_obo_namespace: eco
id: ECO:0000142

Axiom
annotated source: protein:ion binding evidence
annotated property: definition
annotated target: A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site.
database_cross_reference: PMID:2377604

Southwestern blot evidence
type: Class
subclass of: nucleic acid binding evidence
definition: A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
has_obo_namespace: eco
has_related_synonym: Southwestern analysis
id: ECO:0000144

Axiom
annotated source: Southwestern blot evidence
annotated property: definition
annotated target: A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
database_cross_reference: ECO:RCT
database_cross_reference: TAIR:TED

Northwestern blot evidence
type: Class
subclass of: nucleic acid binding evidence
definition: A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
has_obo_namespace: eco
has_related_synonym: Northwestern analysis
id: ECO:0000146

Axiom
annotated source: Northwestern blot evidence
annotated property: definition
annotated target: A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
database_cross_reference: ECO:RCT
database_cross_reference: TAIR:TED

in vitro binding evidence
type: Class
has_obo_namespace: eco
id: ECO:0000148
deprecated: true

in vitro transcription reconstitution assay evidence
type: Class
subclass of: reconstitution assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0034645
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002622
example of usage: As shown in Fig. 5, addition of reconstituted RNA polymerase holoenzyme, but not the core enzyme, generated expected size bands of 193-nt and 158-nt when P1882 and Pami, respectively, were used as template (lanes 2 and 7). However, the addition of CovR did not lead to any observable increase in transcription from P1882.
definition: A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis.
has_obo_namespace: eco
has_related_synonym: in vitro reconstitution assay with recombinant protein
id: ECO:0000150

Axiom
annotated source: in vitro transcription reconstitution assay evidence
annotated property: example of usage
annotated target: As shown in Fig. 5, addition of reconstituted RNA polymerase holoenzyme, but not the core enzyme, generated expected size bands of 193-nt and 158-nt when P1882 and Pami, respectively, were used as template (lanes 2 and 7). However, the addition of CovR did not lead to any observable increase in transcription from P1882.
database_cross_reference: PMID:21124877

Axiom
annotated source: in vitro transcription reconstitution assay evidence
annotated property: definition
annotated target: A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis.
database_cross_reference: PMID:9237163

in vitro recombinant protein transcription reconstitution assay evidence
type: Class
subclass of: in vitro transcription reconstitution assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0002622
definition: A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system.
has_obo_namespace: eco
has_related_synonym: in vitro reconstitution assay with recombinant protein
id: ECO:0000152

Axiom
annotated source: in vitro recombinant protein transcription reconstitution assay evidence
annotated property: definition
annotated target: A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system.
database_cross_reference: PMID:9237165

heterologous protein expression evidence
type: Class
subclass of: protein expression evidence
definition: 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.
has_obo_namespace: eco
has_related_synonym: protein expression in heterologous system
id: ECO:0000154

Axiom
annotated source: heterologous protein expression evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:KAV

protein separation evidence
type: Class
subclass of: fractionation evidence
definition: A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture.
has_obo_namespace: eco
id: ECO:0000156

Axiom
annotated source: protein separation evidence
annotated property: definition
annotated target: A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture.
database_cross_reference: ERO:0000526

protein separation followed by direct sequencing evidence
type: Class
subclass of: protein separation evidence
definition: A type of protein separation evidence that is followed by direct protein sequencing whereby a protein's amino acid sequence is determined experimentally by Edman degradation or by mass spectrometry.
has_obo_namespace: eco
has_related_synonym: protein separation and direct sequencing
id: ECO:0000158

protein separation followed by fragment identification evidence
type: Class
subclass of: protein separation evidence
definition: A type of protein separation evidence which then utilizes the screening and identification of small-molecules that bind to proteins.
has_obo_namespace: eco
has_related_synonym: protein separation and fragment identification
id: ECO:0000160

Axiom
annotated source: protein separation followed by fragment identification evidence
annotated property: definition
annotated target: A type of protein separation evidence which then utilizes the screening and identification of small-molecules that bind to proteins.
database_cross_reference: https://pubs.acs.org/doi/10.1021/bi3005126
database_cross_reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5632530/

heterologous system uptake evidence
type: Class
subclass of: transport assay evidence
definition: 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.
has_obo_namespace: eco
has_related_synonym: uptake assay in heterologous system
id: ECO:0000162
comment: The transporter is a recombinant protein.

Axiom
annotated source: heterologous system uptake evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT
database_cross_reference: doi:10.1146/annurev.pp.46.060195.002223

electrophysiology assay evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002176
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: A type of direct assay evidence where electrical properties of cells or tissues are studied.
has_obo_namespace: eco
id: ECO:0000164
comment: 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.

Axiom
annotated source: electrophysiology assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where electrical properties of cells or tissues are studied.
database_cross_reference: ECO:KAV

two-electrode voltage clamp recording evidence
type: Class
subclass of: voltage clamp recording evidence
definition: 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.
has_obo_namespace: eco
has_related_synonym: two-electrode voltage clamp technique
id: ECO:0000166

Axiom
annotated source: two-electrode voltage clamp recording evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:23529422

transcription assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence resulting from the detection and quantification of transcribed RNA.
has_obo_namespace: eco
id: ECO:0000168

Axiom
annotated source: transcription assay evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from the detection and quantification of transcribed RNA.
database_cross_reference: MeSH:D014158
database_cross_reference: url:https://bmcmolbiol.biomedcentral.com/articles/10.1186/1471-2199-15-7

transcriptional activation assay evidence
type: Class
subclass of: transcription assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0001047
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001430
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000424
    intersection of: OBI_0000913
definition: 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.
has_obo_namespace: eco
has_related_synonym: transcriptional activation assay
id: ECO:0000170

Axiom
annotated source: transcriptional activation assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://smcg.ccg.unam.mx/enp-unam/05-TranscripYRegulacion/transcription.pdf

biochemical trait analysis evidence
type: Class
subclass of: experimental phenotypic evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000366
definition: A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed.
has_obo_namespace: eco
has_related_synonym: analysis of biochemical trait
id: ECO:0000172
comment: For example, the accumulation of a biosynthetic intermediate.

Axiom
annotated source: biochemical trait analysis evidence
annotated property: definition
annotated target: A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed.
database_cross_reference: ECO:RCT

mutant physiological response evidence
type: Class
subclass of: mutant phenotype evidence
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: GO_0050896
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: OBI_0100026
        intersection of: Restriction
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000807
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001396
definition: A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined.
has_obo_namespace: eco
has_related_synonym: analysis of physiological response
id: ECO:0000174
comment: Examples include: abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions.

Axiom
annotated source: mutant physiological response evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined.
database_cross_reference: ECO:RCT

mutant visible phenotype evidence
type: Class
subclass of: mutant phenotype evidence
definition: A type of mutant phenotype evidence in which traits arising from a mutation are visually examined.
has_obo_namespace: eco
has_related_synonym: analysis of visible trait
id: ECO:0000176

Axiom
annotated source: mutant visible phenotype evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence in which traits arising from a mutation are visually examined.
database_cross_reference: ECO:RCT

genomic context evidence
type: Class
subclass of: similarity evidence
definition: A type of similarity evidence in which the location of the gene within the genome provides insight into the gene's function or evolutionary insight.
has_obo_namespace: eco
id: ECO:0000177
comment: This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis.

Axiom
annotated source: genomic context evidence
annotated property: definition
annotated target: A type of similarity evidence in which the location of the gene within the genome provides insight into the gene's function or evolutionary insight.
database_cross_reference: PMID:10958625
database_cross_reference: PMID:21609955

in vivo assay evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000964
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001199
definition: A type of direct assay evidence resulting from a sample of microorganisms or living tissue grown in a medium.
has_obo_namespace: eco
id: ECO:0000178

Axiom
annotated source: in vivo assay evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from a sample of microorganisms or living tissue grown in a medium.
database_cross_reference: ECO:RCT
database_cross_reference: url:https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=46352

animal model system study evidence
type: Class
subclass of: experimental evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0008150
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000966
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001199
definition: A type of experimental evidence arising from the investigation of an animal model system.
has_obo_namespace: eco
id: ECO:0000179

Axiom
annotated source: animal model system study evidence
annotated property: definition
annotated target: A type of experimental evidence arising from the investigation of an animal model system.
database_cross_reference: ECO:MCC

clinical study evidence
type: Class
subclass of: experimental evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0500001
definition: A type of experimental evidence arising from a controlled investigation that uses human subjects.
has_obo_namespace: eco
id: ECO:0000180

Axiom
annotated source: clinical study evidence
annotated property: definition
annotated target: A type of experimental evidence arising from a controlled investigation that uses human subjects.
database_cross_reference: ECO:MCC

in vitro assay evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000978
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001285
definition: 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.
has_alternative_id: ECO:0005013
has_obo_namespace: eco
id: ECO:0000181

Axiom
annotated source: in vitro assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT
database_cross_reference: url:https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=45733

in vitro culture assay evidence
type: Class
has_obo_namespace: eco
id: ECO:0000182
comment: Use ECO:0001563 (cell growth assay evidence) in place of this term.
deprecated: true

cell-free assay evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0008152
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000978
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001285
definition: 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.
has_broad_synonym: in vitro assay
has_obo_namespace: eco
id: ECO:0000183

Axiom
annotated source: cell-free assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18453125

enzyme inhibition evidence
type: Class
subclass of: enzymatic activity assay evidence
subclass of: protein inhibition evidence
definition: A type of protein inhibition evidence and enzymatic acitivty evidence where the protein under study is an enzyme.
has_obo_namespace: eco
id: ECO:0000184

Axiom
annotated source: enzyme inhibition evidence
annotated property: definition
annotated target: A type of protein inhibition evidence and enzymatic acitivty evidence where the protein under study is an enzyme.
database_cross_reference: ECO:MCC

sequence alignment evidence
type: Class
subclass of: sequence similarity evidence
definition: A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment
created_by: mchibucos
creation_date: 2010-03-18T12:21:31Z
has_alternative_id: ECO:00000057
has_obo_namespace: eco
id: ECO:0000200
comment: Such alignments may be pairwise alignments or multiple alignments.

Axiom
annotated source: sequence alignment evidence
annotated property: definition
annotated target: A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment
database_cross_reference: url:http://www.geneontology.org/GO.evidence.shtml

sequence orthology evidence
type: Class
subclass of: sequence similarity evidence
definition: 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.
created_by: mchibucos
creation_date: 2010-03-18T12:30:06Z
has_alternative_id: ECO:00000060
has_obo_namespace: eco
has_related_synonym: ortholog evidence
id: ECO:0000201
comment: Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor.

Axiom
annotated source: sequence orthology evidence
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://www.geneontology.org/GO.evidence.shtml

match to sequence model evidence
type: Class
subclass of: sequence similarity evidence
example of usage: A putative rho-independent terminator sequence (GCCTGACTACATAGATGTCAGGC) was identified at position 402-bp downstream of SMU.1882 by TransTerm (transterm.dev.java.net) program.
definition: A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model.
created_by: mchibucos
creation_date: 2010-03-18T12:32:30Z
has_alternative_id: ECO:00000063
has_obo_namespace: eco
id: ECO:0000202
comment: 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.

Axiom
annotated source: match to sequence model evidence
annotated property: example of usage
annotated target: A putative rho-independent terminator sequence (GCCTGACTACATAGATGTCAGGC) was identified at position 402-bp downstream of SMU.1882 by TransTerm (transterm.dev.java.net) program.
database_cross_reference: PMID:21124877

Axiom
annotated source: match to sequence model evidence
annotated property: definition
annotated target: A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model.
database_cross_reference: ECO:MCC
comment: url:http://www.geneontology.org/GO.evidence.shtml

automatic assertion
type: Class
subclass of: assertion method
disjoint with: manual assertion
definition: An assertion method that does not involve human review.
created_by: mchibucos
creation_date: 2010-03-18T12:36:04Z
has_alternative_id: ECO:00000067
has_obo_namespace: eco
id: ECO:0000203
comment: 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.

Axiom
annotated source: automatic assertion
annotated property: definition
annotated target: An assertion method that does not involve human review.
database_cross_reference: ECO:MCC

author statement
type: Class
equivalent class: Class
  union of: author statement supported by traceable reference
  union of: author statement without traceable support
subclass of: documented statement evidence
definition: A type of documented statement evidence that is based on an assertion by the author of a paper, which is read by a curator.
created_by: mchibucos
creation_date: 2010-06-21T11:17:21Z
has_alternative_id: ECO:0007010
has_obo_namespace: eco
id: ECO:0000204

Axiom
annotated source: author statement
annotated property: definition
annotated target: A type of documented statement evidence that is based on an assertion by the author of a paper, which is read by a curator.
database_cross_reference: ECO:MCC

curator inference
type: Class
subclass of: inferential evidence
definition: A type of inferential evidence that is based on a conclusion drawn by a curator.
created_by: mchibucos
creation_date: 2010-08-18T05:55:12Z
has_obo_namespace: eco
id: ECO:0000205

Axiom
annotated source: curator inference
annotated property: definition
annotated target: A type of inferential evidence that is based on a conclusion drawn by a curator.
database_cross_reference: ECO:MCC

BLAST evidence
type: Class
subclass of: pairwise sequence alignment evidence
definition: A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST).
created_by: mchibucos
creation_date: 2010-08-06T04:48:24Z
has_obo_namespace: eco
id: ECO:0000206

Axiom
annotated source: BLAST evidence
annotated property: definition
annotated target: A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST).
database_cross_reference: ECO:MCC

nucleotide BLAST evidence
type: Class
subclass of: BLAST evidence
definition: A type of BLAST evidence in which nucleotide sequences are aligned.
created_by: mchibucos
creation_date: 2010-08-06T04:49:58Z
has_obo_namespace: eco
id: ECO:0000207

Axiom
annotated source: nucleotide BLAST evidence
annotated property: definition
annotated target: A type of BLAST evidence in which nucleotide sequences are aligned.
database_cross_reference: ECO:MCC

protein BLAST evidence
type: Class
subclass of: BLAST evidence
example of usage: Blast search of S. meliloti genome for homologues of X. campestris Ohr protein revealed two paralogues, SMa2389 and SMc00040, showing 52 and 57% identity respectively with Ohr of X. campestris.
definition: A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned.
created_by: mchibucos
creation_date: 2010-08-06T04:50:45Z
has_obo_namespace: eco
id: ECO:0000208

Axiom
annotated source: protein BLAST evidence
annotated property: example of usage
annotated target: Blast search of S. meliloti genome for homologues of X. campestris Ohr protein revealed two paralogues, SMa2389 and SMc00040, showing 52 and 57% identity respectively with Ohr of X. campestris.
database_cross_reference: PMID:21569462

Axiom
annotated source: protein BLAST evidence
annotated property: definition
annotated target: A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned.
database_cross_reference: ECO:MCC

BLAST evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: BLAST evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: BLAST evidence
subclass of: pairwise sequence alignment evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of BLAST evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-08-06T04:55:21Z
has_obo_namespace: eco
id: ECO:0000209

Axiom
annotated source: BLAST evidence used in automatic assertion
annotated property: subClassOf
annotated target: pairwise sequence alignment evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: BLAST evidence used in automatic assertion
annotated property: definition
annotated target: A type of BLAST evidence that is used in an automatic assertion.
database_cross_reference: ECO:MCC

nucleotide BLAST evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: nucleotide BLAST evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: nucleotide BLAST evidence
subclass of: BLAST evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of nucleotide BLAST evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-08-06T05:09:51Z
has_obo_namespace: eco
id: ECO:0000210

Axiom
annotated source: nucleotide BLAST evidence used in automatic assertion
annotated property: subClassOf
annotated target: BLAST evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: nucleotide BLAST evidence used in automatic assertion
annotated property: definition
annotated target: A type of nucleotide BLAST evidence that is used in an automatic assertion.
database_cross_reference: ECO:RCT

protein BLAST evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: protein BLAST evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: protein BLAST evidence
subclass of: BLAST evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of protein BLAST evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-08-06T05:11:04Z
has_obo_namespace: eco
id: ECO:0000211

Axiom
annotated source: protein BLAST evidence used in automatic assertion
annotated property: subClassOf
annotated target: BLAST evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: protein BLAST evidence used in automatic assertion
annotated property: definition
annotated target: A type of protein BLAST evidence that is used in an automatic assertion.
database_cross_reference: ECO:RCT

combinatorial evidence
type: Class
equivalent class: Class
  intersection of: evidence
  intersection of: Restriction
    on property: has part
    some values from: evidence
subclass of: evidence
definition: A type of evidence in which at least two distinct types of evidence have been integrated.
created_by: mchibucos
creation_date: 2010-08-06T05:24:57Z
has_alternative_id: ECO:0000036
has_alternative_id: ECO:0000043
has_obo_namespace: eco
has_related_synonym: inferred from in-silico analysis
id: ECO:0000212
comment: 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.

Axiom
annotated source: combinatorial evidence
annotated property: definition
annotated target: A type of evidence in which at least two distinct types of evidence have been integrated.
database_cross_reference: ECO:MCC
database_cross_reference: ECO:RCT

combinatorial evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: combinatorial evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: combinatorial evidence
subclass of: evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of combinatorial analysis that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-08-06T05:28:33Z
has_obo_namespace: eco
has_related_synonym: inferred from in-silico analysis
id: ECO:0000213
comment: 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.

Axiom
annotated source: combinatorial evidence used in automatic assertion
annotated property: subClassOf
annotated target: evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: combinatorial evidence used in automatic assertion
annotated property: definition
annotated target: A type of combinatorial analysis that is used in an automatic assertion.
database_cross_reference: ECO:MCC

biological aspect of descendant evidence
type: Class
subclass of: phylogenetic evidence
definition: A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
created_by: mchibucos
creation_date: 2010-10-05T11:16:50Z
has_obo_namespace: eco
id: ECO:0000214
comment: 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.

Axiom
annotated source: biological aspect of descendant evidence
annotated property: definition
annotated target: A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
database_cross_reference: ECO:MCC

rapid divergence from ancestral sequence evidence
type: Class
subclass of: phylogenetic evidence
definition: A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
created_by: mchibucos
creation_date: 2010-10-05T03:41:34Z
has_obo_namespace: eco
id: ECO:0000215
comment: Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence.

Axiom
annotated source: rapid divergence from ancestral sequence evidence
annotated property: definition
annotated target: A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
database_cross_reference: ECO:MCC

phylogenetic determination of loss of key residues evidence
type: Class
subclass of: phylogenetic evidence
definition: A type of phylogenetic evidence characterized by the absence of key sequence residues.
created_by: mchibucos
creation_date: 2010-10-05T03:43:17Z
has_obo_namespace: eco
id: ECO:0000216
comment: The loss of certain residues important for function can indicate that a sequence lacks a particular function.

Axiom
annotated source: phylogenetic determination of loss of key residues evidence
annotated property: definition
annotated target: A type of phylogenetic evidence characterized by the absence of key sequence residues.
database_cross_reference: ECO:MCC

assertion method
type: Class
equivalent class: Class
  union of: automatic assertion
  union of: manual assertion
definition: A means by which a statement is made about an entity.
created_by: mchibucos
creation_date: 2010-11-12T04:17:37Z
has_obo_namespace: eco
id: ECO:0000217

Axiom
annotated source: assertion method
annotated property: definition
annotated target: A means by which a statement is made about an entity.
database_cross_reference: ECO:MCC

manual assertion
type: Class
subclass of: assertion method
definition: An assertion method that involves human review.
created_by: mchibucos
creation_date: 2010-11-12T04:20:02Z
has_obo_namespace: eco
id: ECO:0000218
comment: 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.

Axiom
annotated source: manual assertion
annotated property: definition
annotated target: An assertion method that involves human review.
database_cross_reference: ECO:MCC

nucleotide sequencing assay evidence
type: Class
subclass of: sequencing assay evidence
definition: A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides.
created_by: mchibucos
creation_date: 2010-11-15T12:22:40Z
has_obo_namespace: eco
has_related_synonym: DNA sequencing
id: ECO:0000219

Axiom
annotated source: nucleotide sequencing assay evidence
annotated property: definition
annotated target: A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides.
database_cross_reference: ECO:MCC

Axiom
annotated source: nucleotide sequencing assay evidence
annotated property: has_related_synonym
annotated target: DNA sequencing
database_cross_reference: OBI:0000626

sequencing assay evidence
type: Class
subclass of: experimental evidence
definition: A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
created_by: mchibucos
creation_date: 2010-11-15T01:44:45Z
has_obo_namespace: eco
id: ECO:0000220

Axiom
annotated source: sequencing assay evidence
annotated property: definition
annotated target: A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
database_cross_reference: ECO:MCC
database_cross_reference: OBI:0600047

high throughput nucleotide sequencing assay evidence
type: Class
subclass of: nucleotide sequencing assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001247
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001200
definition: A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique.
created_by: mchibucos
creation_date: 2010-11-15T02:19:34Z
has_obo_namespace: eco
has_related_synonym: next generation sequencing evidence
id: ECO:0000221
comment: Typically thousands to millions of reads are produced in parallel.

Axiom
annotated source: high throughput nucleotide sequencing assay evidence
annotated property: definition
annotated target: A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique.
database_cross_reference: ECO:MCC

Illumina sequencing evidence
type: Class
subclass of: high throughput nucleotide sequencing assay evidence
definition: 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.
created_by: mchibucos
creation_date: 2010-11-15T02:38:03Z
has_obo_namespace: eco
has_related_synonym: Solexa sequencing result
id: ECO:0000222
comment: 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.

Axiom
annotated source: Illumina sequencing evidence
annotated property: definition
annotated target: 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.
database_cross_reference: OBI:0000724
database_cross_reference: PMID:26000844

Axiom
annotated source: Illumina sequencing evidence
annotated property: has_related_synonym
annotated target: Solexa sequencing result
database_cross_reference: OBI:0000724

454 pyrosequencing evidence
type: Class
subclass of: high throughput nucleotide sequencing assay evidence
definition: 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.
created_by: mchibucos
creation_date: 2010-11-15T03:50:14Z
has_broad_synonym: pyrosequencing
has_obo_namespace: eco
id: ECO:0000223
comment: 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.

Axiom
annotated source: 454 pyrosequencing evidence
annotated property: definition
annotated target: 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.
database_cross_reference: EFO:0005016

Axiom
annotated source: 454 pyrosequencing evidence
annotated property: has_broad_synonym
annotated target: pyrosequencing
database_cross_reference: OBI:0000730

SOLiD sequencing evidence
type: Class
subclass of: high throughput nucleotide sequencing assay evidence
definition: 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.
created_by: mchibucos
creation_date: 2010-11-15T04:17:41Z
has_obo_namespace: eco
id: ECO:0000224
comment: 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.

Axiom
annotated source: SOLiD sequencing evidence
annotated property: definition
annotated target: 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.
database_cross_reference: OBI:0000706

chain termination sequencing evidence
type: Class
subclass of: nucleotide sequencing assay evidence
definition: 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.
created_by: mchibucos
creation_date: 2010-11-15T04:46:31Z
has_exact_synonym: Sanger sequencing
has_exact_synonym: dye terminator sequencing
has_obo_namespace: eco
id: ECO:0000225
comment: 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.

Axiom
annotated source: chain termination sequencing evidence
annotated property: definition
annotated target: 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.
database_cross_reference: OBI:0000695

chromatin immunoprecipitation evidence
type: Class
subclass of: immunoprecipitation evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0043565
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001956
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001425
definition: A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
created_by: mchibucos
creation_date: 2010-11-16T01:29:08Z
database_cross_reference: MI:0402
has_exact_synonym: ChIP evidence
has_obo_namespace: eco
id: ECO:0000226
comment: 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).

Axiom
annotated source: chromatin immunoprecipitation evidence
annotated property: definition
annotated target: A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
database_cross_reference: ECO:MCC

chromatin immunoprecipitation assay
type: Axiom
annotated source: chromatin immunoprecipitation evidence
annotated property: database_cross_reference
annotated target: MI:0402

chromatin immunoprecipitation-PCR evidence
type: Class
subclass of: chromatin immunoprecipitation evidence
definition: 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.
ontology term requester: CollecTF
created_by: mchibucos
creation_date: 2010-11-16T05:02:00Z
has_exact_synonym: ChIP-PCR evidence
has_obo_namespace: eco
id: ECO:0000227
comment: ChIP-PCR is often used to validate ChIP-chip results and less frequently,ChIP-Seq results.

Axiom
annotated source: chromatin immunoprecipitation-PCR evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: ECO:SW
database_cross_reference: PMID:18388953

chromatin immunoprecipitation-qPCR evidence
type: Class
subclass of: chromatin immunoprecipitation evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002169
example of usage: To confirm the in vivo binding of FimR to pfim, and to determine the impact of Mn2+ and Fe2+ on the binding activity of FimR, chromatin immunoprecipitation (ChIP) assay-quantitative real time PCR (qPCR) with anti-FimR antibody was employed as detailed in the materials and methods. The strongest binding of FimR to pfim was detected in cells grown in the presence of 50 microM MnCl2 and 50 microM FeSO4 (Figure 5, lane IV), whereas minimal amounts of MnCl2 (0.01 microM) and FeSO4 (0.1 microM) led to the weakest binding (Figure 5, lane I).
definition: 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.
created_by: mchibucos
creation_date: 2010-11-16T05:26:47Z
has_exact_synonym: ChIP-qPCR evidence
has_obo_namespace: eco
id: ECO:0000228

Axiom
annotated source: chromatin immunoprecipitation-qPCR evidence
annotated property: example of usage
annotated target: To confirm the in vivo binding of FimR to pfim, and to determine the impact of Mn2+ and Fe2+ on the binding activity of FimR, chromatin immunoprecipitation (ChIP) assay-quantitative real time PCR (qPCR) with anti-FimR antibody was employed as detailed in the materials and methods. The strongest binding of FimR to pfim was detected in cells grown in the presence of 50 microM MnCl2 and 50 microM FeSO4 (Figure 5, lane IV), whereas minimal amounts of MnCl2 (0.01 microM) and FeSO4 (0.1 microM) led to the weakest binding (Figure 5, lane I).
database_cross_reference: PMID:23823757

Axiom
annotated source: chromatin immunoprecipitation-qPCR evidence
annotated property: definition
annotated target: 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.
database_cross_reference: url:https://www.diagenode.com/applications/chip-qpcr

chromatin immunoprecipitation-seq evidence
type: Class
subclass of: chromatin immunoprecipitation evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000716
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001258
definition: 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.
ontology term requester: CollecTF
created_by: mchibucos
creation_date: 2010-11-16T05:30:41Z
has_exact_synonym: ChIP-SEQ evidence
has_exact_synonym: ChIP-seq evidence
has_obo_namespace: eco
id: ECO:0000229
comment: 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.

Axiom
annotated source: chromatin immunoprecipitation-seq evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: ECO:SW
database_cross_reference: OBI:0000716
database_cross_reference: PMID:22955991

Axiom
annotated source: chromatin immunoprecipitation-seq evidence
annotated property: has_exact_synonym
annotated target: ChIP-SEQ evidence
database_cross_reference: OBI:0000716

Axiom
annotated source: chromatin immunoprecipitation-seq evidence
annotated property: has_exact_synonym
annotated target: ChIP-seq evidence
database_cross_reference: PMID:22955991

chromatin immunoprecipitation-chip evidence
type: Class
subclass of: chromatin immunoprecipitation evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001248
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001403
definition: 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.
ontology term requester: CollecTF
created_by: mchibucos
creation_date: 2010-11-16T05:43:55Z
database_cross_reference: MI:0225
has_exact_synonym: ChIP-chip evidence
has_exact_synonym: ChIP-on-chip evidence
has_obo_namespace: eco
id: ECO:0000230
comment: 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.

Axiom
annotated source: chromatin immunoprecipitation-chip evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: ECO:SW
database_cross_reference: PMID:18388953
database_cross_reference: PMID:19381927

chromatin immunoprecipitation array
type: Axiom
annotated source: chromatin immunoprecipitation-chip evidence
annotated property: database_cross_reference
annotated target: MI:0225

quantitative polymerase chain reaction evidence
type: Class
subclass of: DNA detection assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000893
definition: 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.
ontology term requester: CollecTF
created_by: mchibucos
creation_date: 2010-11-16T05:57:20Z
has_exact_synonym: Q-PCR evidence
has_exact_synonym: qPCR evidence
has_exact_synonym: quantitative PCR evidence
has_exact_synonym: quantitative real-time PCR evidence
has_exact_synonym: real time polymerase chain reaction evidence
has_exact_synonym: real-time PCR evidence
has_exact_synonym: real-time quantitative PCR
has_obo_namespace: eco
has_related_synonym: qRT-PCR evidence
id: ECO:0000231
comment: 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.

Axiom
annotated source: quantitative polymerase chain reaction evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: ECO:SW

chromosome conformation-based evidence
type: Class
subclass of: experimental evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002438
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
definition: 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.
created_by: mchibucos
creation_date: 2010-11-17T12:27:14Z
has_exact_synonym: chromosome conformation capture-based evidence
has_narrow_synonym: 3C
has_narrow_synonym: chromosome conformation capture
has_obo_namespace: eco
id: ECO:0000232
comment: 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.

Axiom
annotated source: chromosome conformation-based evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

3C evidence
type: Class
subclass of: chromosome conformation-based evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002439
definition: 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.
created_by: mchibucos
creation_date: 2010-11-17T12:46:15Z
has_exact_synonym: 3C
has_exact_synonym: chromosome conformation capture evidence
has_narrow_synonym: chromosome conformation capture-PCR evidence
has_obo_namespace: eco
id: ECO:0000233
comment: 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.

Axiom
annotated source: 3C evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

4C evidence
type: Class
subclass of: chromosome conformation-based evidence
definition: 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.
created_by: mchibucos
creation_date: 2010-11-19T01:20:28Z
has_exact_synonym: chromosome conformation capture on chip
has_exact_synonym: circularized 3C
has_exact_synonym: circularized chromosome conformation capture evidence
has_obo_namespace: eco
id: ECO:0000234
comment: 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.

Axiom
annotated source: 4C evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: PMID:17033624

5C evidence
type: Class
subclass of: chromosome conformation-based evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001919
definition: A type of chromosome conformation-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
created_by: mchibucos
creation_date: 2010-11-19T01:22:20Z
has_exact_synonym: 5C
has_exact_synonym: carbon-copy 3C
has_exact_synonym: carbon-copy chromosome conformation capture evidence
has_obo_namespace: eco
id: ECO:0000235
comment: 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.

Axiom
annotated source: 5C evidence
annotated property: definition
annotated target: A type of chromosome conformation-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
database_cross_reference: ECO:MCC

chromosome conformation capture-PCR evidence
type: Class
definition: A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
created_by: mchibucos
creation_date: 2010-11-19T03:00:47Z
has_broad_synonym: 3C
has_exact_synonym: 3C-PCR
has_obo_namespace: eco
id: ECO:0000236
comment: See 3C evidence. 3C evidence was initially developed using PCR.
deprecated: true

Axiom
annotated source: chromosome conformation capture-PCR evidence
annotated property: definition
annotated target: A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
database_cross_reference: ECO:MCC

3C-qPCR evidence
type: Class
subclass of: 3C evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000893
    intersection of: OBI_0002439
definition: 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.
created_by: mchibucos
creation_date: 2010-11-19T03:06:47Z
has_exact_synonym: 3C-quantitative PCR
has_exact_synonym: 3C-real-time PCR
has_exact_synonym: chromosome conformation capture-qPCR evidence
has_obo_namespace: eco
id: ECO:0000237

Axiom
annotated source: 3C-qPCR evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: PMID:17641637
database_cross_reference: PMID:26025624

Hi-C evidence
type: Class
subclass of: chromosome conformation-based evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002440
definition: 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.
created_by: mchibucos
creation_date: 2010-11-19T04:24:03Z
has_obo_namespace: eco
id: ECO:0000238
comment: 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.

Axiom
annotated source: Hi-C evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

3C-seq evidence
type: Class
subclass of: chromosome conformation-based evidence
definition: 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.
created_by: mchibucos
creation_date: 2010-11-30T03:22:25Z
has_exact_synonym: 3C sequencing
has_exact_synonym: circularized 3C sequencing
has_exact_synonym: circularized 3C-seq
has_obo_namespace: eco
has_related_synonym: chromosome conformation capture sequencing evidence
id: ECO:0000239
comment: 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.

Axiom
annotated source: 3C-seq evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: PMID:23411633

anatomical perturbation phenotypic evidence
type: Class
subclass of: experimental phenotypic evidence
definition: A type of experimental phenotypic evidence resulting from the disruption of a structural feature.
created_by: mchibucos
creation_date: 2010-12-06T12:24:16Z
has_exact_synonym: anatomical perturbation evidence
has_obo_namespace: eco
id: ECO:0000240

Axiom
annotated source: anatomical perturbation phenotypic evidence
annotated property: definition
annotated target: A type of experimental phenotypic evidence resulting from the disruption of a structural feature.
database_cross_reference: ECO:MCC

environmental perturbation phenotypic evidence
type: Class
subclass of: experimental phenotypic evidence
definition: A type of experimental phenotypic evidence resulting from modification to the surroundings or conditions in which an organism lives or operates.
created_by: mchibucos
creation_date: 2010-12-06T12:33:58Z
has_exact_synonym: environmental perturbation evidence
has_obo_namespace: eco
has_related_synonym: mechanical constraint evidence
id: ECO:0000241
comment: Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth.

Axiom
annotated source: environmental perturbation phenotypic evidence
annotated property: definition
annotated target: A type of experimental phenotypic evidence resulting from modification to the surroundings or conditions in which an organism lives or operates.
database_cross_reference: ECO:MCC

tissue ablation phenotypic evidence
type: Class
subclass of: anatomical perturbation phenotypic evidence
definition: A type of anatomical perturbation phenotypic evidence resulting from the surgical removal of tissue or subcellular components.
created_by: mchibucos
creation_date: 2010-12-06T12:33:58Z
has_exact_synonym: ablated tissue evidence
has_exact_synonym: tissue ablation evidence
has_obo_namespace: eco
id: ECO:0000242

Axiom
annotated source: tissue ablation phenotypic evidence
annotated property: definition
annotated target: A type of anatomical perturbation phenotypic evidence resulting from the surgical removal of tissue or subcellular components.
database_cross_reference: ECO:MCC

tissue grafting phenotypic evidence
type: Class
subclass of: anatomical perturbation phenotypic evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000105
definition: A type of anatomical perturbation phenotypic evidence resulting from the addition of tissue to an organism through a graft procedure.
created_by: mchibucos
creation_date: 2010-12-06T12:33:58Z
has_exact_synonym: tissue grafting evidence
has_obo_namespace: eco
id: ECO:0000243

Axiom
annotated source: tissue grafting phenotypic evidence
annotated property: definition
annotated target: A type of anatomical perturbation phenotypic evidence resulting from the addition of tissue to an organism through a graft procedure.
database_cross_reference: ECO:MCC

combinatorial evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: combinatorial evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: combinatorial evidence
subclass of: evidence used in manual assertion
definition: A type of combinatorial analysis that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-09T02:02:12Z
has_obo_namespace: eco
has_related_synonym: inferred from in-silico analysis
id: ECO:0000244
comment: 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.

Axiom
annotated source: combinatorial evidence used in manual assertion
annotated property: subClassOf
annotated target: evidence used in manual assertion
is_inferred: true

Axiom
annotated source: combinatorial evidence used in manual assertion
annotated property: definition
annotated target: A type of combinatorial analysis that is used in a manual assertion.
database_cross_reference: ECO:MCC

automatically integrated combinatorial evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: ECO_0007673
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: combinatorial evidence used in manual assertion
subclass of: ECO_0007673
has GO evidence code: RCA
definition: A type of automatically integrated combinatorial evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-09T02:37:54Z
database_cross_reference: GOECO:RCA
has_exact_synonym: RCA
has_exact_synonym: inferred from reviewed computational analysis
has_obo_namespace: eco
has_related_synonym: computational combinatorial evidence used in manual assertion
id: ECO:0000245
in_subset: valid_with_gene
in_subset: valid_with_protein
in_subset: valid_with_protein_complex

Axiom
annotated source: automatically integrated combinatorial evidence used in manual assertion
annotated property: subClassOf
annotated target: combinatorial evidence used in manual assertion
is_inferred: true

Axiom
annotated source: automatically integrated combinatorial evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007673
is_inferred: true

Axiom
annotated source: automatically integrated combinatorial evidence used in manual assertion
annotated property: has GO evidence code
annotated target: RCA
comment: Default

Axiom
annotated source: automatically integrated combinatorial evidence used in manual assertion
annotated property: definition
annotated target: A type of automatically integrated combinatorial evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

inferred from reviewed computational analysis
type: Axiom
annotated source: automatically integrated combinatorial evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:RCA

Axiom
annotated source: automatically integrated combinatorial evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: RCA
database_cross_reference: GOECO:RCA

Axiom
annotated source: automatically integrated combinatorial evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from reviewed computational analysis
database_cross_reference: GOECO:RCA

computational combinatorial evidence used in automatic assertion
type: Class
definition: A type of computational combinatorial analysis that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-12-09T02:37:54Z
has_obo_namespace: eco
id: ECO:0000246
comment: Merged with ECO:0000053.
deprecated: true

Axiom
annotated source: computational combinatorial evidence used in automatic assertion
annotated property: definition
annotated target: A type of computational combinatorial analysis that is used in an automatic assertion.
database_cross_reference: ECO:MCC

sequence alignment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: sequence alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: sequence alignment evidence
subclass of: sequence similarity evidence used in manual assertion
has GO evidence code: ISA
definition: A type of sequence alignment evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-09T05:12:27Z
database_cross_reference: GOECO:ISA
has_exact_synonym: ISA
has_exact_synonym: inferred from sequence alignment
has_obo_namespace: eco
id: ECO:0000247
in_subset: valid_with_gene
in_subset: valid_with_protein

Axiom
annotated source: sequence alignment evidence used in manual assertion
annotated property: subClassOf
annotated target: sequence similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: sequence alignment evidence used in manual assertion
annotated property: has GO evidence code
annotated target: ISA
comment: Default

Axiom
annotated source: sequence alignment evidence used in manual assertion
annotated property: definition
annotated target: A type of sequence alignment evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

inferred from sequence alignment
type: Axiom
annotated source: sequence alignment evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:ISA

Axiom
annotated source: sequence alignment evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: ISA
database_cross_reference: GOECO:ISA

Axiom
annotated source: sequence alignment evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from sequence alignment
database_cross_reference: GOECO:ISA

sequence alignment evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: sequence alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: sequence alignment evidence
subclass of: sequence similarity evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of sequence alignment evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-12-09T05:12:27Z
has_obo_namespace: eco
id: ECO:0000248

Axiom
annotated source: sequence alignment evidence used in automatic assertion
annotated property: subClassOf
annotated target: sequence similarity evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: sequence alignment evidence used in automatic assertion
annotated property: definition
annotated target: A type of sequence alignment evidence that is used in an automatic assertion.
database_cross_reference: ECO:RCT

sequence similarity evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: sequence similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: sequence similarity evidence
subclass of: similarity evidence used in automatic assertion
subclass of: ECO_0007669
has GO evidence code: IEA
definition: A type of sequence similarity evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-12-09T05:22:30Z
database_cross_reference: GO_REF:0000107
has_obo_namespace: eco
id: ECO:0000249

Axiom
annotated source: sequence similarity evidence used in automatic assertion
annotated property: subClassOf
annotated target: similarity evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: sequence similarity evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007669
is_inferred: true

Axiom
annotated source: sequence similarity evidence used in automatic assertion
annotated property: definition
annotated target: A type of sequence similarity evidence that is used in an automatic assertion.
database_cross_reference: ECO:RCT

Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl
type: Axiom
annotated source: sequence similarity evidence used in automatic assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000107

sequence similarity evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: sequence similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: sequence similarity evidence
subclass of: similarity evidence used in manual assertion
subclass of: ECO_0007668
has GO evidence code: ISS
definition: A type of sequence similarity evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-09T05:22:30Z
database_cross_reference: GOECO:ISS
has_exact_synonym: ISS
has_exact_synonym: inferred from sequence or structural similarity
has_obo_namespace: eco
id: ECO:0000250
in_subset: valid_with_gene
in_subset: valid_with_protein
in_subset: valid_with_protein_complex

Axiom
annotated source: sequence similarity evidence used in manual assertion
annotated property: subClassOf
annotated target: similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: sequence similarity evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007668
is_inferred: true

Axiom
annotated source: sequence similarity evidence used in manual assertion
annotated property: has GO evidence code
annotated target: ISS
comment: Default

Axiom
annotated source: sequence similarity evidence used in manual assertion
annotated property: definition
annotated target: A type of sequence similarity evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from sequence or structural similarity
type: Axiom
annotated source: sequence similarity evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:ISS

Axiom
annotated source: sequence similarity evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: ISS
database_cross_reference: GOECO:ISS

Axiom
annotated source: sequence similarity evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from sequence or structural similarity
database_cross_reference: GOECO:ISS

similarity evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: similarity evidence
subclass of: evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of similarity evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-12-09T05:28:12Z
has_broad_synonym: IS
has_obo_namespace: eco
has_related_synonym: inferred from similarity
id: ECO:0000251

Axiom
annotated source: similarity evidence used in automatic assertion
annotated property: subClassOf
annotated target: evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: similarity evidence used in automatic assertion
annotated property: definition
annotated target: A type of similarity evidence that is used in an automatic assertion.
database_cross_reference: ECO:RCT

similarity evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: similarity evidence
subclass of: evidence used in manual assertion
definition: A type of similarity evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-09T05:28:12Z
has_broad_synonym: IS
has_obo_namespace: eco
has_related_synonym: inferred from similarity
id: ECO:0000252
in_subset: go_groupings

Axiom
annotated source: similarity evidence used in manual assertion
annotated property: subClassOf
annotated target: evidence used in manual assertion
is_inferred: true

Axiom
annotated source: similarity evidence used in manual assertion
annotated property: definition
annotated target: A type of similarity evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

genetic similarity evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: genetic similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: genetic similarity evidence
subclass of: similarity evidence used in manual assertion
definition: A type of genetic similarity evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-10T01:42:44Z
has_broad_synonym: IGTS
has_obo_namespace: eco
has_related_synonym: inferred from genetic similarity
id: ECO:0000253

Axiom
annotated source: genetic similarity evidence used in manual assertion
annotated property: subClassOf
annotated target: similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: genetic similarity evidence used in manual assertion
annotated property: definition
annotated target: A type of genetic similarity evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

genetic similarity evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: genetic similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: genetic similarity evidence
subclass of: similarity evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of genetic similarity evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-12-10T01:42:44Z
has_broad_synonym: IGTS
has_obo_namespace: eco
has_related_synonym: inferred from genetic similarity
id: ECO:0000254

Axiom
annotated source: genetic similarity evidence used in automatic assertion
annotated property: subClassOf
annotated target: similarity evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: genetic similarity evidence used in automatic assertion
annotated property: definition
annotated target: A type of genetic similarity evidence that is used in an automatic assertion.
database_cross_reference: ECO:RCT

match to sequence model evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: match to sequence model evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: match to sequence model evidence
subclass of: sequence similarity evidence used in manual assertion
has GO evidence code: ISM
definition: A type of match to sequence model evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-10T02:26:35Z
database_cross_reference: GOECO:ISM
database_cross_reference: GO_REF:0000011
has_exact_synonym: ISM
has_exact_synonym: inferred from sequence model
has_obo_namespace: eco
id: ECO:0000255

Axiom
annotated source: match to sequence model evidence used in manual assertion
annotated property: subClassOf
annotated target: sequence similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: match to sequence model evidence used in manual assertion
annotated property: has GO evidence code
annotated target: ISM
comment: Default

Axiom
annotated source: match to sequence model evidence used in manual assertion
annotated property: definition
annotated target: A type of match to sequence model evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

inferred from sequence model
type: Axiom
annotated source: match to sequence model evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:ISM

Hidden Markov Models (TIGR)
type: Axiom
annotated source: match to sequence model evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000011

Axiom
annotated source: match to sequence model evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: ISM
database_cross_reference: GOECO:ISM

Axiom
annotated source: match to sequence model evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from sequence model
database_cross_reference: GOECO:ISM

match to sequence model evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: match to sequence model evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: match to sequence model evidence
subclass of: sequence similarity evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of match to sequence model evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-12-10T02:26:35Z
database_cross_reference: GO_REF:0000002
has_obo_namespace: eco
id: ECO:0000256

Axiom
annotated source: match to sequence model evidence used in automatic assertion
annotated property: subClassOf
annotated target: sequence similarity evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: match to sequence model evidence used in automatic assertion
annotated property: definition
annotated target: A type of match to sequence model evidence that is used in an automatic assertion.
database_cross_reference: ECO:RCT

Gene Ontology annotation through association of InterPro records with GO terms.
type: Axiom
annotated source: match to sequence model evidence used in automatic assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000002

motif similarity evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: motif similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: motif similarity evidence
subclass of: match to sequence model evidence used in manual assertion
has GO evidence code: ISM
definition: A type of motif similarity evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-10T02:44:34Z
has_obo_namespace: eco
has_related_synonym: recognized domains
id: ECO:0000257

Axiom
annotated source: motif similarity evidence used in manual assertion
annotated property: subClassOf
annotated target: match to sequence model evidence used in manual assertion
is_inferred: true

Axiom
annotated source: motif similarity evidence used in manual assertion
annotated property: definition
annotated target: A type of motif similarity evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

motif similarity evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: motif similarity evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: motif similarity evidence
subclass of: match to sequence model evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of motif similarity evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-12-10T02:44:34Z
has_obo_namespace: eco
has_related_synonym: recognized domains
id: ECO:0000258

Axiom
annotated source: motif similarity evidence used in automatic assertion
annotated property: subClassOf
annotated target: match to sequence model evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: motif similarity evidence used in automatic assertion
annotated property: definition
annotated target: A type of motif similarity evidence that is used in an automatic assertion.
database_cross_reference: ECO:RCT

match to InterPro member signature evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: match to InterPro member signature evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: match to InterPro member signature evidence
subclass of: match to sequence model evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of match to InterPro member signature evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-12-10T02:54:51Z
has_obo_namespace: eco
id: ECO:0000259

Axiom
annotated source: match to InterPro member signature evidence used in automatic assertion
annotated property: subClassOf
annotated target: match to sequence model evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: match to InterPro member signature evidence used in automatic assertion
annotated property: definition
annotated target: A type of match to InterPro member signature evidence that is used in an automatic assertion.
database_cross_reference: ECO:RCT

match to InterPro member signature evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: match to InterPro member signature evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: match to InterPro member signature evidence
subclass of: match to sequence model evidence used in manual assertion
has GO evidence code: ISM
definition: A type of match to InterPro member signature evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-10T02:54:51Z
has_obo_namespace: eco
id: ECO:0000260

Axiom
annotated source: match to InterPro member signature evidence used in manual assertion
annotated property: subClassOf
annotated target: match to sequence model evidence used in manual assertion
is_inferred: true

Axiom
annotated source: match to InterPro member signature evidence used in manual assertion
annotated property: definition
annotated target: A type of match to InterPro member signature evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

targeting sequence prediction evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: targeting sequence prediction evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: targeting sequence prediction evidence
subclass of: motif similarity evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of targeting sequence prediction that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-12-10T03:02:49Z
has_obo_namespace: eco
has_related_synonym: targeting sequence prediction
id: ECO:0000261

Axiom
annotated source: targeting sequence prediction evidence used in automatic assertion
annotated property: subClassOf
annotated target: motif similarity evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: targeting sequence prediction evidence used in automatic assertion
annotated property: definition
annotated target: A type of targeting sequence prediction that is used in an automatic assertion.
database_cross_reference: ECO:RCT

targeting sequence prediction evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: targeting sequence prediction evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: targeting sequence prediction evidence
subclass of: motif similarity evidence used in manual assertion
has GO evidence code: ISM
definition: A type of targeting sequence prediction that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-10T03:02:49Z
has_obo_namespace: eco
has_related_synonym: targeting sequence prediction
id: ECO:0000262

Axiom
annotated source: targeting sequence prediction evidence used in manual assertion
annotated property: subClassOf
annotated target: motif similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: targeting sequence prediction evidence used in manual assertion
annotated property: definition
annotated target: A type of targeting sequence prediction that is used in a manual assertion.
database_cross_reference: ECO:RCT

transmembrane domain prediction evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: transmembrane domain prediction evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: transmembrane domain prediction evidence
subclass of: motif similarity evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of transmembrane domain prediction that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-12-10T03:28:35Z
has_obo_namespace: eco
has_related_synonym: transmembrane domain prediction
id: ECO:0000263

Axiom
annotated source: transmembrane domain prediction evidence used in automatic assertion
annotated property: subClassOf
annotated target: motif similarity evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: transmembrane domain prediction evidence used in automatic assertion
annotated property: definition
annotated target: A type of transmembrane domain prediction that is used in an automatic assertion.
database_cross_reference: ECO:RCT

transmembrane domain prediction evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: transmembrane domain prediction evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: transmembrane domain prediction evidence
subclass of: motif similarity evidence used in manual assertion
has GO evidence code: ISM
definition: A type of transmembrane domain prediction that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-10T03:28:35Z
has_obo_namespace: eco
has_related_synonym: transmembrane domain prediction
id: ECO:0000264

Axiom
annotated source: transmembrane domain prediction evidence used in manual assertion
annotated property: subClassOf
annotated target: motif similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: transmembrane domain prediction evidence used in manual assertion
annotated property: definition
annotated target: A type of transmembrane domain prediction that is used in a manual assertion.
database_cross_reference: ECO:RCT

sequence orthology evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: sequence orthology evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: sequence orthology evidence
subclass of: sequence similarity evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of sequence orthology evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2010-12-10T03:39:41Z
database_cross_reference: GO_REF:0000035
has_obo_namespace: eco
has_related_synonym: Ortholog evidence
has_related_synonym: ortholog evidence
id: ECO:0000265

Axiom
annotated source: sequence orthology evidence used in automatic assertion
annotated property: subClassOf
annotated target: sequence similarity evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: sequence orthology evidence used in automatic assertion
annotated property: definition
annotated target: A type of sequence orthology evidence that is used in an automatic assertion.
database_cross_reference: ECO:RCT

Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara
type: Axiom
annotated source: sequence orthology evidence used in automatic assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000035

sequence orthology evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: sequence orthology evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: sequence orthology evidence
subclass of: sequence similarity evidence used in manual assertion
has GO evidence code: ISO
definition: A type of sequence orthology evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-10T03:39:41Z
database_cross_reference: GOECO:ISO
has_exact_synonym: ISO
has_exact_synonym: inferred from sequence orthology
has_obo_namespace: eco
has_related_synonym: Ortholog evidence
has_related_synonym: ortholog evidence
id: ECO:0000266
in_subset: valid_with_gene
in_subset: valid_with_protein
in_subset: valid_with_protein_complex

Axiom
annotated source: sequence orthology evidence used in manual assertion
annotated property: subClassOf
annotated target: sequence similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: sequence orthology evidence used in manual assertion
annotated property: has GO evidence code
annotated target: ISO
comment: Default

Axiom
annotated source: sequence orthology evidence used in manual assertion
annotated property: definition
annotated target: A type of sequence orthology evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from sequence orthology
type: Axiom
annotated source: sequence orthology evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:ISO

Axiom
annotated source: sequence orthology evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: ISO
database_cross_reference: GOECO:ISO

GOECO:ISO
type: Axiom
annotated source: sequence orthology evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from sequence orthology

enzyme-linked immunoabsorbent assay evidence
type: Class
subclass of: protein detection assay evidence
definition: 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.
ontology term requester: CollecTF
created_by: mchibucos
creation_date: 2010-12-14T01:57:13Z
database_cross_reference: MI:0411
has_exact_synonym: ELISA evidence
has_narrow_synonym: enzyme-linked immunosorbent assay
has_obo_namespace: eco
id: ECO:0000267
comment: ELISA is sometimes used in the study of transcriptional regulation to identify a produced protein, especially secreted protein.

Axiom
annotated source: enzyme-linked immunoabsorbent assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: ECO:SW
database_cross_reference: PMID:23949770

enzyme linked immunosorbent assay
type: Axiom
annotated source: enzyme-linked immunoabsorbent assay evidence
annotated property: database_cross_reference
annotated target: MI:0411

flow cytometry evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000916
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
definition: 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.
created_by: mchibucos
creation_date: 2010-12-14T02:07:08Z
has_exact_synonym: FCM
has_obo_namespace: eco
id: ECO:0000268

Axiom
annotated source: flow cytometry evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

experimental evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: experimental evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence
subclass of: evidence used in manual assertion
has GO evidence code: EXP
definition: A type of experimental evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T05:36:49Z
database_cross_reference: GOECO:EXP
has_exact_synonym: EXP
has_exact_synonym: inferred from experiment
has_obo_namespace: eco
id: ECO:0000269

Axiom
annotated source: experimental evidence used in manual assertion
annotated property: subClassOf
annotated target: evidence used in manual assertion
is_inferred: true

Axiom
annotated source: experimental evidence used in manual assertion
annotated property: has GO evidence code
annotated target: EXP
comment: Default

Axiom
annotated source: experimental evidence used in manual assertion
annotated property: definition
annotated target: A type of experimental evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from experiment
type: Axiom
annotated source: experimental evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:EXP

Axiom
annotated source: experimental evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: EXP
database_cross_reference: GOECO:EXP

Axiom
annotated source: experimental evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from experiment
database_cross_reference: GOECO:EXP

expression pattern evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: expression pattern evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence
subclass of: experimental evidence used in manual assertion
has GO evidence code: IEP
definition: A type of expression pattern evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T05:46:39Z
database_cross_reference: GOECO:IEP
has_exact_synonym: IEP
has_exact_synonym: inferred from expression pattern
has_obo_namespace: eco
id: ECO:0000270

Axiom
annotated source: expression pattern evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: expression pattern evidence used in manual assertion
annotated property: has GO evidence code
annotated target: IEP
comment: Default

Axiom
annotated source: expression pattern evidence used in manual assertion
annotated property: definition
annotated target: A type of expression pattern evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from expression pattern
type: Axiom
annotated source: expression pattern evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:IEP

Axiom
annotated source: expression pattern evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: IEP
database_cross_reference: GOECO:IEP

Axiom
annotated source: expression pattern evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from expression pattern
database_cross_reference: GOECO:IEP

array experiment evidence used in manual assertion
type: Class
created_by: mchibucos
creation_date: 2010-12-20T05:51:58Z
has_obo_namespace: eco
id: ECO:0000271
comment: 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.)
deprecated: true

Affymetrix GeneChip evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Affymetrix GeneChip evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: Affymetrix GeneChip evidence
subclass of: cRNA to DNA expression microarray evidence used in manual assertion
has GO evidence code: IEP
definition: A type of Affymetrix GeneChip evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T05:53:36Z
has_broad_synonym: Affymetrix array experiment evidence
has_obo_namespace: eco
id: ECO:0000272

Axiom
annotated source: Affymetrix GeneChip evidence used in manual assertion
annotated property: subClassOf
annotated target: cRNA to DNA expression microarray evidence used in manual assertion
is_inferred: true

Axiom
annotated source: Affymetrix GeneChip evidence used in manual assertion
annotated property: definition
annotated target: A type of Affymetrix GeneChip evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

cDNA to DNA expression microarray evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cDNA to DNA expression microarray evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: cDNA to DNA expression microarray evidence
subclass of: expression microarray evidence used in manual assertion
has GO evidence code: IEP
definition: A type of cDNA to DNA expression microarray evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T05:55:49Z
has_alternative_id: ECO:0001178
has_alternative_id: ECO:0005525
has_obo_namespace: eco
has_related_synonym: DNA microarray|RNA microarray
id: ECO:0000273

Axiom
annotated source: cDNA to DNA expression microarray evidence used in manual assertion
annotated property: subClassOf
annotated target: expression microarray evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cDNA to DNA expression microarray evidence used in manual assertion
annotated property: definition
annotated target: A type of cDNA to DNA expression microarray evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

differential methylation hybridization evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: differential methylation hybridization evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: differential methylation hybridization evidence
subclass of: in vitro methylation assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of differential methylation hybridization evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T05:58:44Z
has_broad_synonym: CpG island microarray evidence
has_exact_synonym: CpG island microarray evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0000274

Axiom
annotated source: differential methylation hybridization evidence used in manual assertion
annotated property: subClassOf
annotated target: in vitro methylation assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: differential methylation hybridization evidence used in manual assertion
annotated property: definition
annotated target: A type of differential methylation hybridization evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

expression microarray evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: expression microarray evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression microarray evidence
subclass of: transcript expression evidence used in manual assertion
has GO evidence code: IEP
definition: A type of expression microarray evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:01:26Z
has_obo_namespace: eco
has_related_synonym: differential gene expression evidence from microarray experiment
id: ECO:0000275

Axiom
annotated source: expression microarray evidence used in manual assertion
annotated property: subClassOf
annotated target: transcript expression evidence used in manual assertion
is_inferred: true

Axiom
annotated source: expression microarray evidence used in manual assertion
annotated property: definition
annotated target: A type of expression microarray evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

cRNA to DNA expression microarray evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cRNA to DNA expression microarray evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: cRNA to DNA expression microarray evidence
subclass of: expression microarray evidence used in manual assertion
has GO evidence code: IEP
definition: A type of cRNA to DNA expression microarray evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:03:28Z
has_broad_synonym: genomic microarray evidence
has_exact_synonym: genomic microarray evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0000276

Axiom
annotated source: cRNA to DNA expression microarray evidence used in manual assertion
annotated property: subClassOf
annotated target: expression microarray evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cRNA to DNA expression microarray evidence used in manual assertion
annotated property: definition
annotated target: A type of cRNA to DNA expression microarray evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

Nimblegen array evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Nimblegen array evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: Nimblegen array evidence
subclass of: cDNA to DNA expression microarray evidence used in manual assertion
has GO evidence code: IEP
definition: A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:05:20Z
has_obo_namespace: eco
id: ECO:0000277

Axiom
annotated source: Nimblegen array evidence used in manual assertion
annotated property: subClassOf
annotated target: cDNA to DNA expression microarray evidence used in manual assertion
is_inferred: true

Axiom
annotated source: Nimblegen array evidence used in manual assertion
annotated property: definition
annotated target: A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
database_cross_reference: ECO:MCC

array-based sequence capture evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: array-based sequence capture evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: array-based sequence capture evidence
subclass of: experimental evidence used in manual assertion
has GO evidence code: EXP
definition: A type of array-based sequence capture evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:09:45Z
has_broad_synonym: DNA microarray
has_broad_synonym: oligonucleotide microarray evidence
has_broad_synonym: oligonucleotide microarray evidence used in manual assertion
has_obo_namespace: eco
has_related_synonym: SNP array evidence
has_related_synonym: single nucleotide polymorphism array evidence
id: ECO:0000278

Axiom
annotated source: array-based sequence capture evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: array-based sequence capture evidence used in manual assertion
annotated property: definition
annotated target: A type of array-based sequence capture evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

qualitative western immunoblotting evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: qualitative western immunoblotting evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: qualitative western immunoblotting evidence
subclass of: protein expression evidence used in manual assertion
subclass of: direct assay evidence used in manual assertion
has GO evidence code: IEP
definition: A type of qualitative western immunoblotting evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:20:01Z
has_alternative_id: ECO:0007183
has_exact_synonym: protein expression level evidence based on western blot used in manual assertion
has_obo_namespace: eco
has_related_synonym: Western blot expression analysis
has_related_synonym: protein immunoblot
has_related_synonym: protein levels (e.g. Western blots)
id: ECO:0000279

Axiom
annotated source: qualitative western immunoblotting evidence used in manual assertion
annotated property: subClassOf
annotated target: protein expression evidence used in manual assertion
is_inferred: true

Axiom
annotated source: qualitative western immunoblotting evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: qualitative western immunoblotting evidence used in manual assertion
annotated property: definition
annotated target: A type of qualitative western immunoblotting evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

expression library screen evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: expression library screen evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression library screen evidence
subclass of: protein expression evidence used in manual assertion
has GO evidence code: IEP
definition: A type of expression library screen evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:24:05Z
has_obo_namespace: eco
has_related_synonym: expression library screening
id: ECO:0000281

Axiom
annotated source: expression library screen evidence used in manual assertion
annotated property: subClassOf
annotated target: protein expression evidence used in manual assertion
is_inferred: true

Axiom
annotated source: expression library screen evidence used in manual assertion
annotated property: definition
annotated target: A type of expression library screen evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

heterologous protein expression evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: heterologous protein expression evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: heterologous protein expression evidence
subclass of: protein expression evidence used in manual assertion
has GO evidence code: IEP
definition: A type of heterologous protein expression analysis that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:27:04Z
has_obo_namespace: eco
has_related_synonym: protein expression in heterologous system
id: ECO:0000282

Axiom
annotated source: heterologous protein expression evidence used in manual assertion
annotated property: subClassOf
annotated target: protein expression evidence used in manual assertion
is_inferred: true

Axiom
annotated source: heterologous protein expression evidence used in manual assertion
annotated property: definition
annotated target: A type of heterologous protein expression analysis that is used in a manual assertion.
database_cross_reference: ECO:MCC

spatial pattern of protein expression evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: spatial pattern of protein expression evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: spatial pattern of protein expression evidence
subclass of: protein expression evidence used in manual assertion
has GO evidence code: IEP
definition: A type of protein expression spatial pattern analysis that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:31:44Z
has_obo_namespace: eco
id: ECO:0000283

Axiom
annotated source: spatial pattern of protein expression evidence used in manual assertion
annotated property: subClassOf
annotated target: protein expression evidence used in manual assertion
is_inferred: true

Axiom
annotated source: spatial pattern of protein expression evidence used in manual assertion
annotated property: definition
annotated target: A type of protein expression spatial pattern analysis that is used in a manual assertion.
database_cross_reference: ECO:MCC

protein expression evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein expression evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: protein expression evidence
subclass of: expression pattern evidence used in manual assertion
has GO evidence code: IEP
definition: A type of protein expression analysis that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:33:46Z
has_alternative_id: ECO:0000280
has_exact_synonym: protein expression level evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0000284

Axiom
annotated source: protein expression evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

Axiom
annotated source: protein expression evidence used in manual assertion
annotated property: definition
annotated target: A type of protein expression analysis that is used in a manual assertion.
database_cross_reference: ECO:MCC

DNA to cDNA expression microarray evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: DNA to cDNA expression microarray evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: DNA to cDNA expression microarray evidence
subclass of: expression microarray evidence used in manual assertion
has GO evidence code: IEP
definition: A type of DNA to cDNA expression microarray evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:41:33Z
has_broad_synonym: REM evidence
has_broad_synonym: RNA expression microarray evidence
has_broad_synonym: microarray RNA expression level evidence
has_obo_namespace: eco
has_related_synonym: transcript levels (e.g. microarray data)
id: ECO:0000285

Axiom
annotated source: DNA to cDNA expression microarray evidence used in manual assertion
annotated property: subClassOf
annotated target: expression microarray evidence used in manual assertion
is_inferred: true

Axiom
annotated source: DNA to cDNA expression microarray evidence used in manual assertion
annotated property: definition
annotated target: A type of DNA to cDNA expression microarray evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

differential hybridization evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: differential hybridization evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: differential hybridization evidence
subclass of: transcript expression evidence used in manual assertion
has GO evidence code: IEP
definition: A type of differential hybridization experiment that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:55:14Z
has_obo_namespace: eco
has_related_synonym: differential hybridization
id: ECO:0000287

Axiom
annotated source: differential hybridization evidence used in manual assertion
annotated property: subClassOf
annotated target: transcript expression evidence used in manual assertion
is_inferred: true

Axiom
annotated source: differential hybridization evidence used in manual assertion
annotated property: definition
annotated target: A type of differential hybridization experiment that is used in a manual assertion.
database_cross_reference: ECO:MCC

RNA protection assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: RNA protection assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: RNA protection assay evidence
subclass of: nuclease protection assay evidence used in manual assertion
has GO evidence code: EXP
definition: A type of RNA protection assay that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:57:33Z
has_broad_synonym: ribonuclease protection assay
has_obo_namespace: eco
has_related_synonym: RNA protection assay|RPA
has_related_synonym: RNAse protection assay
id: ECO:0000288

Axiom
annotated source: RNA protection assay evidence used in manual assertion
annotated property: subClassOf
annotated target: nuclease protection assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: RNA protection assay evidence used in manual assertion
annotated property: definition
annotated target: A type of RNA protection assay that is used in a manual assertion.
database_cross_reference: ECO:MCC

spatial pattern of transcript expression evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: spatial pattern of transcript expression evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: spatial pattern of transcript expression evidence
subclass of: transcript expression evidence used in manual assertion
has GO evidence code: IEP
definition: A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T06:59:18Z
has_obo_namespace: eco
id: ECO:0000289

Axiom
annotated source: spatial pattern of transcript expression evidence used in manual assertion
annotated property: subClassOf
annotated target: transcript expression evidence used in manual assertion
is_inferred: true

Axiom
annotated source: spatial pattern of transcript expression evidence used in manual assertion
annotated property: definition
annotated target: A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
database_cross_reference: ECO:MCC

subtractive hybridization evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: subtractive hybridization evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: subtractive hybridization evidence
subclass of: transcript expression evidence used in manual assertion
has GO evidence code: IEP
definition: A type of subtractive hybridization experiment that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T07:00:48Z
has_obo_namespace: eco
has_related_synonym: subtractive hybridization
id: ECO:0000290

Axiom
annotated source: subtractive hybridization evidence used in manual assertion
annotated property: subClassOf
annotated target: transcript expression evidence used in manual assertion
is_inferred: true

Axiom
annotated source: subtractive hybridization evidence used in manual assertion
annotated property: definition
annotated target: A type of subtractive hybridization experiment that is used in a manual assertion.
database_cross_reference: ECO:MCC

transcript expression evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: transcript expression evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: transcript expression evidence
subclass of: expression pattern evidence used in manual assertion
has GO evidence code: IEP
definition: A type of transcript expression evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2010-12-20T07:02:08Z
has_alternative_id: ECO:0000286
has_broad_synonym: transcript expression level evidence
has_exact_synonym: transcriptomics evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0000291

Axiom
annotated source: transcript expression evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

Axiom
annotated source: transcript expression evidence used in manual assertion
annotated property: definition
annotated target: A type of transcript expression evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

morpholino experiment evidence
type: Class
subclass of: mutant phenotype evidence
definition: A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
created_by: mchibucos
creation_date: 2011-01-10T03:36:25Z
has_broad_synonym: anti-sense
has_obo_namespace: eco
id: ECO:0000292
comment: 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.

Axiom
annotated source: morpholino experiment evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
database_cross_reference: ECO:MCC

systematic evolution of ligands by exponential amplification evidence
type: Class
subclass of: physical interaction evidence
example of usage: A total of 160 SELEX fragments were cloned and sequenced, which were classified into 29 CRP-binding sequences, including 13 previously identified loci and 16 newly identified sites (Table S2). When the CRP-binding sequences are located upstream or near promoters of the flanking genes, these genes are predicted to be under the control of CRP.
definition: 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.
created_by: mchibucos
creation_date: 2011-01-10T04:23:50Z
database_cross_reference: MI:0657
has_exact_synonym: SELEX evidence
has_exact_synonym: in vitro selection evidence
has_obo_namespace: eco
has_related_synonym: in vitro evolution evidence
id: ECO:0000293
comment: 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.

Axiom
annotated source: systematic evolution of ligands by exponential amplification evidence
annotated property: example of usage
annotated target: A total of 160 SELEX fragments were cloned and sequenced, which were classified into 29 CRP-binding sequences, including 13 previously identified loci and 16 newly identified sites (Table S2). When the CRP-binding sequences are located upstream or near promoters of the flanking genes, these genes are predicted to be under the control of CRP.
database_cross_reference: PMID:21673794

Axiom
annotated source: systematic evolution of ligands by exponential amplification evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: url:http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment

systematic evolution of ligands by exponential enrichment
type: Axiom
annotated source: systematic evolution of ligands by exponential amplification evidence
annotated property: database_cross_reference
annotated target: MI:0657

bacterial one-hybrid evidence
type: Class
subclass of: bait-prey hybrid interaction evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0043565
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001682
example of usage: Bacterial one-hybrid assays confirmed the interaction between MtrA and the regulatory sequence of the dnaA initiator gene.
definition: A type of bait-prey 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).
created_by: mchibucos
creation_date: 2011-01-10T06:16:20Z
has_exact_synonym: B1H evidence
has_obo_namespace: eco
id: ECO:0000294
comment: 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.

Axiom
annotated source: bacterial one-hybrid evidence
annotated property: example of usage
annotated target: Bacterial one-hybrid assays confirmed the interaction between MtrA and the regulatory sequence of the dnaA initiator gene.
database_cross_reference: PMID:20843371

Axiom
annotated source: bacterial one-hybrid evidence
annotated property: definition
annotated target: A type of bait-prey 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).
database_cross_reference: ECO:MCC

RNA-sequencing evidence
type: Class
subclass of: transcript expression evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001271
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001239
definition: A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
created_by: mchibucos
creation_date: 2011-01-11T12:54:50Z
has_alternative_id: ECO:0000357
has_exact_synonym: RNA-seq evidence
has_exact_synonym: RNAseq evidence
has_exact_synonym: WTSS
has_exact_synonym: whole transcriptome shotgun sequencing
has_narrow_synonym: differential gene expression evidence from RNA-seq experiment
has_obo_namespace: eco
has_related_synonym: RNA sequencing
id: ECO:0000295
comment: 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.

Axiom
annotated source: RNA-sequencing evidence
annotated property: definition
annotated target: A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
database_cross_reference: ECO:MCC

Axiom
annotated source: RNA-sequencing evidence
annotated property: has_exact_synonym
annotated target: whole transcriptome shotgun sequencing
database_cross_reference: PMID:18611170

cleavage arrested development evidence
type: Class
subclass of: experimental phenotypic evidence
definition: A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
created_by: mchibucos
creation_date: 2011-01-11T03:28:49Z
has_obo_namespace: eco
id: ECO:0000298
comment: 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.

Axiom
annotated source: cleavage arrested development evidence
annotated property: definition
annotated target: A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
database_cross_reference: ECO:MCC

cytochalasin experiment evidence
type: Class
subclass of: cleavage arrested development evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0072749
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001689
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000807
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0000985
definition: A type of cleavage arrested development that arises after treatment with cytochalasin.
created_by: mchibucos
creation_date: 2011-01-11T03:30:29Z
has_obo_namespace: eco
id: ECO:0000299
comment: Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments.

Axiom
annotated source: cytochalasin experiment evidence
annotated property: definition
annotated target: A type of cleavage arrested development that arises after treatment with cytochalasin.
database_cross_reference: ECO:MCC

green fluorescent protein immunolocalization evidence
type: Class
subclass of: immunolocalization evidence
definition: A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
created_by: mchibucos
creation_date: 2011-01-11T03:48:50Z
has_exact_synonym: GFP immunolocalization evidence
has_obo_namespace: eco
id: ECO:0000300
comment: This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript".

Axiom
annotated source: green fluorescent protein immunolocalization evidence
annotated property: definition
annotated target: A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
database_cross_reference: ECO:MCC

beta-galactosidase protein immunolocalization evidence
type: Class
subclass of: immunolocalization evidence
definition: A type of immunolocalization evidence that was generated using LacZ protein as a marker.
created_by: mchibucos
creation_date: 2011-01-11T04:06:40Z
has_exact_synonym: LacZ protein immunolocalization evidence
has_obo_namespace: eco
id: ECO:0000301
comment: This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript".

Axiom
annotated source: beta-galactosidase protein immunolocalization evidence
annotated property: definition
annotated target: A type of immunolocalization evidence that was generated using LacZ protein as a marker.
database_cross_reference: ECO:MCC

author statement used in manual assertion
type: Class
equivalent class: Class
  intersection of: author statement
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: author statement
subclass of: documented statement evidence used in manual assertion
definition: A type of author statement that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-01-20T02:26:47Z
has_alternative_id: ECO:0007764
has_exact_synonym: author inference used in manual assertion
has_obo_namespace: eco
id: ECO:0000302

Axiom
annotated source: author statement used in manual assertion
annotated property: subClassOf
annotated target: documented statement evidence used in manual assertion
is_inferred: true

Axiom
annotated source: author statement used in manual assertion
annotated property: definition
annotated target: A type of author statement that is used in a manual assertion.
database_cross_reference: ECO:MCC

author statement without traceable support used in manual assertion
type: Class
equivalent class: Class
  intersection of: author statement without traceable support
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: author statement without traceable support
subclass of: author statement used in manual assertion
has GO evidence code: NAS
definition: A type of author statement without traceable support that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-01-20T02:29:50Z
database_cross_reference: GOECO:NAS
has_exact_synonym: NAS
has_obo_namespace: eco
has_related_synonym: non-traceable author statement
id: ECO:0000303

Axiom
annotated source: author statement without traceable support used in manual assertion
annotated property: subClassOf
annotated target: author statement used in manual assertion
is_inferred: true

Axiom
annotated source: author statement without traceable support used in manual assertion
annotated property: has GO evidence code
annotated target: NAS
comment: Default

Axiom
annotated source: author statement without traceable support used in manual assertion
annotated property: definition
annotated target: A type of author statement without traceable support that is used in a manual assertion.
database_cross_reference: ECO:MCC

non-traceable author statement
type: Axiom
annotated source: author statement without traceable support used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:NAS

Axiom
annotated source: author statement without traceable support used in manual assertion
annotated property: has_exact_synonym
annotated target: NAS
database_cross_reference: GOECO:NAS

Axiom
annotated source: author statement without traceable support used in manual assertion
annotated property: has_related_synonym
annotated target: non-traceable author statement
database_cross_reference: GOECO:NAS

author statement supported by traceable reference used in manual assertion
type: Class
equivalent class: Class
  intersection of: author statement supported by traceable reference
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: author statement supported by traceable reference
subclass of: author statement used in manual assertion
has GO evidence code: TAS
definition: A type of author statement supported by traceable reference that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-01-20T02:31:03Z
database_cross_reference: GOECO:TAS
has_exact_synonym: TAS
has_obo_namespace: eco
has_related_synonym: traceable author statement
id: ECO:0000304

Axiom
annotated source: author statement supported by traceable reference used in manual assertion
annotated property: subClassOf
annotated target: author statement used in manual assertion
is_inferred: true

Axiom
annotated source: author statement supported by traceable reference used in manual assertion
annotated property: has GO evidence code
annotated target: TAS
comment: Default

Axiom
annotated source: author statement supported by traceable reference used in manual assertion
annotated property: definition
annotated target: A type of author statement supported by traceable reference that is used in a manual assertion.
database_cross_reference: ECO:MCC

traceable author statement
type: Axiom
annotated source: author statement supported by traceable reference used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:TAS

Axiom
annotated source: author statement supported by traceable reference used in manual assertion
annotated property: has_exact_synonym
annotated target: TAS
database_cross_reference: GOECO:TAS

Axiom
annotated source: author statement supported by traceable reference used in manual assertion
annotated property: has_related_synonym
annotated target: traceable author statement
database_cross_reference: GOECO:TAS

curator inference used in manual assertion
type: Class
equivalent class: Class
  intersection of: curator inference
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: curator inference
subclass of: ECO_0007751
has GO evidence code: IC
definition: A type of curator inference that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-01-20T02:33:32Z
database_cross_reference: GOECO:IC
has_exact_synonym: IC
has_exact_synonym: inferred by curator
has_obo_namespace: eco
id: ECO:0000305
in_subset: valid_with_biological_process
in_subset: valid_with_cellular_component
in_subset: valid_with_molecular_function

Axiom
annotated source: curator inference used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007751
is_inferred: true

Axiom
annotated source: curator inference used in manual assertion
annotated property: has GO evidence code
annotated target: IC
comment: Default

Axiom
annotated source: curator inference used in manual assertion
annotated property: definition
annotated target: A type of curator inference that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred by curator
type: Axiom
annotated source: curator inference used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:IC

Axiom
annotated source: curator inference used in manual assertion
annotated property: has_exact_synonym
annotated target: IC
database_cross_reference: GOECO:IC

Axiom
annotated source: curator inference used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred by curator
database_cross_reference: GOECO:IC

inference from background scientific knowledge used in manual assertion
type: Class
equivalent class: Class
  intersection of: inference from background scientific knowledge
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: inference from background scientific knowledge
subclass of: curator inference used in manual assertion
has GO evidence code: IC
definition: A type of inference from background scientific knowledge that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-01-20T02:35:11Z
has_obo_namespace: eco
id: ECO:0000306

Axiom
annotated source: inference from background scientific knowledge used in manual assertion
annotated property: subClassOf
annotated target: curator inference used in manual assertion
is_inferred: true

Axiom
annotated source: inference from background scientific knowledge used in manual assertion
annotated property: definition
annotated target: A type of inference from background scientific knowledge that is used in a manual assertion.
database_cross_reference: ECO:MCC

no evidence data found used in manual assertion
type: Class
equivalent class: Class
  intersection of: no evidence data found
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: no evidence data found
subclass of: curator inference used in manual assertion
has GO evidence code: ND
definition: An inference that results when research finds no evidence information in the scientific literature, at reference databases, or from other resources that is used in an manual assertion.
created_by: mchibucos
creation_date: 2011-01-20T02:43:18Z
database_cross_reference: GOECO:ND
has_exact_synonym: ND
has_exact_synonym: no biological data available
has_obo_namespace: eco
id: ECO:0000307

Axiom
annotated source: no evidence data found used in manual assertion
annotated property: subClassOf
annotated target: curator inference used in manual assertion
is_inferred: true

Axiom
annotated source: no evidence data found used in manual assertion
annotated property: has GO evidence code
annotated target: ND
comment: Default

Axiom
annotated source: no evidence data found used in manual assertion
annotated property: definition
annotated target: An inference that results when research finds no evidence information in the scientific literature, at reference databases, or from other resources that is used in an manual assertion.
database_cross_reference: ECO:MCC

no biological data available
type: Axiom
annotated source: no evidence data found used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:ND

Axiom
annotated source: no evidence data found used in manual assertion
annotated property: has_exact_synonym
annotated target: ND
database_cross_reference: GOECO:ND

Axiom
annotated source: no evidence data found used in manual assertion
annotated property: has_exact_synonym
annotated target: no biological data available
database_cross_reference: GOECO:ND

biological aspect of ancestor evidence
type: Class
subclass of: phylogenetic evidence
definition: A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
created_by: mchibucos
creation_date: 2011-02-04T05:41:26Z
has_obo_namespace: eco
id: ECO:0000308
comment: 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.

Axiom
annotated source: biological aspect of ancestor evidence
annotated property: definition
annotated target: A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
database_cross_reference: ECO:MCC

cap analysis of gene expression evidence
type: Class
subclass of: transcript expression evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001674
definition: 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.
created_by: mchibucos
creation_date: 2011-02-17T01:33:09Z
has_exact_synonym: CAGE
has_obo_namespace: eco
id: ECO:0000309
comment: 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.

Axiom
annotated source: cap analysis of gene expression evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

Axiom
annotated source: cap analysis of gene expression evidence
annotated property: has_exact_synonym
annotated target: CAGE
database_cross_reference: PMID:16489339

nano-cap analysis of gene expression evidence
type: Class
subclass of: transcript expression evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001673
definition: 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.
created_by: mchibucos
creation_date: 2011-02-17T01:33:34Z
has_obo_namespace: eco
has_related_synonym: nanoCAGE
id: ECO:0000310
comment: 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.

Axiom
annotated source: nano-cap analysis of gene expression evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

Axiom
annotated source: nano-cap analysis of gene expression evidence
annotated property: has_related_synonym
annotated target: nanoCAGE
database_cross_reference: PMID:20543846

imported information
type: Class
subclass of: documented statement evidence
definition: A type of documented statement evidence that is based on work performed by a person or group prior to a use by a different person or group.
created_by: mchibucos
creation_date: 2011-03-02T05:24:13Z
has_obo_namespace: eco
id: ECO:0000311

Axiom
annotated source: imported information
annotated property: definition
annotated target: A type of documented statement evidence that is based on work performed by a person or group prior to a use by a different person or group.
database_cross_reference: ECO:MCC

imported information used in manual assertion
type: Class
equivalent class: Class
  intersection of: imported information
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: imported information
subclass of: documented statement evidence used in manual assertion
definition: A type of imported information that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-03-02T05:29:44Z
has_obo_namespace: eco
id: ECO:0000312

Axiom
annotated source: imported information used in manual assertion
annotated property: subClassOf
annotated target: documented statement evidence used in manual assertion
is_inferred: true

Axiom
annotated source: imported information used in manual assertion
annotated property: definition
annotated target: A type of imported information that is used in a manual assertion.
database_cross_reference: ECO:MCC

imported information used in automatic assertion
type: Class
equivalent class: Class
  intersection of: imported information
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: imported information
subclass of: documented statement evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of imported information that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2011-03-02T05:33:43Z
has_obo_namespace: eco
id: ECO:0000313

Axiom
annotated source: imported information used in automatic assertion
annotated property: subClassOf
annotated target: documented statement evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: imported information used in automatic assertion
annotated property: definition
annotated target: A type of imported information that is used in an automatic assertion.
database_cross_reference: ECO:MCC

direct assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: direct assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence
subclass of: experimental evidence used in manual assertion
has GO evidence code: IDA
definition: A type of direct assay evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-10-28T04:59:31Z
database_cross_reference: GOECO:IDA
has_exact_synonym: IDA
has_exact_synonym: inferred from direct assay
has_obo_namespace: eco
id: ECO:0000314
in_subset: valid_with_chemical_entity

Axiom
annotated source: direct assay evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: direct assay evidence used in manual assertion
annotated property: has GO evidence code
annotated target: IDA
comment: Default

Axiom
annotated source: direct assay evidence used in manual assertion
annotated property: definition
annotated target: A type of direct assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from direct assay
type: Axiom
annotated source: direct assay evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:IDA

Axiom
annotated source: direct assay evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: IDA
database_cross_reference: GOECO:IDA

Axiom
annotated source: direct assay evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from direct assay
database_cross_reference: GOECO:IDA

mutant phenotype evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: mutant phenotype evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mutant phenotype evidence
subclass of: ECO_0007634
has GO evidence code: IMP
definition: A type of mutant phenotype evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-10-28T05:12:49Z
database_cross_reference: GOECO:IMP
has_exact_synonym: IMP
has_exact_synonym: inferred from mutant phenotype
has_obo_namespace: eco
id: ECO:0000315
in_subset: valid_with_chemical_entity
in_subset: valid_with_gene
in_subset: valid_with_protein
in_subset: valid_with_protein_complex

Axiom
annotated source: mutant phenotype evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: mutant phenotype evidence used in manual assertion
annotated property: has GO evidence code
annotated target: IMP
comment: Default

Axiom
annotated source: mutant phenotype evidence used in manual assertion
annotated property: definition
annotated target: A type of mutant phenotype evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from mutant phenotype
type: Axiom
annotated source: mutant phenotype evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:IMP

Axiom
annotated source: mutant phenotype evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: IMP
database_cross_reference: GOECO:IMP

Axiom
annotated source: mutant phenotype evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from mutant phenotype
database_cross_reference: GOECO:IMP

genetic interaction evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: genetic interaction evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: genetic interaction evidence
subclass of: ECO_0007634
has GO evidence code: IGI
definition: A type of genetic interaction experiment evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-10-28T05:14:42Z
database_cross_reference: GOECO:IGI
has_exact_synonym: IGI
has_exact_synonym: inferred from genetic interaction
has_obo_namespace: eco
id: ECO:0000316
in_subset: valid_with_gene
in_subset: valid_with_protein
in_subset: valid_with_protein_complex

Axiom
annotated source: genetic interaction evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: genetic interaction evidence used in manual assertion
annotated property: has GO evidence code
annotated target: IGI
comment: Default

Axiom
annotated source: genetic interaction evidence used in manual assertion
annotated property: definition
annotated target: A type of genetic interaction experiment evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from genetic interaction
type: Axiom
annotated source: genetic interaction evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:IGI

Axiom
annotated source: genetic interaction evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: IGI
database_cross_reference: GOECO:IGI

Axiom
annotated source: genetic interaction evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from genetic interaction
database_cross_reference: GOECO:IGI

genomic context evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: genomic context evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: genomic context evidence
subclass of: similarity evidence used in manual assertion
has GO evidence code: IGC
definition: A type of genomic context evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-10-28T05:22:53Z
database_cross_reference: GOECO:IGC
has_exact_synonym: IGC
has_exact_synonym: inferred from genomic context
has_obo_namespace: eco
id: ECO:0000317
in_subset: valid_with_gene
in_subset: valid_with_protein

Axiom
annotated source: genomic context evidence used in manual assertion
annotated property: subClassOf
annotated target: similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: genomic context evidence used in manual assertion
annotated property: has GO evidence code
annotated target: IGC
comment: Default

Axiom
annotated source: genomic context evidence used in manual assertion
annotated property: definition
annotated target: A type of genomic context evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from genomic context
type: Axiom
annotated source: genomic context evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:IGC

Axiom
annotated source: genomic context evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: IGC
database_cross_reference: GOECO:IGC

Axiom
annotated source: genomic context evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from genomic context
database_cross_reference: GOECO:IGC

biological aspect of ancestor evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: biological aspect of ancestor evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: similarity evidence used in manual assertion
subclass of: biological aspect of ancestor evidence
has GO evidence code: IBA
definition: A type of biological aspect of ancestor evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-10-28T05:23:51Z
database_cross_reference: GOECO:IBA
has_exact_synonym: IBA
has_exact_synonym: inferred from biological aspect of ancestor
has_obo_namespace: eco
id: ECO:0000318
in_subset: valid_with_gene
in_subset: valid_with_protein

Axiom
annotated source: biological aspect of ancestor evidence used in manual assertion
annotated property: subClassOf
annotated target: similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: biological aspect of ancestor evidence used in manual assertion
annotated property: has GO evidence code
annotated target: IBA
comment: Default

Axiom
annotated source: biological aspect of ancestor evidence used in manual assertion
annotated property: definition
annotated target: A type of biological aspect of ancestor evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from biological aspect of ancestor
type: Axiom
annotated source: biological aspect of ancestor evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:IBA

Axiom
annotated source: biological aspect of ancestor evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: IBA
database_cross_reference: GOECO:IBA

Axiom
annotated source: biological aspect of ancestor evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from biological aspect of ancestor
database_cross_reference: GOECO:IBA

biological aspect of descendant evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: biological aspect of descendant evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: biological aspect of descendant evidence
subclass of: similarity evidence used in manual assertion
has GO evidence code: IBD
definition: A type of biological aspect of descendant evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-10-28T05:25:09Z
database_cross_reference: GOECO:IBD
has_exact_synonym: IBD
has_exact_synonym: inferred from biological aspect of descendant
has_obo_namespace: eco
id: ECO:0000319
in_subset: valid_with_gene
in_subset: valid_with_protein

Axiom
annotated source: biological aspect of descendant evidence used in manual assertion
annotated property: subClassOf
annotated target: similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: biological aspect of descendant evidence used in manual assertion
annotated property: has GO evidence code
annotated target: IBD
comment: Default

Axiom
annotated source: biological aspect of descendant evidence used in manual assertion
annotated property: definition
annotated target: A type of biological aspect of descendant evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from biological aspect of descendant
type: Axiom
annotated source: biological aspect of descendant evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:IBD

Axiom
annotated source: biological aspect of descendant evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: IBD
database_cross_reference: GOECO:IBD

Axiom
annotated source: biological aspect of descendant evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from biological aspect of descendant
database_cross_reference: GOECO:IBD

phylogenetic determination of loss of key residues evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: phylogenetic determination of loss of key residues evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: phylogenetic determination of loss of key residues evidence
subclass of: similarity evidence used in manual assertion
has GO evidence code: IKR
definition: A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-10-28T05:25:48Z
database_cross_reference: GOECO:IKR
database_cross_reference: GOECO:IMR
has_exact_synonym: IKR
has_exact_synonym: IMR
has_exact_synonym: inferred from key residues
has_exact_synonym: inferred from missing residues
has_obo_namespace: eco
id: ECO:0000320

Axiom
annotated source: phylogenetic determination of loss of key residues evidence used in manual assertion
annotated property: subClassOf
annotated target: similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: phylogenetic determination of loss of key residues evidence used in manual assertion
annotated property: has GO evidence code
annotated target: IKR
comment: Default

Axiom
annotated source: phylogenetic determination of loss of key residues evidence used in manual assertion
annotated property: definition
annotated target: A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from key residues
type: Axiom
annotated source: phylogenetic determination of loss of key residues evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:IKR

inferred from missing residues
type: Axiom
annotated source: phylogenetic determination of loss of key residues evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:IMR

Axiom
annotated source: phylogenetic determination of loss of key residues evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: IKR
database_cross_reference: GOECO:IKR

Axiom
annotated source: phylogenetic determination of loss of key residues evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: IMR
database_cross_reference: GOECO:IKR

Axiom
annotated source: phylogenetic determination of loss of key residues evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from key residues
database_cross_reference: GOECO:IKR

Axiom
annotated source: phylogenetic determination of loss of key residues evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from missing residues
database_cross_reference: GOECO:IKR

rapid divergence from ancestral sequence evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: rapid divergence from ancestral sequence evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: rapid divergence from ancestral sequence evidence
subclass of: similarity evidence used in manual assertion
has GO evidence code: IRD
definition: A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2011-10-28T05:26:42Z
database_cross_reference: GOECO:IRD
has_exact_synonym: IRD
has_exact_synonym: inferred from rapid divergence
has_obo_namespace: eco
id: ECO:0000321
in_subset: valid_with_gene
in_subset: valid_with_protein

Axiom
annotated source: rapid divergence from ancestral sequence evidence used in manual assertion
annotated property: subClassOf
annotated target: similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: rapid divergence from ancestral sequence evidence used in manual assertion
annotated property: has GO evidence code
annotated target: IRD
comment: Default

Axiom
annotated source: rapid divergence from ancestral sequence evidence used in manual assertion
annotated property: definition
annotated target: A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from rapid divergence
type: Axiom
annotated source: rapid divergence from ancestral sequence evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:IRD

Axiom
annotated source: rapid divergence from ancestral sequence evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: IRD
database_cross_reference: GOECO:IRD

Axiom
annotated source: rapid divergence from ancestral sequence evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from rapid divergence
database_cross_reference: GOECO:IRD

imported manually asserted information used in automatic assertion
type: Class
subclass of: imported information used in automatic assertion
has GO evidence code: IEA
definition: 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.
created_by: mchibucos
creation_date: 2011-12-13T12:04:48Z
has_obo_namespace: eco
id: ECO:0000322

Axiom
annotated source: imported manually asserted information used in automatic assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

imported automatically asserted information used in automatic assertion
type: Class
subclass of: imported information used in automatic assertion
has GO evidence code: IEA
definition: 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.
created_by: mchibucos
creation_date: 2011-12-13T02:06:25Z
has_obo_namespace: eco
id: ECO:0000323

Axiom
annotated source: imported automatically asserted information used in automatic assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

imaging assay evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000185
example of usage: In the images shown in Figure 9, the MelR focus is 15 x 33 nm across the shortest and longest axes of the oval in the complex with the shortened arm (right hand panel), compared to 9 x 12 nm in the other complex (centre panel). The simplest explanation for these observations, that is consistent with the location of sites in the DNA fragment (Figure 9), is that one type of complex contains 3 MelR molecules bound at sites 2, 1 and 1' (centre panel), whilst the other contains 4 MelR molecules bound at sites 2, 1, 1' and R (right panel).
definition: A type of direct assay evidence in which an image is created and analyzed.
created_by: mchibucos
creation_date: 2012-02-23T12:01:43Z
has_alternative_id: ECO:0001122
has_alternative_id: ECO:0005024
database_cross_reference: ECO:MCC
has_narrow_synonym: radiologic test evidence
has_obo_namespace: eco
id: ECO:0000324

Axiom
annotated source: imaging assay evidence
annotated property: example of usage
annotated target: In the images shown in Figure 9, the MelR focus is 15 x 33 nm across the shortest and longest axes of the oval in the complex with the shortened arm (right hand panel), compared to 9 x 12 nm in the other complex (centre panel). The simplest explanation for these observations, that is consistent with the location of sites in the DNA fragment (Figure 9), is that one type of complex contains 3 MelR molecules bound at sites 2, 1 and 1' (centre panel), whilst the other contains 4 MelR molecules bound at sites 2, 1, 1' and R (right panel).
database_cross_reference: PMID:18346968

chromatography evidence
type: Class
subclass of: experimental evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001630
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600046
definition: 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.
created_by: mchibucos
creation_date: 2012-05-16T11:46:27Z
has_exact_synonym: chromatographic evidence
has_obo_namespace: eco
id: ECO:0000325

Axiom
annotated source: chromatography evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

transcript splice pattern evidence
type: Class
subclass of: sequence alignment evidence
definition: 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.
created_by: mchibucos
creation_date: 2012-06-08T11:03:59Z
has_obo_namespace: eco
id: ECO:0000326

Axiom
annotated source: transcript splice pattern evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

whole transcript splice pattern evidence
type: Class
subclass of: transcript splice pattern evidence
definition: A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
created_by: mchibucos
creation_date: 2012-06-08T11:11:24Z
has_obo_namespace: eco
id: ECO:0000327
comment: 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.

Axiom
annotated source: whole transcript splice pattern evidence
annotated property: definition
annotated target: A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
database_cross_reference: ECO:MCC

coding sequence splice pattern evidence
type: Class
subclass of: transcript splice pattern evidence
definition: 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.
created_by: mchibucos
creation_date: 2012-06-08T11:21:57Z
has_obo_namespace: eco
id: ECO:0000328
comment: 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.

Axiom
annotated source: coding sequence splice pattern evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

whole transcript splice pattern evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: whole transcript splice pattern evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: sequence alignment evidence used in manual assertion
subclass of: whole transcript splice pattern evidence
has GO evidence code: ISA
definition: 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.
created_by: mchibucos
creation_date: 2012-06-08T11:40:03Z
has_obo_namespace: eco
id: ECO:0000329
comment: 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.

Axiom
annotated source: whole transcript splice pattern evidence used in manual assertion
annotated property: subClassOf
annotated target: sequence alignment evidence used in manual assertion
is_inferred: true

Axiom
annotated source: whole transcript splice pattern evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

coding sequence splice pattern evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: coding sequence splice pattern evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: sequence alignment evidence used in manual assertion
subclass of: coding sequence splice pattern evidence
has GO evidence code: ISA
definition: 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.
created_by: mchibucos
creation_date: 2012-06-08T11:43:47Z
has_obo_namespace: eco
id: ECO:0000330
comment: 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.

Axiom
annotated source: coding sequence splice pattern evidence used in manual assertion
annotated property: subClassOf
annotated target: sequence alignment evidence used in manual assertion
is_inferred: true

Axiom
annotated source: coding sequence splice pattern evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

coding sequence splice pattern evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: coding sequence splice pattern evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: coding sequence splice pattern evidence
subclass of: ECO_0007825
has GO evidence code: IEA
definition: 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.
created_by: mchibucos
creation_date: 2012-06-08T11:48:09Z
has_obo_namespace: eco
id: ECO:0000331
comment: 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.

Axiom
annotated source: coding sequence splice pattern evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007825
is_inferred: true

Axiom
annotated source: coding sequence splice pattern evidence used in automatic assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

whole transcript splice pattern evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: whole transcript splice pattern evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: whole transcript splice pattern evidence
subclass of: ECO_0007825
has GO evidence code: IEA
definition: 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.
created_by: mchibucos
creation_date: 2012-06-08T11:49:17Z
has_obo_namespace: eco
id: ECO:0000332
comment: 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.

Axiom
annotated source: whole transcript splice pattern evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007825
is_inferred: true

Axiom
annotated source: whole transcript splice pattern evidence used in automatic assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence
type: Class
subclass of: gel electrophoresis evidence
definition: A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
created_by: mchibucos
creation_date: 2012-07-31T02:56:43Z
has_exact_synonym: SDS-PAGE evidence
has_obo_namespace: eco
id: ECO:0000333
comment: 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.

Axiom
annotated source: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence
annotated property: definition
annotated target: A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
database_cross_reference: ECO:MCC
database_cross_reference: PubMed:4861258
database_cross_reference: url:http://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html
database_cross_reference: url:http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Protein/protein18.html

particle size and count assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined.
created_by: mchibucos
creation_date: 2012-07-31T03:19:32Z
has_obo_namespace: eco
id: ECO:0000334
comment: An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system.

Axiom
annotated source: particle size and count assay evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined.
database_cross_reference: ECO:MCC

substance quantification evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
created_by: mchibucos
creation_date: 2012-07-31T03:52:46Z
has_obo_namespace: eco
id: ECO:0000335
comment: 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.

Axiom
annotated source: substance quantification evidence
annotated property: definition
annotated target: A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
database_cross_reference: ECO:MCC

competitive growth assay evidence
type: Class
subclass of: cell proliferation assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000978
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000153
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001285
definition: 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.
created_by: mchibucos
creation_date: 2012-08-24T12:03:58Z
has_exact_synonym: fitness profiling
has_obo_namespace: eco
id: ECO:0000336

Axiom
annotated source: competitive growth assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:MAH
database_cross_reference: PMID:14718172
database_cross_reference: PMID:20537132

Axiom
annotated source: competitive growth assay evidence
annotated property: has_exact_synonym
annotated target: fitness profiling
database_cross_reference: GOC:MAH
database_cross_reference: PMID:20537132

gel electrophoresis evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is about
  some values from: OBI_0600051
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600053
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0001121
example of usage: We analyzed the electrophoretic pattern of cytosolic proteins extracted from LM3 and LM3-2 cells, grown under standard conditions up to mid-exponential phase (Fig. 1). The presence of differentially expressed proteins in the two strains, together with results of previous studies [28,29] demonstrated the role of CcpA as global regulator in L. plantarum.
definition: 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.
created_by: mchibucos
creation_date: 2012-08-24T12:11:51Z
has_alternative_id: ECO:0005026
has_obo_namespace: eco
id: ECO:0000337
comment: Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch.

Axiom
annotated source: gel electrophoresis evidence
annotated property: example of usage
annotated target: We analyzed the electrophoretic pattern of cytosolic proteins extracted from LM3 and LM3-2 cells, grown under standard conditions up to mid-exponential phase (Fig. 1). The presence of differentially expressed proteins in the two strains, together with results of previous studies [28,29] demonstrated the role of CcpA as global regulator in L. plantarum.
database_cross_reference: PMID:17129387

Axiom
annotated source: gel electrophoresis evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: wikipedia:Gel_electrophoresis

pulsed-field gel electrophoresis evidence
type: Class
subclass of: gel electrophoresis evidence
definition: 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.
created_by: mchibucos
creation_date: 2012-08-24T12:34:01Z
has_exact_synonym: PFGE
has_obo_namespace: eco
id: ECO:0000338

Axiom
annotated source: pulsed-field gel electrophoresis evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:6373014

two-dimensional agarose gel electrophoresis evidence
type: Class
subclass of: gel electrophoresis evidence
definition: 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.
created_by: mchibucos
creation_date: 2012-08-24T12:42:37Z
has_exact_synonym: 2-D agarose gel electrophoresis
has_obo_namespace: eco
id: ECO:0000339
comment: 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.

Axiom
annotated source: two-dimensional agarose gel electrophoresis evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:16118435
database_cross_reference: PMID:8594382

plasmid maintenance assay evidence
type: Class
subclass of: experimental evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0006276
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000964
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600000
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: A type of experimental evidence in which a plasmid that is capable of being replicated is introduced into cells, cells are grown without selection for several generations, and retention of the plasmid is determined.
created_by: mchibucos
creation_date: 2012-08-24T01:27:58Z
has_exact_synonym: minichromosome maintenance assay evidence
has_obo_namespace: eco
id: ECO:0000340
comment: Loss per generation is determined by comparing colony numbers on selective and non-selective media.

Axiom
annotated source: plasmid maintenance assay evidence
annotated property: definition
annotated target: A type of experimental evidence in which a plasmid that is capable of being replicated is introduced into cells, cells are grown without selection for several generations, and retention of the plasmid is determined.
comment: ECO:MCC
comment: PMID:6323245

Axiom
annotated source: plasmid maintenance assay evidence
annotated property: has_exact_synonym
annotated target: minichromosome maintenance assay evidence
database_cross_reference: PMID:6323245

specific protein inhibition by antibody evidence
type: Class
subclass of: protein inhibition evidence
definition: A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
created_by: mchibucos
creation_date: 2012-08-24T01:48:24Z
has_obo_namespace: eco
id: ECO:0000341

Axiom
annotated source: specific protein inhibition by antibody evidence
annotated property: definition
annotated target: A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
database_cross_reference: ECO:MCC

support of intron positions by RNA-sequencing alignment evidence
type: Class
subclass of: RNA-sequencing evidence
definition: A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
created_by: mchibucos
creation_date: 2013-04-03T04:22:05Z
has_exact_synonym: Support of intron positions by RNA-seq alignment evidence
has_obo_namespace: eco
id: ECO:0000342
comment: 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.

Axiom
annotated source: support of intron positions by RNA-sequencing alignment evidence
annotated property: definition
annotated target: A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
database_cross_reference: ECO:MCC

full support of intron positions by RNA-sequencing alignment evidence
type: Class
subclass of: support of intron positions by RNA-sequencing alignment evidence
definition: A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
created_by: mchibucos
creation_date: 2013-04-03T04:41:48Z
has_exact_synonym: Full support of intron positions by RNA-seq alignment evidence
has_obo_namespace: eco
id: ECO:0000343
comment: 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.

Axiom
annotated source: full support of intron positions by RNA-sequencing alignment evidence
annotated property: definition
annotated target: A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
database_cross_reference: ECO:MCC

partial support of intron positions by RNA-sequencing alignment evidence
type: Class
subclass of: support of intron positions by RNA-sequencing alignment evidence
definition: A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript.
created_by: mchibucos
creation_date: 2013-04-03T04:50:46Z
has_exact_synonym: Partial support of intron positions by RNA-seq alignment evidence
has_obo_namespace: eco
id: ECO:0000344
comment: 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.

Axiom
annotated source: partial support of intron positions by RNA-sequencing alignment evidence
annotated property: definition
annotated target: A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript.
database_cross_reference: ECO:MCC

single exon transcript confirmation via alignment evidence
type: Class
subclass of: sequence alignment evidence
definition: A type of sequence alignment evidence resulting from the comparison of a single exon transcript to a collection / database of known single exon genes.
created_by: mchibucos
creation_date: 2013-04-03T05:10:34Z
has_obo_namespace: eco
id: ECO:0000345

Axiom
annotated source: single exon transcript confirmation via alignment evidence
annotated property: definition
annotated target: A type of sequence alignment evidence resulting from the comparison of a single exon transcript to a collection / database of known single exon genes.
database_cross_reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4897596/

support of intron positions by RNA-sequencing alignment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: support of intron positions by RNA-sequencing alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: support of intron positions by RNA-sequencing alignment evidence
subclass of: RNA-sequencing evidence used in manual assertion
has GO evidence code: IEP
definition: A type of support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2013-04-04T04:37:35Z
has_exact_synonym: Support of intron positions by RNA-seq alignment evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0000346

Axiom
annotated source: support of intron positions by RNA-sequencing alignment evidence used in manual assertion
annotated property: subClassOf
annotated target: RNA-sequencing evidence used in manual assertion
is_inferred: true

Axiom
annotated source: support of intron positions by RNA-sequencing alignment evidence used in manual assertion
annotated property: definition
annotated target: A type of support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: support of intron positions by RNA-sequencing alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: support of intron positions by RNA-sequencing alignment evidence
subclass of: RNA-sequencing evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2013-04-04T04:38:45Z
has_exact_synonym: Support of intron positions by RNA-seq alignment evidence used in automatic assertion
has_obo_namespace: eco
id: ECO:0000347

Axiom
annotated source: support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
annotated property: subClassOf
annotated target: RNA-sequencing evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
annotated property: definition
annotated target: A type of support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
database_cross_reference: ECO:MCC

full support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: full support of intron positions by RNA-sequencing alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: full support of intron positions by RNA-sequencing alignment evidence
subclass of: support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of full support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2013-04-04T04:40:19Z
has_exact_synonym: Full support of intron positions by RNA-seq alignment evidence used in automatic assertion
has_obo_namespace: eco
id: ECO:0000348

Axiom
annotated source: full support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
annotated property: subClassOf
annotated target: support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: full support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
annotated property: definition
annotated target: A type of full support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
database_cross_reference: ECO:MCC

full support of intron positions by RNA-sequencing alignment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: full support of intron positions by RNA-sequencing alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: full support of intron positions by RNA-sequencing alignment evidence
subclass of: support of intron positions by RNA-sequencing alignment evidence used in manual assertion
has GO evidence code: IEP
definition: A type of full support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2013-04-04T04:41:34Z
has_exact_synonym: Full support of intron positions by RNA-seq alignment evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0000349

Axiom
annotated source: full support of intron positions by RNA-sequencing alignment evidence used in manual assertion
annotated property: subClassOf
annotated target: support of intron positions by RNA-sequencing alignment evidence used in manual assertion
is_inferred: true

Axiom
annotated source: full support of intron positions by RNA-sequencing alignment evidence used in manual assertion
annotated property: definition
annotated target: A type of full support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

partial support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: partial support of intron positions by RNA-sequencing alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: partial support of intron positions by RNA-sequencing alignment evidence
subclass of: support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of partial support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2013-04-04T04:42:53Z
has_exact_synonym: Partial support of intron positions by RNA-seq alignment evidence used in automatic assertion
has_obo_namespace: eco
id: ECO:0000350

Axiom
annotated source: partial support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
annotated property: subClassOf
annotated target: support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: partial support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
annotated property: definition
annotated target: A type of partial support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
database_cross_reference: ECO:MCC

partial support of intron positions by RNA-sequencing alignment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: partial support of intron positions by RNA-sequencing alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: partial support of intron positions by RNA-sequencing alignment evidence
subclass of: support of intron positions by RNA-sequencing alignment evidence used in manual assertion
has GO evidence code: IEP
definition: A type of partial support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2013-04-04T04:43:56Z
has_exact_synonym: Partial support of intron positions by RNA-seq alignment evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0000351

Axiom
annotated source: partial support of intron positions by RNA-sequencing alignment evidence used in manual assertion
annotated property: subClassOf
annotated target: support of intron positions by RNA-sequencing alignment evidence used in manual assertion
is_inferred: true

Axiom
annotated source: partial support of intron positions by RNA-sequencing alignment evidence used in manual assertion
annotated property: definition
annotated target: A type of partial support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: evidence
subclass of: Restriction
  on property: used_in
  some values from: manual assertion
definition: A type of evidence that is used in an manual assertion.
created_by: mchibucos
has_obo_namespace: eco
id: ECO:0000352

Axiom
annotated source: evidence used in manual assertion
annotated property: subClassOf
annotated target: evidence
is_inferred: true

Axiom
annotated source: evidence used in manual assertion
annotated property: subClassOf
annotated target: Restriction
  on property: used_in
  some values from: manual assertion
is_inferred: true

Axiom
annotated source: evidence used in manual assertion
annotated property: definition
annotated target: A type of evidence that is used in an manual assertion.
database_cross_reference: ECO:MCC

physical interaction evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: physical interaction evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: physical interaction evidence
subclass of: direct assay evidence used in manual assertion
has GO evidence code: IPI
definition: A type of physical interaction evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2013-10-31T21:01:27Z
database_cross_reference: GOECO:IPI
has_exact_synonym: IPI
has_exact_synonym: inferred from physical interaction
has_obo_namespace: eco
id: ECO:0000353
in_subset: valid_with_chemical_entity
in_subset: valid_with_gene
in_subset: valid_with_protein
in_subset: valid_with_protein_complex

Axiom
annotated source: physical interaction evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: physical interaction evidence used in manual assertion
annotated property: has GO evidence code
annotated target: IPI
comment: Default

Axiom
annotated source: physical interaction evidence used in manual assertion
annotated property: definition
annotated target: A type of physical interaction evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

inferred from physical interaction
type: Axiom
annotated source: physical interaction evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:IPI

Axiom
annotated source: physical interaction evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: IPI
database_cross_reference: GOECO:IPI

Axiom
annotated source: physical interaction evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from physical interaction
database_cross_reference: GOECO:IPI

gene neighbors evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: gene neighbors evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: gene neighbors evidence
subclass of: genomic context evidence used in manual assertion
has GO evidence code: IGC
definition: A type of gene neighbors evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2013-11-19T13:37:24Z
has_broad_synonym: inferred from genome cluster
database_cross_reference: GO_REF:0000025
has_obo_namespace: eco
has_related_synonym: ICL
id: ECO:0000354

Axiom
annotated source: gene neighbors evidence used in manual assertion
annotated property: subClassOf
annotated target: genomic context evidence used in manual assertion
is_inferred: true

Axiom
annotated source: gene neighbors evidence used in manual assertion
annotated property: definition
annotated target: A type of gene neighbors evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

operon structure as IGC evidence
type: Axiom
annotated source: gene neighbors evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000025

phylogenetic distribution evidence
type: Class
subclass of: phylogenetic evidence
definition: A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
created_by: mchibucos
creation_date: 2014-04-22T17:02:31Z
has_obo_namespace: eco
id: ECO:0000355
comment: 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.

Axiom
annotated source: phylogenetic distribution evidence
annotated property: definition
annotated target: A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
database_cross_reference: ECO:MCC
database_cross_reference: PMID:21238344

differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact)
type: Class
subclass of: transcript expression evidence
definition: 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.
created_by: mchibucos
creation_date: 2014-09-26T16:25:47Z
has_obo_namespace: eco
id: ECO:0000358

Axiom
annotated source: differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact)
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:19725948

differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact)
type: Class
subclass of: transcript expression evidence
definition: 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.
created_by: mchibucos
creation_date: 2014-09-26T16:26:48Z
has_obo_namespace: eco
id: ECO:0000359

Axiom
annotated source: differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact)
annotated property: definition
annotated target: 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.
database_cross_reference: PMC:2881125

biological target-disease association via drug evidence
type: Class
subclass of: experimental evidence
definition: A type of experimental evidence resulting from the prediction of drug-target interactions by computational means.
created_by: mchibucos
creation_date: 2014-09-26T16:39:11Z
has_obo_namespace: eco
id: ECO:0000360

Axiom
annotated source: biological target-disease association via drug evidence
annotated property: definition
annotated target: A type of experimental evidence resulting from the prediction of drug-target interactions by computational means.
database_cross_reference: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2199-x

inferential evidence
type: Class
subclass of: evidence
definition: A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
created_by: mchibucos
creation_date: 2015-07-14T11:19:37Z
has_obo_namespace: eco
id: ECO:0000361
comment: 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.

Axiom
annotated source: inferential evidence
annotated property: definition
annotated target: A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
database_cross_reference: ECO:MCC

computational inference
type: Class
subclass of: inferential evidence
subclass of: ECO_0007672
definition: 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.
created_by: mchibucos
creation_date: 2015-07-14T11:24:27Z
has_exact_synonym: evidence based on computational logical inference
has_obo_namespace: eco
id: ECO:0000362

Axiom
annotated source: computational inference
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC
database_cross_reference: GOC:MC

computational inference used in automatic assertion
type: Class
equivalent class: Class
  intersection of: computational inference
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: computational inference
subclass of: ECO_0007669
subclass of: ECO_0007832
has GO evidence code: IEA
definition: A type of evidence based on computational logical inference that is used in automatic assertion.
created_by: mchibucos
creation_date: 2015-07-14T11:35:08Z
database_cross_reference: GO_REF:0000108
has_exact_synonym: evidence based on computational logical inference used in automatic assertion
has_obo_namespace: eco
id: ECO:0000363

Axiom
annotated source: computational inference used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007669
is_inferred: true

Axiom
annotated source: computational inference used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007832
is_inferred: true

Axiom
annotated source: computational inference used in automatic assertion
annotated property: definition
annotated target: A type of evidence based on computational logical inference that is used in automatic assertion.
database_cross_reference: ECO:MCC

Automatic assignment of GO terms using logical inference, based on on inter-ontology links
type: Axiom
annotated source: computational inference used in automatic assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000108

evidence based on logical inference from manual annotation used in automatic assertion
type: Class
subclass of: computational inference used in automatic assertion
has GO evidence code: IEA
definition: A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2015-07-14T11:44:19Z
has_obo_namespace: eco
id: ECO:0000364

Axiom
annotated source: evidence based on logical inference from manual annotation used in automatic assertion
annotated property: definition
annotated target: A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
database_cross_reference: ECO:MCC

evidence based on logical inference from automatic annotation used in automatic assertion
type: Class
subclass of: computational inference used in automatic assertion
has GO evidence code: IEA
definition: A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
created_by: mchibucos
creation_date: 2015-07-14T11:45:25Z
has_obo_namespace: eco
id: ECO:0000366

Axiom
annotated source: evidence based on logical inference from automatic annotation used in automatic assertion
annotated property: definition
annotated target: A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
database_cross_reference: ECO:MCC

evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: evidence
subclass of: Restriction
  on property: used_in
  some values from: automatic assertion
has GO evidence code: IEA
definition: A type of evidence that is used in an automatic assertion.
created_by: cjm
database_cross_reference: GOECO:IEA
database_cross_reference: GO_REF:0000003
database_cross_reference: GO_REF:0000004
database_cross_reference: GO_REF:0000020
database_cross_reference: GO_REF:0000041
database_cross_reference: GO_REF:0000043
database_cross_reference: GO_REF:0000044
database_cross_reference: GO_REF:0000116
has_exact_synonym: IEA
has_exact_synonym: inferred from electronic annotation
has_obo_namespace: eco
id: ECO:0000501
in_subset: valid_with_gene
in_subset: valid_with_protein
in_subset: valid_with_protein_complex

Axiom
annotated source: evidence used in automatic assertion
annotated property: subClassOf
annotated target: evidence
is_inferred: true

Axiom
annotated source: evidence used in automatic assertion
annotated property: subClassOf
annotated target: Restriction
  on property: used_in
  some values from: automatic assertion
is_inferred: true

Axiom
annotated source: evidence used in automatic assertion
annotated property: has GO evidence code
annotated target: IEA
comment: Default

Axiom
annotated source: evidence used in automatic assertion
annotated property: definition
annotated target: A type of evidence that is used in an automatic assertion.
database_cross_reference: ECO:cjm

inferred from electronic annotation
type: Axiom
annotated source: evidence used in automatic assertion
annotated property: database_cross_reference
annotated target: GOECO:IEA

Gene Ontology annotation based on Enzyme Commission mapping.
type: Axiom
annotated source: evidence used in automatic assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000003

Gene Ontology annotation based on Swiss-Prot keyword mapping.
type: Axiom
annotated source: evidence used in automatic assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000004

Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins.
type: Axiom
annotated source: evidence used in automatic assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000020

IEA (UniProt UniPathway)
type: Axiom
annotated source: evidence used in automatic assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000041

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping.
type: Axiom
annotated source: evidence used in automatic assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt.
type: Axiom
annotated source: evidence used in automatic assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000044

Automatic Gene Ontology annotation based on Rhea mapping.
type: Axiom
annotated source: evidence used in automatic assertion
annotated property: database_cross_reference
annotated target: GO_REF:0000116

Axiom
annotated source: evidence used in automatic assertion
annotated property: has_exact_synonym
annotated target: IEA
database_cross_reference: GOECO:IEA

Axiom
annotated source: evidence used in automatic assertion
annotated property: has_exact_synonym
annotated target: inferred from electronic annotation
database_cross_reference: GOECO:IEA

3D cell culture evidence
type: Class
subclass of: cell proliferation assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0001147
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001285
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001001

Axiom
annotated source: 3D cell culture evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:21042962
database_cross_reference: url:http://volttecnologia.com.br/wp-content/uploads/2016/03/Drug-discovery.pdf

[3H]arachidonic acid release assay evidence
type: Class
subclass of: cell-based assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0050482
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000366
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001002

Axiom
annotated source: [3H]arachidonic acid release assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ISBN:0323152295
database_cross_reference: PMID:20693009

[3H]-thymidine incorporation assay evidence
type: Class
subclass of: DNA synthesis cell proliferation assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000669
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001003

Axiom
annotated source: [3H]-thymidine incorporation assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: OBI:0000669
database_cross_reference: url:http://www.scientistsolutions.com/forum/cell-culture-and-tissue-culture-proliferationapoptosis/3h-thymidine-incorporation-assay-rat-1a

51Cr release assay evidence
type: Class
subclass of: cytotoxicity assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0001906
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_9999994
definition: 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).
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001004

Axiom
annotated source: 51Cr release assay evidence
annotated property: definition
annotated target: 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).
database_cross_reference: PMC:3929704

7-aminoactinomycin staining evidence
type: Class
subclass of: staining evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: 7-AAD staining evidence
has_exact_synonym: 7-amino-actinomycin D staining evidence
has_obo_namespace: eco
id: ECO:0001005

Axiom
annotated source: 7-aminoactinomycin staining evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT

adhesion assay evidence
type: Class
subclass of: cell-based assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0060352
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000964
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0002590
definition: A type of cell-based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001006

Axiom
annotated source: adhesion assay evidence
annotated property: definition
annotated target: A type of cell-based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells.
database_cross_reference: PMID:15576904
database_cross_reference: PMID:21909903

adoptive cell transfer evidence
type: Class
subclass of: ex vivo assay evidence
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: GO_0008150
    intersection of: Restriction
      on property: has participant
      some values from: lymphocyte
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000978
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000105
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: Adoptive immunotherapy
has_exact_synonym: passive immunization
has_obo_namespace: eco
id: ECO:0001007

Axiom
annotated source: adoptive cell transfer evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://jco.ascopubs.org/content/23/10/2346.full.pdf+html
database_cross_reference: url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf

alamarBlue assay evidence
type: Class
subclass of: cell viability assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000443
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600000
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001008

Axiom
annotated source: alamarBlue assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMC:3478843
database_cross_reference: url:https://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/cell-profilteration-assay-protocols/cell-viability-with-alamarblue.html

allograft transplantation phenotypic evidence
type: Class
subclass of: anatomical perturbation phenotypic evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000057
definition: A type of anatomical perturbation phenotypic evidence resulting from the transplantation of an organ or tissue from one individual of the same species with a different genotype.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: Allotransplantation
has_exact_synonym: allograft transplantation experiment evidence
has_exact_synonym: allografting
has_narrow_synonym: tissue grafting
has_obo_namespace: eco
id: ECO:0001009

Axiom
annotated source: allograft transplantation phenotypic evidence
annotated property: definition
annotated target: A type of anatomical perturbation phenotypic evidence resulting from the transplantation of an organ or tissue from one individual of the same species with a different genotype.
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.nature.com/subjects/allograft
database_cross_reference: url:http://www.organdonor.gov/about/terms_and_topics/

anion-exchange chromatography evidence
type: Class
subclass of: chromatography evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001010

Axiom
annotated source: anion-exchange chromatography evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:20978968
database_cross_reference: url:http://www.bio-rad.com/en-us/applications-technologies/anion-exchange-chromatography

annexin-V staining evidence
type: Class
subclass of: apoptotic assay evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001011

Axiom
annotated source: annexin-V staining evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMC:3169266

cognitive assay phenotypic evidence
type: Class
subclass of: experimental phenotypic evidence
definition: A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: behavioral assay evidence
has_obo_namespace: eco
id: ECO:0001012

Axiom
annotated source: cognitive assay phenotypic evidence
annotated property: definition
annotated target: A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning.
database_cross_reference: PMID:24462904

blocking monoclonal antibody evidence
type: Class
subclass of: immunological assay evidence
subclass of: Restriction
  on property: is about
  some values from: OBI_0001702
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001593
definition: A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001013

Axiom
annotated source: blocking monoclonal antibody evidence
annotated property: definition
annotated target: A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies.
database_cross_reference: PMID:11292349
database_cross_reference: url:http://www.sciencedirect.com/science/article/pii/S0140673600034966

blocking peptide evidence
type: Class
subclass of: immunological assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0042605
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001593
definition: A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001014

Axiom
annotated source: blocking peptide evidence
annotated property: definition
annotated target: A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets.
database_cross_reference: ECO:RCT

blocking polyclonal antibody evidence
type: Class
subclass of: immunological assay evidence
definition: A type of immunological assay evidence resulting from the inhibitory effect of polyclonal antibodies (antibodies secreted by different B cell lineages), which while not reacting with a specific antigen, serve to prevent other antibodies from doing so.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001015

blood test evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: Class
        intersection of: OBI_0000094
        intersection of: Restriction
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000443
    intersection of: OBI_0000630
definition: A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001016

Axiom
annotated source: blood test evidence
annotated property: definition
annotated target: A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
database_cross_reference: ECO:SN
database_cross_reference: url:https://www.nhlbi.nih.gov/health/health-topics/topics/bdt

Boyden chamber assay evidence
type: Class
subclass of: chemotaxis assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0060326
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001017

Axiom
annotated source: Boyden chamber assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:13872176
database_cross_reference: PMID:15576901

bromodeoxyuridine incorporation assay evidence
type: Class
subclass of: nucleotide analog incorporation assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000664
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: Class
        intersection of: OBI_0600038
        intersection of: Restriction
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_alternative_id: ECO:0005010
has_broad_synonym: cell proliferation marker detection assay evidence
has_exact_synonym: 5-bromo-2'-deoxyuridine incorporation assay evidence
has_exact_synonym: BUdR incorporation assay evidence
has_exact_synonym: BrdU incorporation assay evidence
has_exact_synonym: BrdUrd incorporation assay evidence
has_obo_namespace: eco
id: ECO:0001018

Axiom
annotated source: bromodeoxyuridine incorporation assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:23690005

caspase assay evidence
type: Class
subclass of: apoptotic assay evidence
definition: A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001019

Axiom
annotated source: caspase assay evidence
annotated property: definition
annotated target: A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis.
database_cross_reference: PMID:18314058
database_cross_reference: PMID:25086023

cell counting evidence
type: Class
subclass of: cell-based assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0008283
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000978
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001285
definition: A type of cell-based assay evidence resulting from the quantification of a sample of cells.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001020

Axiom
annotated source: cell counting evidence
annotated property: definition
annotated target: A type of cell-based assay evidence resulting from the quantification of a sample of cells.
database_cross_reference: ECO:RCT

cell permeability assay evidence
type: Class
subclass of: cell-based assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0009987
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001977
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: A type of cell-based assay evidence resulting from the quantification of cell permeability.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001021

Axiom
annotated source: cell permeability assay evidence
annotated property: definition
annotated target: A type of cell-based assay evidence resulting from the quantification of cell permeability.
database_cross_reference: PMID:16962665

carboxyfluorescein diacetate succinimidyl ester staining evidence
type: Class
subclass of: staining evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: CFDA-SE staining evidence
has_exact_synonym: CFSE-staining evidence
has_obo_namespace: eco
id: ECO:0001022

Axiom
annotated source: carboxyfluorescein diacetate succinimidyl ester staining evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMC:3185625

chemiluminescence-linked immunoassay evidence
type: Class
subclass of: protein detection assay evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: CLIA evidence
has_obo_namespace: eco
id: ECO:0001023

Axiom
annotated source: chemiluminescence-linked immunoassay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:659901

chimeric protein phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
definition: A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: chimeric protein evidence
has_obo_namespace: eco
id: ECO:0001024

Axiom
annotated source: chimeric protein phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product.
database_cross_reference: PMID:22588898
database_cross_reference: PMID:25832756

co-electrophoresis evidence
type: Class
subclass of: gel electrophoresis evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0005488
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: Class
        intersection of: OBI_0600051
        intersection of: OBI_0600053
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001146
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0001121
definition: A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001025

Axiom
annotated source: co-electrophoresis evidence
annotated property: definition
annotated target: A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions.
database_cross_reference: PMID:7668395

co-localization evidence
type: Class
subclass of: imaging assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0033036
definition: A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001026

Axiom
annotated source: co-localization evidence
annotated property: definition
annotated target: A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location.
database_cross_reference: PMC:3074624

colony counting evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001285
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000978
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0100060
definition: A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001027

Axiom
annotated source: colony counting evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish.
database_cross_reference: PMID:16558698
database_cross_reference: PMID:23457446

co-sedimentation assay evidence
type: Class
subclass of: physical interaction evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000288
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001028

Axiom
annotated source: co-sedimentation assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: MI:0027

comet assay evidence
type: Class
subclass of: gel electrophoresis evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0006974
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0302736
definition: A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001029

Axiom
annotated source: comet assay evidence
annotated property: definition
annotated target: A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration.
database_cross_reference: OBI:0302736
database_cross_reference: PMID:10737956

conditional knockout evidence
type: Class
subclass of: knockout phenotypic evidence
definition: A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001030

Axiom
annotated source: conditional knockout evidence
annotated property: definition
annotated target: A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal.
database_cross_reference: PMC:3572410

conditional knockin evidence
type: Class
subclass of: knockin evidence
definition: A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001031

Axiom
annotated source: conditional knockin evidence
annotated property: definition
annotated target: A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation.
database_cross_reference: PMID:16832820

constitutively active mutant evidence
type: Class
subclass of: experimental phenotypic evidence
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: GO_0009058
    intersection of: GO_0010467
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001032

Axiom
annotated source: constitutively active mutant evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:12217490

cross-linking evidence
type: Class
subclass of: protein binding evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0005515
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001591
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000800
example of usage: To confirm this intriguing observation, we cross-linked AdpA and DNA in the presence of increasing amounts of ATP (figure 2b(iii)). In this assay, ATP prevented the formation of AdpA - DNA complexes in a concentration-dependent manner, an outcome consistent with the results obtained by SPR analysis.
definition: 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
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001033

Axiom
annotated source: cross-linking evidence
annotated property: example of usage
annotated target: To confirm this intriguing observation, we cross-linked AdpA and DNA in the presence of increasing amounts of ATP (figure 2b(iii)). In this assay, ATP prevented the formation of AdpA - DNA complexes in a concentration-dependent manner, an outcome consistent with the results obtained by SPR analysis.
database_cross_reference: PMID:22870392

Axiom
annotated source: cross-linking evidence
annotated property: definition
annotated target: 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
database_cross_reference: PMID:15530987
database_cross_reference: PMID:19241040

crystallography evidence
type: Class
subclass of: structure determination evidence
example of usage: The crystal structures of E. coli MarR and Enterococcus faecalis SlyA-like proteins show their cross-sections are ~70 angstroms, suggesting they would protect ~20 bp of DNA (Alekshun et al., 2001; Wu et al., 2003). This suggests the presence of two SlyA dimers at the SlyA I site and at least three dimers at the SlyA II site.
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001034

Axiom
annotated source: crystallography evidence
annotated property: example of usage
annotated target: The crystal structures of E. coli MarR and Enterococcus faecalis SlyA-like proteins show their cross-sections are ~70 angstroms, suggesting they would protect ~20 bp of DNA (Alekshun et al., 2001; Wu et al., 2003). This suggests the presence of two SlyA dimers at the SlyA I site and at least three dimers at the SlyA II site.
database_cross_reference: PMID:17892462

Axiom
annotated source: crystallography evidence
annotated property: definition
annotated target: 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.
database_cross_reference: MI:0114

cytochemistry evidence
type: Class
subclass of: histochemistry evidence
definition: A type of histochemistry evidence resulting from localizing chemical components of cells and organelles on histological sections.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001035

Axiom
annotated source: cytochemistry evidence
annotated property: definition
annotated target: A type of histochemistry evidence resulting from localizing chemical components of cells and organelles on histological sections.
database_cross_reference: PMID:11597006

cytochrome C release assay evidence
type: Class
subclass of: apoptotic assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000443
    intersection of: OBI_0001977
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001036

Axiom
annotated source: cytochrome C release assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:10914021
database_cross_reference: PMID:12815469

4',6-diamidino-2-phenylindole staining evidence
type: Class
subclass of: staining evidence
definition: A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: DAPI staining evidence
has_exact_synonym: diaminophenylindole staining
has_obo_namespace: eco
id: ECO:0001037

Axiom
annotated source: 4',6-diamidino-2-phenylindole staining evidence
annotated property: definition
annotated target: A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence.
database_cross_reference: PMID:8580206
database_cross_reference: url:https://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/protocols/dapi-imaging-protocol.html

deletion mutation phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
example of usage: In contrast, and in full agreement with the previous results of Wade et al. (17), the longer deletion in the TB23 fragment, that removes MelR binding site 2, results in a sharp reduction in the repression of the melR promoter by MelR.
definition: A type of mutant phenotype evidence resulting from a mutation in which there is the removal of one or more contiguous nucleotides that may result in altered function or other measurable properties.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_alternative_id: ECO:0005510
has_exact_synonym: deletion mutation evidence
has_obo_namespace: eco
id: ECO:0001038
comment: As a child of 'experimental phenotypic evidence', this is not to be confused with the biological processes deletion mutation / deletion deficiency in which DNA is lost during DNA replication.
comment: Contrast with knockout phenotypic evidence in which any number of changes to the DNA result in elimination of the function of the gene in question.
comment: The length of the DNA deleted can range from a single nucleotide to enough material that could include multiple genes.

Axiom
annotated source: deletion mutation phenotypic evidence
annotated property: example of usage
annotated target: In contrast, and in full agreement with the previous results of Wade et al. (17), the longer deletion in the TB23 fragment, that removes MelR binding site 2, results in a sharp reduction in the repression of the melR promoter by MelR.
database_cross_reference: PMID:18346968

Axiom
annotated source: deletion mutation phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from a mutation in which there is the removal of one or more contiguous nucleotides that may result in altered function or other measurable properties.
database_cross_reference: SO:0000159

DNA laddering assay evidence
type: Class
subclass of: apoptotic assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0006309
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001039

Axiom
annotated source: DNA laddering assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMC:4401164

RNA dot blot assay evidence
type: Class
subclass of: RNA detection assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0302903
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0002171
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0000880
definition: 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.
ontology term requester: CollecTF
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
has_related_synonym: RNA dot blot
id: ECO:0001040

Axiom
annotated source: RNA dot blot assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:21424648

dominant-negative mutant phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
definition: A type of mutant phenotype evidence resulting from a mutated gene producing mutant polypeptides that disrupt the activity of the wild-type genes.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: dominant-negative mutant evidence
has_obo_namespace: eco
id: ECO:0001042

Axiom
annotated source: dominant-negative mutant phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from a mutated gene producing mutant polypeptides that disrupt the activity of the wild-type genes.
database_cross_reference: PMC:2217636
database_cross_reference: PMID:8018332

Edman degradation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Edman degradation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: Edman degradation evidence
has GO evidence code: EXP
definition: A type of Edman degradation evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:59:00Z
has_obo_namespace: eco
id: ECO:0001043

Axiom
annotated source: Edman degradation evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: Edman degradation evidence used in manual assertion
annotated property: definition
annotated target: A type of Edman degradation evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

Edman degradation evidence
type: Class
subclass of: protein detection assay evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001044

Axiom
annotated source: Edman degradation evidence
annotated property: definition
annotated target: 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.
database_cross_reference: OBI:0000705
database_cross_reference: doi:10.3891/acta.chem.scand.04-0283

eTag assay evidence
type: Class
subclass of: affinity evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0010467
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000443
    intersection of: Class
      intersection of: Restriction
        on property: has part
        some values from: OBI_0600038
      intersection of: Restriction
        on property: has participant
        some values from: Class
definition: A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001045

Axiom
annotated source: eTag assay evidence
annotated property: definition
annotated target: A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters.
database_cross_reference: PMID:15137949

filter binding assay evidence
type: Class
subclass of: physical interaction evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001591
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0000151
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001046

Axiom
annotated source: filter binding assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:23028069

fluorescence in situ hybridization evidence
type: Class
subclass of: nucleic acid localization evidence
subclass of: in situ hybridization evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0051276
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001683
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001047

Axiom
annotated source: fluorescence in situ hybridization evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMC:346675
database_cross_reference: PMID:6812046

fluorescence resonance energy transfer evidence
type: Class
subclass of: dynamic fluorescence quenching evidence
definition: A type of dynamic fluorescence quenching 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: FRET
has_obo_namespace: eco
id: ECO:0001048

Axiom
annotated source: fluorescence resonance energy transfer evidence
annotated property: definition
annotated target: A type of dynamic fluorescence quenching 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.
database_cross_reference: PMID:11516318
database_cross_reference: PMID:15696158

gel-filtration evidence
type: Class
subclass of: chromatography evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001630
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0000535
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001049

Axiom
annotated source: gel-filtration evidence
annotated property: definition
annotated target: 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.
database_cross_reference: CHMO:0001011
database_cross_reference: doi:10.1038/nmeth0506-410

histochemistry evidence
type: Class
subclass of: histology evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001211
definition: A type of histology evidence resulting from the identification of chemical components in cells and tissues.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001050

Axiom
annotated source: histochemistry evidence
annotated property: definition
annotated target: A type of histology evidence resulting from the identification of chemical components in cells and tissues.
database_cross_reference: MMO:0000497

histology evidence
type: Class
subclass of: imaging assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0048532
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600020
definition: A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001051

Axiom
annotated source: histology evidence
annotated property: definition
annotated target: A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues.
database_cross_reference: OBI:0600020

high-performance liquid chromatography evidence
type: Class
subclass of: chromatography evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002116
example of usage: No OD increases with the mutant and the wild type were measured with DMSO provided as electron acceptor at 2 and 10 mM; however, HPLC analyses of cultures with 2 mM DMSO revealed that DMSO was completely consumed in wild type cultures, whereas no DMSO consumption was evident in the mutant cultures (Figure 3).
definition: 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.
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: HPLC evidence
has_obo_namespace: eco
id: ECO:0001052

Axiom
annotated source: high-performance liquid chromatography evidence
annotated property: example of usage
annotated target: No OD increases with the mutant and the wild type were measured with DMSO provided as electron acceptor at 2 and 10 mM; however, HPLC analyses of cultures with 2 mM DMSO revealed that DMSO was completely consumed in wild type cultures, whereas no DMSO consumption was evident in the mutant cultures (Figure 3).
database_cross_reference: PMID:21450087

Axiom
annotated source: high-performance liquid chromatography evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:16376355

immunocytochemistry evidence
type: Class
subclass of: protein detection assay evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001053

Axiom
annotated source: immunocytochemistry evidence
annotated property: definition
annotated target: 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.
database_cross_reference: MI:1200
database_cross_reference: OBI:0001986

immunodepletion evidence
type: Class
subclass of: immunological assay evidence
definition: A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001054

Axiom
annotated source: immunodepletion evidence
annotated property: definition
annotated target: A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample.
database_cross_reference: BAO:0002505

immunohistochemistry evidence
type: Class
subclass of: protein detection assay evidence
definition: A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001055

Axiom
annotated source: immunohistochemistry evidence
annotated property: definition
annotated target: A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections.
database_cross_reference: OBI:0001986

induced mutation evidence
type: Class
definition: A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001056
comment: This term was made obsolete for a couple of reasons: the def. doesn’t make sense as the suggested means of mutagenesis fail to introduce exogenous DNA (it is a child of genetic transformation evidence) and the def. is too much like random mutagenesis evidence.
deprecated: true

Axiom
annotated source: induced mutation evidence
annotated property: definition
annotated target: A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation.
database_cross_reference: OBI:0001154

in vitro acetylation assay evidence
type: Class
subclass of: acetylation assay evidence
definition: A type of acetylation assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001057

Axiom
annotated source: in vitro acetylation assay evidence
annotated property: definition
annotated target: A type of acetylation assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml

in vitro cleavage assay evidence
type: Class
subclass of: cleavage assay evidence
definition: A type of cleavage assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001058

Axiom
annotated source: in vitro cleavage assay evidence
annotated property: definition
annotated target: A type of cleavage assay evidence used in an in vitro experiment.
database_cross_reference: PMID:21121091

in vitro deubiquitination assay evidence
type: Class
subclass of: deubiquitination assay evidence
definition: A type of deubiquitination assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001059

Axiom
annotated source: in vitro deubiquitination assay evidence
annotated property: definition
annotated target: A type of deubiquitination assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:19692941
database_cross_reference: SIB:PG

in vitro deacetylation assay evidence
type: Class
subclass of: deacetylation assay evidence
definition: A type of deacetylation assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001060

Axiom
annotated source: in vitro deacetylation assay evidence
annotated property: definition
annotated target: A type of deacetylation assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml

in vitro defarnesylation assay evidence
type: Class
subclass of: defarnesylation assay evidence
definition: A type of defarnesylation assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001061

Axiom
annotated source: in vitro defarnesylation assay evidence
annotated property: definition
annotated target: A type of defarnesylation assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:16126733
database_cross_reference: SIB:PG

in vitro demethylation assay evidence
type: Class
subclass of: demethylation assay evidence
definition: A type of demethylation assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001062

Axiom
annotated source: in vitro demethylation assay evidence
annotated property: definition
annotated target: A type of demethylation assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Demethylation

in vitro desumoylation assay evidence
type: Class
subclass of: desumoylation assay evidence
definition: A type of desumoylation assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001063

Axiom
annotated source: in vitro desumoylation assay evidence
annotated property: definition
annotated target: A type of desumoylation assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/

in vitro farnesylation assay evidence
type: Class
subclass of: farnesylation assay evidence
definition: A type of farnesylation assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001064

Axiom
annotated source: in vitro farnesylation assay evidence
annotated property: definition
annotated target: A type of farnesylation assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Farnesyltransferase

in vitro methylation assay evidence
type: Class
subclass of: methylation assay evidence
definition: A type of methylation assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001065

Axiom
annotated source: in vitro methylation assay evidence
annotated property: definition
annotated target: A type of methylation assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Methylation

in vitro palmitoylation assay evidence
type: Class
subclass of: palmitoylation assay evidence
definition: A type of palmitoylation assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001066

Axiom
annotated source: in vitro palmitoylation assay evidence
annotated property: definition
annotated target: A type of palmitoylation assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:17077383
database_cross_reference: SIB:PG

in vitro phosphatase assay evidence
type: Class
subclass of: phosphatase assay evidence
definition: A type of phosphatase assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001067

Axiom
annotated source: in vitro phosphatase assay evidence
annotated property: definition
annotated target: A type of phosphatase assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Phosphatase

in vitro protein kinase assay evidence
type: Class
subclass of: protein kinase assay evidence
definition: A type of protein kinase assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001068

Axiom
annotated source: in vitro protein kinase assay evidence
annotated property: definition
annotated target: A type of protein kinase assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Protein_kinase
database_cross_reference: url:http://en.wikipedia.org/wiki/Protein_phosphorylation

in vitro polyADP-ribosylation assay evidence
type: Class
subclass of: polyADP-ribosylation assay evidence
definition: A type of polyADP-ribosylation assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001069

Axiom
annotated source: in vitro polyADP-ribosylation assay evidence
annotated property: definition
annotated target: A type of polyADP-ribosylation assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:21870253
database_cross_reference: SIB:PG

in vitro sumoylation assay evidence
type: Class
subclass of: sumoylation assay evidence
definition: A type of sumoylation assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001070

Axiom
annotated source: in vitro sumoylation assay evidence
annotated property: definition
annotated target: A type of sumoylation assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/

in vitro transcription assay evidence
type: Class
subclass of: transcription assay evidence
definition: A type of transcription assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001071

Axiom
annotated source: in vitro transcription assay evidence
annotated property: definition
annotated target: A type of transcription assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: ECO:SW
database_cross_reference: PMID:21125481
database_cross_reference: SIB:PG

in vitro translation assay evidence
type: Class
subclass of: translation assay evidence
definition: A type of translation assay evidence used in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001072

Axiom
annotated source: in vitro translation assay evidence
annotated property: definition
annotated target: A type of translation assay evidence used in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:18230759
database_cross_reference: SIB:PG

in vitro ubiquitination assay evidence
type: Class
subclass of: ubiquitination assay evidence
definition: A type of ubiquitination assay evidenceused in an in vitro experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001073

Axiom
annotated source: in vitro ubiquitination assay evidence
annotated property: definition
annotated target: A type of ubiquitination assay evidenceused in an in vitro experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:19692941
database_cross_reference: SIB:PG

in vivo acetylation assay evidence
type: Class
subclass of: acetylation assay evidence
definition: A type of acetylation assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001074

Axiom
annotated source: in vivo acetylation assay evidence
annotated property: definition
annotated target: A type of acetylation assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml

in vivo cleavage assay evidence
type: Class
subclass of: cleavage assay evidence
definition: A type of cleavage assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001075

Axiom
annotated source: in vivo cleavage assay evidence
annotated property: definition
annotated target: A type of cleavage assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:22154596

in vivo deacetylation assay evidence
type: Class
subclass of: deacetylation assay evidence
definition: A type of deacetylation assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001076

Axiom
annotated source: in vivo deacetylation assay evidence
annotated property: definition
annotated target: A type of deacetylation assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml

in vivo defarnesylation assay evidence
type: Class
subclass of: defarnesylation assay evidence
definition: A type of defarnesylation assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001077

Axiom
annotated source: in vivo defarnesylation assay evidence
annotated property: definition
annotated target: A type of defarnesylation assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:15556768
database_cross_reference: PMID:16507103
database_cross_reference: SIB:PG

in vivo demethylation assay evidence
type: Class
subclass of: demethylation assay evidence
definition: A type of demethylation assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001078

Axiom
annotated source: in vivo demethylation assay evidence
annotated property: definition
annotated target: A type of demethylation assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Demethylation

in vivo deubiquitination assay evidence
type: Class
subclass of: deubiquitination assay evidence
definition: A type of deubiquitination assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001079

Axiom
annotated source: in vivo deubiquitination assay evidence
annotated property: definition
annotated target: A type of deubiquitination assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:19692941
database_cross_reference: SIB:PG

in vivo desumoylation assay evidence
type: Class
subclass of: desumoylation assay evidence
definition: A type of desumoylation assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001080

Axiom
annotated source: in vivo desumoylation assay evidence
annotated property: definition
annotated target: A type of desumoylation assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/

in vivo farnesylation assay evidence
type: Class
subclass of: farnesylation assay evidence
definition: A type of farnesylation assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001081

Axiom
annotated source: in vivo farnesylation assay evidence
annotated property: definition
annotated target: A type of farnesylation assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:9030603
database_cross_reference: SIB:PG

in vivo methylation assay evidence
type: Class
subclass of: methylation assay evidence
definition: A type of methylation assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001082

Axiom
annotated source: in vivo methylation assay evidence
annotated property: definition
annotated target: A type of methylation assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Methylation

in vivo palmitoylation assay evidence
type: Class
subclass of: palmitoylation assay evidence
definition: A type of palmitoylation assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001083

Axiom
annotated source: in vivo palmitoylation assay evidence
annotated property: definition
annotated target: A type of palmitoylation assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:10329400
database_cross_reference: SIB:PG

in vivo phosphatase assay evidence
type: Class
subclass of: phosphatase assay evidence
definition: A type of phosphatase assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001084

Axiom
annotated source: in vivo phosphatase assay evidence
annotated property: definition
annotated target: A type of phosphatase assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Phosphatase

in vivo protein kinase assay evidence
type: Class
subclass of: protein kinase assay evidence
definition: A type of protein kinase assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001085

Axiom
annotated source: in vivo protein kinase assay evidence
annotated property: definition
annotated target: A type of protein kinase assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Protein_kinase
database_cross_reference: url:http://en.wikipedia.org/wiki/Protein_phosphorylation

in vivo sumoylation assay evidence
type: Class
subclass of: sumoylation assay evidence
definition: A type of sumoylation assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001086

Axiom
annotated source: in vivo sumoylation assay evidence
annotated property: definition
annotated target: A type of sumoylation assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: SIB:PG
database_cross_reference: url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/

in vivo transcription assay evidence
type: Class
subclass of: transcription assay evidence
definition: A type of transcription assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001087

Axiom
annotated source: in vivo transcription assay evidence
annotated property: definition
annotated target: A type of transcription assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:12181418
database_cross_reference: SIB:PG

in vivo translation assay evidence
type: Class
subclass of: translation assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0006412
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000966
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001199
definition: A type of translation assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001088

Axiom
annotated source: in vivo translation assay evidence
annotated property: definition
annotated target: A type of translation assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:24901308
database_cross_reference: SIB:PG

in vivo ubiquitination assay evidence
type: Class
subclass of: ubiquitination assay evidence
definition: A type of ubiquitination assay evidence used in an in vivo experiment.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001089

Axiom
annotated source: in vivo ubiquitination assay evidence
annotated property: definition
annotated target: A type of ubiquitination assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:19692941
database_cross_reference: SIB:PG

knockin evidence
type: Class
subclass of: genetic transformation evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0001149
definition: A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001090

Axiom
annotated source: knockin evidence
annotated property: definition
annotated target: A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence.
database_cross_reference: PMID:18077807
database_cross_reference: PMID:21800101

knockout phenotypic evidence
type: Class
subclass of: genetic transformation evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0001148
definition: A type of genetic transformation evidence resulting from a change in the DNA that results in the elimination of the function of the gene, allowing for functional analysis.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: knockout evidence
has_narrow_synonym: gene deletion evidence
has_narrow_synonym: gene knockout evidence
has_obo_namespace: eco
id: ECO:0001091
comment: A change in the DNA may result from any number of processes such (deletion, insertion, frame shift, etc.) Additionally, the gene may be made inoperative via homologous recombination, site-specific nucleases, zinc finger nucleases, transcription activator-like effector nucleases (TALENs), or CRISPR (Clustered regularly interspaced short palindromic repeats).
comment: Contrast with deletion mutation phenotypic evidence in which DNA is deleted which may result in altering the function of the resulting protein(s).

Axiom
annotated source: knockout phenotypic evidence
annotated property: definition
annotated target: A type of genetic transformation evidence resulting from a change in the DNA that results in the elimination of the function of the gene, allowing for functional analysis.
database_cross_reference: PMC:2782548

lipid binding assay evidence
type: Class
subclass of: physical interaction evidence
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: GO_0008289
    intersection of: Restriction
      on property: has participant
      some values from: PR_000000001
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001591
definition: A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001092

Axiom
annotated source: lipid binding assay evidence
annotated property: definition
annotated target: A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid.
database_cross_reference: PMID:22848065
database_cross_reference: PMID:23681540

luminescence-based mammalian interactome mapping assay evidence
type: Class
subclass of: physical interaction evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0005515
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000288
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: LUMIER assay
has_obo_namespace: eco
id: ECO:0001093

Axiom
annotated source: luminescence-based mammalian interactome mapping assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: MI:0729
database_cross_reference: PMID:15761153

macroscopy evidence
type: Class
subclass of: experimental evidence
definition: A type of experimental evidence that is visible to the naked eye cf. microscopy evidence which requires the aid of a microscope.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001094

mammalian 2-hybrid assay evidence
type: Class
subclass of: bait-prey hybrid interaction evidence
definition: A type of bait-prey 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001095

Axiom
annotated source: mammalian 2-hybrid assay evidence
annotated property: definition
annotated target: A type of bait-prey 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.
database_cross_reference: ECO:RCT
database_cross_reference: PMID:9043710

mass spectrometry evidence
type: Class
subclass of: spectrometry evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000470
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0200085
example of usage: The MS analyses showed that two VapB10 peaks (836.437, 1584.789 m/z) and three VapC10-His6 peaks (1049.526, 1299.733 and 1455.853 m/z) were detected in MS-DIGEST program, indicating that both VapB10 and VapC10-His6 had the expected peptide masses (Figure S3). These results suggest that VapB10 binds to VapC10-His6 forming the TA complex VapBC10 in vivo, which may cause the counteraction of the VapC10-induced growth arrest (Figure 2).
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001096

Axiom
annotated source: mass spectrometry evidence
annotated property: example of usage
annotated target: The MS analyses showed that two VapB10 peaks (836.437, 1584.789 m/z) and three VapC10-His6 peaks (1049.526, 1299.733 and 1455.853 m/z) were detected in MS-DIGEST program, indicating that both VapB10 and VapC10-His6 had the expected peptide masses (Figure S3). These results suggest that VapB10 binds to VapC10-His6 forming the TA complex VapBC10 in vivo, which may cause the counteraction of the VapC10-induced growth arrest (Figure 2).
database_cross_reference: PMID:24260461

Axiom
annotated source: mass spectrometry evidence
annotated property: definition
annotated target: 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.
database_cross_reference: OBI:0000470

medical imaging evidence
type: Class
subclass of: imaging assay evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001097

Axiom
annotated source: medical imaging evidence
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://www.fda.gov/Radiation-EmittingProducts/RadiationEmittingProductsandProcedures/MedicalImaging/ucm2005914.htm

microscopy evidence
type: Class
subclass of: imaging assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000185
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0400169
definition: A type of direct assay evidence resulting from the use of a microscope.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001098
comment: Microscopy may include any of the following: optical, electron, scanning probe, or X-ray.

Axiom
annotated source: microscopy evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from the use of a microscope.
database_cross_reference: ECO:MCC

motility wound healing assay evidence
type: Class
subclass of: cell-based assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0042060
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000978
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001285
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_alternative_id: ECO:0001135
has_broad_synonym: wound healing assay evidence
has_obo_namespace: eco
id: ECO:0001099

MTS assay evidence
type: Class
subclass of: apoptotic assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0008283
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000443
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600000
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_narrow_synonym: 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium
has_obo_namespace: eco
id: ECO:0001100

Axiom
annotated source: MTS assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: NBK:144065
database_cross_reference: PMID:1867954

MTT assay evidence
type: Class
subclass of: apoptotic assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0008283
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000443
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600000
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_narrow_synonym: 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
has_obo_namespace: eco
id: ECO:0001101

Axiom
annotated source: MTT assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: NBK:144065
database_cross_reference: PMID:6606682

multiplex bead-based immunoassay evidence
type: Class
subclass of: protein detection assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000443
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001441
definition: 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).
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001102

Axiom
annotated source: multiplex bead-based immunoassay evidence
annotated property: definition
annotated target: 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).
database_cross_reference: PMC:1534009

natural variation mutant evidence
type: Class
subclass of: experimental phenotypic evidence
definition: A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001103

Axiom
annotated source: natural variation mutant evidence
annotated property: definition
annotated target: A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits.
database_cross_reference: ECO:RCT

nuclear fragmentation evidence
type: Class
subclass of: apoptotic assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0007576
definition: A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001104

Axiom
annotated source: nuclear fragmentation evidence
annotated property: definition
annotated target: A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death.
database_cross_reference: PMID:16738861

nuclear magnetic resonance evidence
type: Class
subclass of: magnetic resonance evidence
definition: A type of magnetic resonance evidence in which atomic nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field and the resulting electromagnetic signal is captured.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001105

Axiom
annotated source: nuclear magnetic resonance evidence
annotated property: definition
annotated target: A type of magnetic resonance evidence in which atomic nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field and the resulting electromagnetic signal is captured.
database_cross_reference: url:https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance

nuclease protection assay evidence
type: Class
subclass of: RNA detection assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000424
    intersection of: OBI_0001670
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001106

Axiom
annotated source: nuclease protection assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:17486122
database_cross_reference: PMID:18428580

nucleotide analog incorporation assay evidence
type: Class
subclass of: DNA synthesis cell proliferation assay evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001107

Axiom
annotated source: nucleotide analog incorporation assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMC:3149870

phage display evidence
type: Class
subclass of: protein binding evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0005515
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001476
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0001480
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001108

Axiom
annotated source: phage display evidence
annotated property: definition
annotated target: 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.
database_cross_reference: MI:0084
database_cross_reference: PMID:11680867

phosphoamino acid analysis evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001109

Axiom
annotated source: phosphoamino acid analysis evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis.
database_cross_reference: PMID:11680867
database_cross_reference: PMID:18429115

peptide affinity enrichment evidence
type: Class
subclass of: affinity evidence
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: GO_0005488
    intersection of: Restriction
      on property: has participant
      some values from: PR_000000001
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001591
definition: A type of affinity evidence resulting from the appending of affinity tags on proteins so that they may be purified from their biological source using an affinity technique.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_narrow_synonym: phosphopeptide affinity enrichment evidence
has_obo_namespace: eco
id: ECO:0001110

physical examination evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001111

Axiom
annotated source: physical examination evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample.
database_cross_reference: ECO:RCT

peptide array evidence
type: Class
subclass of: protein binding evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000288
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001441
definition: A type of protein binding 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_narrow_synonym: phosphopeptide array evidence
has_obo_namespace: eco
id: ECO:0001112

Axiom
annotated source: peptide array evidence
annotated property: definition
annotated target: A type of protein binding 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.
database_cross_reference: PMID:21243154

point mutation phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
definition: A type of mutant phenotype evidence resulting from the change in a single nucleotide.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: point mutation evidence
has_obo_namespace: eco
id: ECO:0001113

Axiom
annotated source: point mutation phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from the change in a single nucleotide.
database_cross_reference: SO:1000008

propidium iodide staining evidence
type: Class
subclass of: staining evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001114

Axiom
annotated source: propidium iodide staining evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:17406435

fluorescence evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001501
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600038
definition: A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001115

Axiom
annotated source: fluorescence evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore.
database_cross_reference: url:http://www.nature.com/subjects/biological-fluorescence

protein dot blot assay evidence
type: Class
subclass of: protein detection assay evidence
definition: A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001116

Axiom
annotated source: protein dot blot assay evidence
annotated property: definition
annotated target: A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged.
database_cross_reference: doi:10.1007/978-94-009-0951-9_24

protein microarray evidence
type: Class
subclass of: protein detection assay evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001117

Axiom
annotated source: protein microarray evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMC:1828913

protein sequencing assay evidence
type: Class
subclass of: sequencing assay evidence
definition: A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001118

Axiom
annotated source: protein sequencing assay evidence
annotated property: definition
annotated target: A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein.
database_cross_reference: ERO:0001287

quantitative mass spectrometry evidence
type: Class
subclass of: mass spectrometry evidence
definition: A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001119

Axiom
annotated source: quantitative mass spectrometry evidence
annotated property: definition
annotated target: A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes.
database_cross_reference: PMID:22665296

radioisotope assay evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000201
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600038
definition: A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: radioassay
has_exact_synonym: radioisotopic assay
has_obo_namespace: eco
id: ECO:0001120

Axiom
annotated source: radioisotope assay evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant.
database_cross_reference: ISBN:978-3-642-50036-7

radioimmunoassay evidence
type: Class
subclass of: protein detection assay evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001121

Axiom
annotated source: radioimmunoassay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: MeSH:D011863

resonant mirror biosensor evidence
type: Class
subclass of: direct assay evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001123

Axiom
annotated source: resonant mirror biosensor evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:19151938

restriction fragment detection evidence
type: Class
subclass of: DNA detection assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001444
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000435
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600055
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001124

Axiom
annotated source: restriction fragment detection evidence
annotated property: definition
annotated target: 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.
database_cross_reference: doi:10.1007/978-94-009-0951-9_24
database_cross_reference: url:http://www.ncbi.nlm.nih.gov/probe/docs/techrflp/

spectrophotometry evidence
type: Class
subclass of: spectrometry evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0400115
definition: A type of spectrometry evidence resulting from the evaluation of a molecule in a fluid or solid by its ability to alter the transmission of light at specific wavelengths.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001126

Axiom
annotated source: spectrophotometry evidence
annotated property: definition
annotated target: A type of spectrometry evidence resulting from the evaluation of a molecule in a fluid or solid by its ability to alter the transmission of light at specific wavelengths.
database_cross_reference: MMO:0000173

surface plasmon resonance evidence
type: Class
subclass of: physical interaction evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000923
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: Class
        intersection of: OBI_0000094
        intersection of: Restriction
example of usage: Electrophoretic mobility shift assay (EMSA) and surface plasmon resonance (SPR) demonstrated that AdpAHis6 specifically bound the oriC fragment (283-bp) containing the in silico-predicted A-boxes in a concentration-dependent manner (figures 1b and 2a), but not the remaining part of oriC (data not shown).
example of usage: Further confirmation of the specific interaction was obtained by conducting the competing surface plasmon resonance (SPR) assay with the unlabeled DNA fragments. As shown in Additional file 3, a significantly lower response was observed when either the unlabeled S2 or S5 was added together with MtrA, which indicated that they could compete the binding of MtrA with the promoter DNA on the chip.
example of usage: Our SPR analysis revealed that also housekeeping genes required for ribosome function (rplR) and beta subunit RNA polymerase (rpoB) belong to the LexA regulon, a feature of the SOS network not yet observed in bacteria.
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: SPR evidence
has_obo_namespace: eco
id: ECO:0001127
comment: Plasmons are generated by an incident light beam.

Axiom
annotated source: surface plasmon resonance evidence
annotated property: example of usage
annotated target: Electrophoretic mobility shift assay (EMSA) and surface plasmon resonance (SPR) demonstrated that AdpAHis6 specifically bound the oriC fragment (283-bp) containing the in silico-predicted A-boxes in a concentration-dependent manner (figures 1b and 2a), but not the remaining part of oriC (data not shown).
database_cross_reference: PMID:22870392

Axiom
annotated source: surface plasmon resonance evidence
annotated property: example of usage
annotated target: Further confirmation of the specific interaction was obtained by conducting the competing surface plasmon resonance (SPR) assay with the unlabeled DNA fragments. As shown in Additional file 3, a significantly lower response was observed when either the unlabeled S2 or S5 was added together with MtrA, which indicated that they could compete the binding of MtrA with the promoter DNA on the chip.
database_cross_reference: PMID:20843371

Axiom
annotated source: surface plasmon resonance evidence
annotated property: example of usage
annotated target: Our SPR analysis revealed that also housekeeping genes required for ribosome function (rplR) and beta subunit RNA polymerase (rpoB) belong to the LexA regulon, a feature of the SOS network not yet observed in bacteria.
database_cross_reference: PMID:24713082

Axiom
annotated source: surface plasmon resonance evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:11578932
database_cross_reference: PMID:19151937
database_cross_reference: PMID:8574707

Axiom
annotated source: surface plasmon resonance evidence
annotated property: has_exact_synonym
annotated target: SPR evidence
database_cross_reference: PMID:11578932

syngeneic transplantation experiment evidence
type: Class
subclass of: experimental phenotypic evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000105
definition: A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001128

Axiom
annotated source: syngeneic transplantation experiment evidence
annotated property: definition
annotated target: A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin.
database_cross_reference: PMID:18469352

TACE activity assay evidence
type: Class
subclass of: enzymatic activity assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_1990774
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000443
definition: A type of enzymatic activity 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: Tumor necrosis factor - alpha converting enzyme activity assay
has_obo_namespace: eco
id: ECO:0001129

Axiom
annotated source: TACE activity assay evidence
annotated property: definition
annotated target: A type of enzymatic activity 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.
database_cross_reference: PMC:1808921

tissue microarray evidence
type: Class
subclass of: cytochemistry evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001985
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: OBI_0100051
        intersection of: Restriction
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001130

Axiom
annotated source: tissue microarray evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:11770905

transgenic organism evidence
type: Class
subclass of: genetic transformation evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000966
    intersection of: Restriction
      on property: has participant
      some values from: OBI_1000048
definition: A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001131

Axiom
annotated source: transgenic organism evidence
annotated property: definition
annotated target: A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification.
database_cross_reference: OBI:1000048

tryptic phosphopeptide mapping assay evidence
type: Class
subclass of: mass spectrometry evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002035
definition: A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001132

Axiom
annotated source: tryptic phosphopeptide mapping assay evidence
annotated property: definition
annotated target: A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate.
database_cross_reference: PMID:18429120

terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence
type: Class
subclass of: apoptotic assay evidence
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: TUNEL assay evidence
has_exact_synonym: TdT-mediated dUTP-biotin nick end labeling assay
has_exact_synonym: terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence
has_obo_namespace: eco
id: ECO:0001133

Axiom
annotated source: terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:22566045

urine test evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000443
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: Class
        intersection of: OBI_0000094
        intersection of: Restriction
definition: A type of direct assay evidence resulting from the analysis of a urine sample.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_obo_namespace: eco
id: ECO:0001134

Axiom
annotated source: urine test evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from the analysis of a urine sample.
database_cross_reference: ECO:RCT

WST-1 assay evidence
type: Class
subclass of: cell proliferation assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600000
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000443
    intersection of: OBI_0000891
definition: 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.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_alternative_id: ECO:0005009
has_broad_synonym: metabolic cell proliferation assay evidence
has_obo_namespace: eco
id: ECO:0001136

Axiom
annotated source: WST-1 assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18417231

xenotransplantation phenotypic evidence
type: Class
subclass of: anatomical perturbation phenotypic evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000043
definition: A type of anatomical perturbation phenotypic evidence resulting from the transplantation, implantation, or infusion of live cells, tissues, or organs between individuals of different species.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-16T11:30:54Z
has_exact_synonym: Xenograft transplantation
has_exact_synonym: Xenografting
has_exact_synonym: Xenotransplantation
has_exact_synonym: xenotransplantation experiment evidence
has_narrow_synonym: tissue grafting
has_obo_namespace: eco
id: ECO:0001137

Axiom
annotated source: xenotransplantation phenotypic evidence
annotated property: definition
annotated target: A type of anatomical perturbation phenotypic evidence resulting from the transplantation, implantation, or infusion of live cells, tissues, or organs between individuals of different species.
database_cross_reference: ECO:SN
database_cross_reference: url:http://ilarjournal.oxfordjournals.org/content/37/1/16.full.pdf+html
database_cross_reference: url:http://www.fda.gov/BiologicsBloodVaccines/Xenotransplantation/

3D cell culture evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: 3D cell culture evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: 3D cell culture evidence
has GO evidence code: IDA
definition: A type of 3D cell culture evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:18:35Z
has_obo_namespace: eco
id: ECO:0001138

Axiom
annotated source: 3D cell culture evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: 3D cell culture evidence used in manual assertion
annotated property: definition
annotated target: A type of 3D cell culture evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

51Cr release assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: 51Cr release assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: 51Cr release assay evidence
has GO evidence code: IDA
definition: A type of 51Cr release assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:20:55Z
has_obo_namespace: eco
id: ECO:0001139

Axiom
annotated source: 51Cr release assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: 51Cr release assay evidence used in manual assertion
annotated property: definition
annotated target: A type of 51Cr release assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

7-aminoactinomycin staining evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: 7-aminoactinomycin staining evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: 7-aminoactinomycin staining evidence
has GO evidence code: IDA
definition: A type of 7-aminoactinomycin staining evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:22:01Z
has_broad_synonym: 7-AAD staining evidence
has_broad_synonym: 7-amino-actinomycin D staining evidence
has_obo_namespace: eco
id: ECO:0001140

Axiom
annotated source: 7-aminoactinomycin staining evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: 7-aminoactinomycin staining evidence used in manual assertion
annotated property: definition
annotated target: A type of 7-aminoactinomycin staining evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

[3H]-thymidine incorporation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: [3H]-thymidine incorporation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: [3H]-thymidine incorporation assay evidence
has GO evidence code: IDA
definition: A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:31:52Z
has_obo_namespace: eco
id: ECO:0001141

Axiom
annotated source: [3H]-thymidine incorporation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: [3H]-thymidine incorporation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

[3H]arachidonic acid release assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: [3H]arachidonic acid release assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: [3H]arachidonic acid release assay evidence
has GO evidence code: IDA
definition: A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:32:44Z
has_obo_namespace: eco
id: ECO:0001142

Axiom
annotated source: [3H]arachidonic acid release assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: [3H]arachidonic acid release assay evidence used in manual assertion
annotated property: definition
annotated target: A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

adhesion assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: adhesion assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: adhesion assay evidence
has GO evidence code: IDA
definition: A type of adhesion assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:33:38Z
has_obo_namespace: eco
id: ECO:0001143

Axiom
annotated source: adhesion assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: adhesion assay evidence used in manual assertion
annotated property: definition
annotated target: A type of adhesion assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

adoptive cell transfer evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: adoptive cell transfer evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: adoptive cell transfer evidence
has GO evidence code: IDA
definition: A type of adoptive cell transfer evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:36:19Z
has_broad_synonym: Adoptive immunotherapy
has_broad_synonym: passive immunization
has_obo_namespace: eco
id: ECO:0001144

Axiom
annotated source: adoptive cell transfer evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: adoptive cell transfer evidence used in manual assertion
annotated property: definition
annotated target: A type of adoptive cell transfer evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

alamarBlue assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: alamarBlue assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: alamarBlue assay evidence
has GO evidence code: IDA
definition: A type of alamarBlue assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:37:21Z
has_obo_namespace: eco
id: ECO:0001145

Axiom
annotated source: alamarBlue assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: alamarBlue assay evidence used in manual assertion
annotated property: definition
annotated target: A type of alamarBlue assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

allograft transplantation phenotypic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: allograft transplantation phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: allograft transplantation phenotypic evidence
subclass of: ECO_0007634
has GO evidence code: EXP
definition: A type of allograft transplantation phenotypic evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:38:22Z
has_broad_synonym: Allotransplantation
has_broad_synonym: allografting
has_exact_synonym: allograft transplantation evidence used in manual assertion
has_obo_namespace: eco
has_related_synonym: tissue grafting
id: ECO:0001146

Axiom
annotated source: allograft transplantation phenotypic evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: allograft transplantation phenotypic evidence used in manual assertion
annotated property: definition
annotated target: A type of allograft transplantation phenotypic evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

anion-exchange chromatography evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: anion-exchange chromatography evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: anion-exchange chromatography evidence
subclass of: ECO_0007680
has GO evidence code: EXP
definition: A type of anion-exchange chromatography evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:44:30Z
has_obo_namespace: eco
id: ECO:0001147

Axiom
annotated source: anion-exchange chromatography evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007680
is_inferred: true

Axiom
annotated source: anion-exchange chromatography evidence used in manual assertion
annotated property: definition
annotated target: A type of anion-exchange chromatography evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

annexin-V staining evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: annexin-V staining evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: annexin-V staining evidence
has GO evidence code: IDA
definition: A type of annexin-V staining evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:52:01Z
has_obo_namespace: eco
id: ECO:0001148

Axiom
annotated source: annexin-V staining evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: annexin-V staining evidence used in manual assertion
annotated property: definition
annotated target: A type of annexin-V staining evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

cognitive assay phenotypic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cognitive assay phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: cognitive assay phenotypic evidence
subclass of: ECO_0007634
has GO evidence code: EXP
definition: A type of cognitive assay phenotypic evidence used that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:53:38Z
has_exact_synonym: behavioral assay evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0001149

Axiom
annotated source: cognitive assay phenotypic evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: cognitive assay phenotypic evidence used in manual assertion
annotated property: definition
annotated target: A type of cognitive assay phenotypic evidence used that is used in a manual assertion.
database_cross_reference: ECO:MCC

blocking monoclonal antibody evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: blocking monoclonal antibody evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: blocking monoclonal antibody evidence
subclass of: immunological assay evidence used in manual assertion
has GO evidence code: IPI
definition: A type of blocking monoclonal antibody evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:54:44Z
has_obo_namespace: eco
id: ECO:0001150

Axiom
annotated source: blocking monoclonal antibody evidence used in manual assertion
annotated property: subClassOf
annotated target: immunological assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: blocking monoclonal antibody evidence used in manual assertion
annotated property: definition
annotated target: A type of blocking monoclonal antibody evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

blocking peptide evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: blocking peptide evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: blocking peptide evidence
subclass of: immunological assay evidence used in manual assertion
has GO evidence code: IPI
definition: A type of blocking peptide evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T15:55:33Z
has_obo_namespace: eco
id: ECO:0001151

Axiom
annotated source: blocking peptide evidence used in manual assertion
annotated property: subClassOf
annotated target: immunological assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: blocking peptide evidence used in manual assertion
annotated property: definition
annotated target: A type of blocking peptide evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

blocking polyclonal antibody evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: blocking polyclonal antibody evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: blocking polyclonal antibody evidence
subclass of: immunological assay evidence used in manual assertion
has GO evidence code: IPI
definition: A type of blocking polyclonal antibody evidence tthat is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:01:39Z
has_obo_namespace: eco
id: ECO:0001152

Axiom
annotated source: blocking polyclonal antibody evidence used in manual assertion
annotated property: subClassOf
annotated target: immunological assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: blocking polyclonal antibody evidence used in manual assertion
annotated property: definition
annotated target: A type of blocking polyclonal antibody evidence tthat is used in a manual assertion.
database_cross_reference: ECO:MCC

blood test evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: blood test evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: blood test evidence
has GO evidence code: IDA
definition: A type of blood test evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:02:47Z
has_obo_namespace: eco
id: ECO:0001153

Axiom
annotated source: blood test evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: blood test evidence used in manual assertion
annotated property: definition
annotated target: A type of blood test evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

Boyden chamber assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Boyden chamber assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: Boyden chamber assay evidence
has GO evidence code: IDA
definition: A type of Boyden chamber assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:03:53Z
has_obo_namespace: eco
id: ECO:0001154

Axiom
annotated source: Boyden chamber assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: Boyden chamber assay evidence used in manual assertion
annotated property: definition
annotated target: A type of Boyden chamber assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

bromodeoxyuridine incorporation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: bromodeoxyuridine incorporation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: bromodeoxyuridine incorporation assay evidence
subclass of: nucleotide analog incorporation assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of bromodeoxyuridine incorporation assay evidence used in manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:04:49Z
has_broad_synonym: 5-bromo-2'-deoxyuridine incorporation assay evidence
has_broad_synonym: BUdR incorporation assay evidence
has_broad_synonym: BrdU incorporation assay evidence
has_broad_synonym: BrdUrd incorporation assay evidence
has_obo_namespace: eco
id: ECO:0001155

Axiom
annotated source: bromodeoxyuridine incorporation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: nucleotide analog incorporation assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: bromodeoxyuridine incorporation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of bromodeoxyuridine incorporation assay evidence used in manual assertion.
database_cross_reference: ECO:MCC

caspase assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: caspase assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: caspase assay evidence
has GO evidence code: IDA
definition: A type of caspase assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:06:06Z
has_obo_namespace: eco
id: ECO:0001156

Axiom
annotated source: caspase assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: caspase assay evidence used in manual assertion
annotated property: definition
annotated target: A type of caspase assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

cell counting evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cell counting evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: cell counting evidence
has GO evidence code: IDA
definition: A type of cell counting evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:07:13Z
has_obo_namespace: eco
id: ECO:0001157

Axiom
annotated source: cell counting evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cell counting evidence used in manual assertion
annotated property: definition
annotated target: A type of cell counting evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

cell permeability assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cell permeability assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: cell permeability assay evidence
has GO evidence code: IDA
definition: A type of cell permeability assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:07:58Z
has_obo_namespace: eco
id: ECO:0001158

Axiom
annotated source: cell permeability assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cell permeability assay evidence used in manual assertion
annotated property: definition
annotated target: A type of cell permeability assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: carboxyfluorescein diacetate succinimidyl ester staining evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: carboxyfluorescein diacetate succinimidyl ester staining evidence
has GO evidence code: IDA
definition: A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:08:54Z
has_broad_synonym: CFDA-SE staining evidence
has_broad_synonym: CFSE-staining evidence
has_obo_namespace: eco
id: ECO:0001159

Axiom
annotated source: carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion
annotated property: definition
annotated target: A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

chemiluminescence-linked immunoassay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: chemiluminescence-linked immunoassay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: chemiluminescence-linked immunoassay evidence
has GO evidence code: EXP
definition: A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:09:55Z
has_broad_synonym: CLIA evidence
has_obo_namespace: eco
id: ECO:0001160

Axiom
annotated source: chemiluminescence-linked immunoassay evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: chemiluminescence-linked immunoassay evidence used in manual assertion
annotated property: definition
annotated target: A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

chimeric protein phenotypic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: chimeric protein phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mutant phenotype evidence used in manual assertion
subclass of: chimeric protein phenotypic evidence
has GO evidence code: IMP
definition: A type of chimeric protein phenotypic evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:10:40Z
has_exact_synonym: chimeric protein evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0001161

Axiom
annotated source: chimeric protein phenotypic evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

Axiom
annotated source: chimeric protein phenotypic evidence used in manual assertion
annotated property: definition
annotated target: A type of chimeric protein phenotypic evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

co-electrophoresis evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: co-electrophoresis evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: co-electrophoresis evidence
has GO evidence code: IDA
definition: A type of co-electrophoresis evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:11:22Z
has_obo_namespace: eco
id: ECO:0001162

Axiom
annotated source: co-electrophoresis evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: co-electrophoresis evidence used in manual assertion
annotated property: definition
annotated target: A type of co-electrophoresis evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

co-localization evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: co-localization evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: co-localization evidence
subclass of: imaging assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of co-localization evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:12:04Z
has_obo_namespace: eco
id: ECO:0001163

Axiom
annotated source: co-localization evidence used in manual assertion
annotated property: subClassOf
annotated target: imaging assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: co-localization evidence used in manual assertion
annotated property: definition
annotated target: A type of co-localization evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

co-sedimentation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: co-sedimentation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: physical interaction evidence used in manual assertion
subclass of: co-sedimentation assay evidence
has GO evidence code: IPI
definition: A type of co-sedimentation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:12:55Z
has_obo_namespace: eco
id: ECO:0001164

Axiom
annotated source: co-sedimentation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: co-sedimentation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of co-sedimentation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

colony counting evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: colony counting evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: colony counting evidence
has GO evidence code: IDA
definition: A type of colony counting evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:14:57Z
has_obo_namespace: eco
id: ECO:0001165

Axiom
annotated source: colony counting evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: colony counting evidence used in manual assertion
annotated property: definition
annotated target: A type of colony counting evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

comet assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: comet assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: comet assay evidence
has GO evidence code: IDA
definition: A type of comet assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:16:01Z
has_obo_namespace: eco
id: ECO:0001166

Axiom
annotated source: comet assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: comet assay evidence used in manual assertion
annotated property: definition
annotated target: A type of comet assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

conditional knockin evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: conditional knockin evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: conditional knockin evidence
subclass of: knockin evidence used in manual assertion
has GO evidence code: IMP
definition: A type of conditional knockin evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:17:22Z
has_obo_namespace: eco
id: ECO:0001167

Axiom
annotated source: conditional knockin evidence used in manual assertion
annotated property: subClassOf
annotated target: knockin evidence used in manual assertion
is_inferred: true

Axiom
annotated source: conditional knockin evidence used in manual assertion
annotated property: definition
annotated target: A type of conditional knockin evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

conditional knockout evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: conditional knockout evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: conditional knockout evidence
subclass of: knockout evidence used in manual assertion
has GO evidence code: IMP
definition: A type of conditional knockout evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:17:58Z
has_obo_namespace: eco
id: ECO:0001168

Axiom
annotated source: conditional knockout evidence used in manual assertion
annotated property: subClassOf
annotated target: knockout evidence used in manual assertion
is_inferred: true

Axiom
annotated source: conditional knockout evidence used in manual assertion
annotated property: definition
annotated target: A type of conditional knockout evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

constitutively active mutant evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: constitutively active mutant evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: constitutively active mutant evidence
subclass of: ECO_0007634
has GO evidence code: EXP
definition: A type of constitutively active mutant evidence that is used a in manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:20:23Z
has_obo_namespace: eco
id: ECO:0001169

Axiom
annotated source: constitutively active mutant evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: constitutively active mutant evidence used in manual assertion
annotated property: definition
annotated target: A type of constitutively active mutant evidence that is used a in manual assertion.
database_cross_reference: ECO:MCC

cross-linking evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cross-linking evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: cross-linking evidence
subclass of: protein binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of cross-linking evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:21:29Z
has_obo_namespace: eco
id: ECO:0001170

Axiom
annotated source: cross-linking evidence used in manual assertion
annotated property: subClassOf
annotated target: protein binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cross-linking evidence used in manual assertion
annotated property: definition
annotated target: A type of cross-linking evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

crystallography evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: crystallography evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: crystallography evidence
has GO evidence code: EXP
definition: A type of crystallography evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:22:20Z
has_obo_namespace: eco
id: ECO:0001171

Axiom
annotated source: crystallography evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: crystallography evidence used in manual assertion
annotated property: definition
annotated target: A type of crystallography evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

cytochemistry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cytochemistry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: cytochemistry evidence
subclass of: histochemistry evidence used in manual assertion
has GO evidence code: IDA
definition: A type of cytochemistry evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:23:10Z
has_obo_namespace: eco
id: ECO:0001172

Axiom
annotated source: cytochemistry evidence used in manual assertion
annotated property: subClassOf
annotated target: histochemistry evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cytochemistry evidence used in manual assertion
annotated property: definition
annotated target: A type of cytochemistry evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

cytochrome C release assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cytochrome C release assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: cytochrome C release assay evidence
has GO evidence code: IDA
definition: A type of cytochrome C release assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:23:53Z
has_obo_namespace: eco
id: ECO:0001173

Axiom
annotated source: cytochrome C release assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cytochrome C release assay evidence used in manual assertion
annotated property: definition
annotated target: A type of cytochrome C release assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

4',6-diamidino-2-phenylindole staining evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: 4',6-diamidino-2-phenylindole staining evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: 4',6-diamidino-2-phenylindole staining evidence
has GO evidence code: IDA
definition: A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:25:03Z
has_broad_synonym: DAPI staining evidence
has_obo_namespace: eco
id: ECO:0001174

Axiom
annotated source: 4',6-diamidino-2-phenylindole staining evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: 4',6-diamidino-2-phenylindole staining evidence used in manual assertion
annotated property: definition
annotated target: A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

deletion mutation phenotypic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: deletion mutation phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mutant phenotype evidence used in manual assertion
subclass of: deletion mutation phenotypic evidence
has GO evidence code: IMP
definition: A type of deletion mutation phenotypic evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:25:54Z
has_exact_synonym: deletion mutation evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0001175

Axiom
annotated source: deletion mutation phenotypic evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

Axiom
annotated source: deletion mutation phenotypic evidence used in manual assertion
annotated property: definition
annotated target: A type of deletion mutation phenotypic evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

DNA laddering assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: DNA laddering assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: DNA laddering assay evidence
has GO evidence code: IDA
definition: A type of DNA laddering assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:26:46Z
has_obo_namespace: eco
id: ECO:0001176

Axiom
annotated source: DNA laddering assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: DNA laddering assay evidence used in manual assertion
annotated property: definition
annotated target: A type of DNA laddering assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

RNA dot blot assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: RNA dot blot assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: RNA dot blot assay evidence
has GO evidence code: EXP
definition: A type of RNA dot blot assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:45:52Z
has_broad_synonym: RNA dot blot evidence
has_obo_namespace: eco
id: ECO:0001177

Axiom
annotated source: RNA dot blot assay evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: RNA dot blot assay evidence used in manual assertion
annotated property: definition
annotated target: A type of RNA dot blot assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

dominant-negative mutant phenotypic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: dominant-negative mutant phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mutant phenotype evidence used in manual assertion
subclass of: dominant-negative mutant phenotypic evidence
has GO evidence code: IMP
definition: A type of dominant-negative mutant phenotypic evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:47:44Z
has_exact_synonym: dominant-negative mutant evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0001179

Axiom
annotated source: dominant-negative mutant phenotypic evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

Axiom
annotated source: dominant-negative mutant phenotypic evidence used in manual assertion
annotated property: definition
annotated target: A type of dominant-negative mutant phenotypic evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

eTag assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: eTag assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: eTag assay evidence
subclass of: affinity evidence used in manual assertion
has GO evidence code: IPI
definition: A type of eTag assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T16:59:39Z
has_obo_namespace: eco
id: ECO:0001180

Axiom
annotated source: eTag assay evidence used in manual assertion
annotated property: subClassOf
annotated target: affinity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: eTag assay evidence used in manual assertion
annotated property: definition
annotated target: A type of eTag assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

filter binding assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: filter binding assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: physical interaction evidence used in manual assertion
subclass of: filter binding assay evidence
has GO evidence code: IPI
definition: A type of filter binding assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:03:28Z
has_obo_namespace: eco
id: ECO:0001181

Axiom
annotated source: filter binding assay evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: filter binding assay evidence used in manual assertion
annotated property: definition
annotated target: A type of filter binding assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

fluorescence in situ hybridization evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: fluorescence in situ hybridization evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: fluorescence in situ hybridization evidence
subclass of: in situ hybridization evidence used in manual assertion
has GO evidence code: IEP
definition: A type of fluorescence in situ hybridization evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:04:20Z
has_obo_namespace: eco
id: ECO:0001182

Axiom
annotated source: fluorescence in situ hybridization evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: fluorescence in situ hybridization evidence used in manual assertion
annotated property: subClassOf
annotated target: in situ hybridization evidence used in manual assertion
is_inferred: true

Axiom
annotated source: fluorescence in situ hybridization evidence used in manual assertion
annotated property: definition
annotated target: A type of fluorescence in situ hybridization evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

fluorescence resonance energy transfer evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: fluorescence resonance energy transfer evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: fluorescence resonance energy transfer evidence
subclass of: ECO_0006327
has GO evidence code: IPI
definition: A type of fluorescence resonance energy transfer evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:05:22Z
has_broad_synonym: FRET evidence
has_obo_namespace: eco
id: ECO:0001183

Axiom
annotated source: fluorescence resonance energy transfer evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0006327
is_inferred: true

Axiom
annotated source: fluorescence resonance energy transfer evidence used in manual assertion
annotated property: definition
annotated target: A type of fluorescence resonance energy transfer evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

gel-filtration evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: gel-filtration evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: gel-filtration evidence
subclass of: ECO_0007680
has GO evidence code: EXP
definition: A type of gel-filtration evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:06:14Z
has_obo_namespace: eco
id: ECO:0001184

Axiom
annotated source: gel-filtration evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007680
is_inferred: true

Axiom
annotated source: gel-filtration evidence used in manual assertion
annotated property: definition
annotated target: A type of gel-filtration evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

histochemistry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: histochemistry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: histochemistry evidence
subclass of: histology evidence used in manual assertion
has GO evidence code: IDA
definition: A type of histochemistry evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:07:19Z
has_obo_namespace: eco
id: ECO:0001185

Axiom
annotated source: histochemistry evidence used in manual assertion
annotated property: subClassOf
annotated target: histology evidence used in manual assertion
is_inferred: true

Axiom
annotated source: histochemistry evidence used in manual assertion
annotated property: definition
annotated target: A type of histochemistry evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

immunocytochemistry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunocytochemistry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: immunocytochemistry evidence
has GO evidence code: EXP
definition: A type of immunocytochemistry evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:12:39Z
has_obo_namespace: eco
id: ECO:0001186

Axiom
annotated source: immunocytochemistry evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunocytochemistry evidence used in manual assertion
annotated property: definition
annotated target: A type of immunocytochemistry evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

histology evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: histology evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: histology evidence
subclass of: imaging assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of histology evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:09:50Z
has_obo_namespace: eco
id: ECO:0001187

Axiom
annotated source: histology evidence used in manual assertion
annotated property: subClassOf
annotated target: imaging assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: histology evidence used in manual assertion
annotated property: definition
annotated target: A type of histology evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

immunodepletion evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunodepletion evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: immunodepletion evidence
subclass of: immunological assay evidence used in manual assertion
has GO evidence code: IPI
definition: A type of immunodepletion evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:16:19Z
has_obo_namespace: eco
id: ECO:0001188

Axiom
annotated source: immunodepletion evidence used in manual assertion
annotated property: subClassOf
annotated target: immunological assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunodepletion evidence used in manual assertion
annotated property: definition
annotated target: A type of immunodepletion evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

immunohistochemistry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunohistochemistry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: immunohistochemistry evidence
has GO evidence code: EXP
definition: A type of immunohistochemistry evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:17:22Z
has_obo_namespace: eco
id: ECO:0001189

Axiom
annotated source: immunohistochemistry evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunohistochemistry evidence used in manual assertion
annotated property: definition
annotated target: A type of immunohistochemistry evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro acetylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro acetylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro acetylation assay evidence
has GO evidence code: IDA
definition: A type of in vitro acetylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:19:24Z
has_obo_namespace: eco
id: ECO:0001190

Axiom
annotated source: in vitro acetylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro acetylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro acetylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro cleavage assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro cleavage assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro cleavage assay evidence
has GO evidence code: IDA
definition: A type of in vitro cleavage assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:21:22Z
has_obo_namespace: eco
id: ECO:0001191

Axiom
annotated source: in vitro cleavage assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro cleavage assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro cleavage assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro deacetylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro deacetylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro deacetylation assay evidence
has GO evidence code: IDA
definition: A type of in vitro deacetylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:23:42Z
has_obo_namespace: eco
id: ECO:0001192

Axiom
annotated source: in vitro deacetylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro deacetylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro deacetylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro defarnesylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro defarnesylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro defarnesylation assay evidence
has GO evidence code: IDA
definition: A type of in vitro defarnesylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:25:45Z
has_obo_namespace: eco
id: ECO:0001193

Axiom
annotated source: in vitro defarnesylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro defarnesylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro defarnesylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro demethylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro demethylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro demethylation assay evidence
has GO evidence code: IDA
definition: A type of in vitro demethylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:27:00Z
has_obo_namespace: eco
id: ECO:0001194

Axiom
annotated source: in vitro demethylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro demethylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro demethylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro desumoylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro desumoylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro desumoylation assay evidence
has GO evidence code: IDA
definition: A type of in vitro desumoylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:29:01Z
has_obo_namespace: eco
id: ECO:0001195

Axiom
annotated source: in vitro desumoylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro desumoylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro desumoylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro deubiquitination assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro deubiquitination assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro deubiquitination assay evidence
has GO evidence code: IDA
definition: A type of in vitro deubiquitination assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:29:48Z
has_obo_namespace: eco
id: ECO:0001196

Axiom
annotated source: in vitro deubiquitination assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro deubiquitination assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro deubiquitination assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro farnesylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro farnesylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro farnesylation assay evidence
has GO evidence code: IDA
definition: A type of in vitro farnesylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:30:50Z
has_obo_namespace: eco
id: ECO:0001197

Axiom
annotated source: in vitro farnesylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro farnesylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro farnesylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro methylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro methylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro methylation assay evidence
has GO evidence code: IDA
definition: A type of in vitro methylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:31:54Z
has_obo_namespace: eco
id: ECO:0001198

Axiom
annotated source: in vitro methylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro methylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro methylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro palmitoylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro palmitoylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro palmitoylation assay evidence
has GO evidence code: IDA
definition: A type of in vitro palmitoylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:32:57Z
has_obo_namespace: eco
id: ECO:0001199

Axiom
annotated source: in vitro palmitoylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro palmitoylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro palmitoylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro phosphatase assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro phosphatase assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro phosphatase assay evidence
has GO evidence code: IDA
definition: A type of in vitro phosphatase assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:34:16Z
has_obo_namespace: eco
id: ECO:0001200

Axiom
annotated source: in vitro phosphatase assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro phosphatase assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro phosphatase assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro polyADP-ribosylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro polyADP-ribosylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro polyADP-ribosylation assay evidence
has GO evidence code: IDA
definition: A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:34:57Z
has_obo_namespace: eco
id: ECO:0001201

Axiom
annotated source: in vitro polyADP-ribosylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro polyADP-ribosylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro protein kinase assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro protein kinase assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: in vitro protein kinase assay evidence
subclass of: enzymatic activity assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of in vitro protein kinase assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:39:57Z
has_obo_namespace: eco
id: ECO:0001202

Axiom
annotated source: in vitro protein kinase assay evidence used in manual assertion
annotated property: subClassOf
annotated target: enzymatic activity assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro protein kinase assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro protein kinase assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro sumoylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro sumoylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro sumoylation assay evidence
has GO evidence code: IDA
definition: A type of in vitro sumoylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:41:25Z
has_obo_namespace: eco
id: ECO:0001203

Axiom
annotated source: in vitro sumoylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro sumoylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro sumoylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro transcription assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro transcription assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro transcription assay evidence
has GO evidence code: IDA
definition: A type of in vitro transcription assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:44:40Z
has_obo_namespace: eco
id: ECO:0001204

Axiom
annotated source: in vitro transcription assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro transcription assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro transcription assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro translation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro translation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro translation assay evidence
has GO evidence code: IDA
definition: A type of in vitro translation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:46:30Z
has_obo_namespace: eco
id: ECO:0001205

Axiom
annotated source: in vitro translation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro translation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro translation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vitro ubiquitination assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vitro ubiquitination assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vitro ubiquitination assay evidence
has GO evidence code: IDA
definition: A type of in vitro ubiquitination assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:47:18Z
has_obo_namespace: eco
id: ECO:0001206

Axiom
annotated source: in vitro ubiquitination assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vitro ubiquitination assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vitro ubiquitination assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo acetylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo acetylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo acetylation assay evidence
has GO evidence code: IDA
definition: A type of in vivo acetylation assay evidence that is used in manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:48:56Z
has_obo_namespace: eco
id: ECO:0001207

Axiom
annotated source: in vivo acetylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo acetylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo acetylation assay evidence that is used in manual assertion.
database_cross_reference: ECO:MCC

in vivo cleavage assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo cleavage assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo cleavage assay evidence
has GO evidence code: IDA
definition: A type of in vivo cleavage assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:49:43Z
has_obo_namespace: eco
id: ECO:0001208

Axiom
annotated source: in vivo cleavage assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo cleavage assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo cleavage assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo deacetylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo deacetylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo deacetylation assay evidence
has GO evidence code: IDA
definition: A type of in vivo deacetylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:50:47Z
has_obo_namespace: eco
id: ECO:0001209

Axiom
annotated source: in vivo deacetylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo deacetylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo deacetylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo defarnesylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo defarnesylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo defarnesylation assay evidence
has GO evidence code: IDA
definition: A type of in vivo defarnesylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:52:41Z
has_obo_namespace: eco
id: ECO:0001210

Axiom
annotated source: in vivo defarnesylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo defarnesylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo defarnesylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo demethylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo demethylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo demethylation assay evidence
has GO evidence code: IDA
definition: A type of in vivo demethylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:53:40Z
has_obo_namespace: eco
id: ECO:0001211

Axiom
annotated source: in vivo demethylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo demethylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo demethylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo desumoylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo desumoylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo desumoylation assay evidence
has GO evidence code: IDA
definition: A type of in vivo desumoylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:54:36Z
has_obo_namespace: eco
id: ECO:0001212

Axiom
annotated source: in vivo desumoylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo desumoylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo desumoylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo deubiquitination assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo deubiquitination assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo deubiquitination assay evidence
has GO evidence code: IDA
definition: A type of in vivo deubiquitination assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:56:28Z
has_obo_namespace: eco
id: ECO:0001213

Axiom
annotated source: in vivo deubiquitination assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo deubiquitination assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo deubiquitination assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo farnesylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo farnesylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo farnesylation assay evidence
has GO evidence code: IDA
definition: A type of in vivo farnesylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T17:57:18Z
has_obo_namespace: eco
id: ECO:0001214

Axiom
annotated source: in vivo farnesylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo farnesylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo farnesylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo methylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo methylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo methylation assay evidence
has GO evidence code: IDA
definition: A type of in vivo methylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:03:16Z
has_obo_namespace: eco
id: ECO:0001215

Axiom
annotated source: in vivo methylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo methylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo methylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo palmitoylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo palmitoylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo palmitoylation assay evidence
has GO evidence code: IDA
definition: A type of in vivo palmitoylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:04:07Z
has_obo_namespace: eco
id: ECO:0001216

Axiom
annotated source: in vivo palmitoylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo palmitoylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo palmitoylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo phosphatase assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo phosphatase assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo phosphatase assay evidence
has GO evidence code: IDA
definition: A type of in vivo phosphatase assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:06:08Z
has_obo_namespace: eco
id: ECO:0001217

Axiom
annotated source: in vivo phosphatase assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo phosphatase assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo phosphatase assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo protein kinase assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo protein kinase assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: in vivo protein kinase assay evidence
subclass of: enzymatic activity assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of in vivo protein kinase assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:07:58Z
has_obo_namespace: eco
id: ECO:0001218

Axiom
annotated source: in vivo protein kinase assay evidence used in manual assertion
annotated property: subClassOf
annotated target: enzymatic activity assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo protein kinase assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo protein kinase assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo sumoylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo sumoylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo sumoylation assay evidence
has GO evidence code: IDA
definition: A type of in vivo sumoylation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:09:49Z
has_obo_namespace: eco
id: ECO:0001219

Axiom
annotated source: in vivo sumoylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo sumoylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo sumoylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo transcription assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo transcription assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo transcription assay evidence
has GO evidence code: IDA
definition: A type of in vivo transcription assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:11:20Z
has_obo_namespace: eco
id: ECO:0001220

Axiom
annotated source: in vivo transcription assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo transcription assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo transcription assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo translation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo translation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo translation assay evidence
has GO evidence code: IDA
definition: A type of in vivo translation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:42:50Z
has_obo_namespace: eco
id: ECO:0001221

Axiom
annotated source: in vivo translation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo translation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo translation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

in vivo ubiquitination assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo ubiquitination assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo ubiquitination assay evidence
has GO evidence code: IDA
definition: A type of in vivo ubiquitination assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:44:11Z
has_obo_namespace: eco
id: ECO:0001222

Axiom
annotated source: in vivo ubiquitination assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo ubiquitination assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo ubiquitination assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

induced mutation evidence used in manual assertion
type: Class
definition: A type of induced mutation evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:45:56Z
has_obo_namespace: eco
id: ECO:0001223
deprecated: true

Axiom
annotated source: induced mutation evidence used in manual assertion
annotated property: definition
annotated target: A type of induced mutation evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

knockin evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: knockin evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: knockin evidence
subclass of: genetic transformation evidence used in manual assertion
has GO evidence code: IMP
definition: A type of knockin evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:49:35Z
has_obo_namespace: eco
id: ECO:0001224

Axiom
annotated source: knockin evidence used in manual assertion
annotated property: subClassOf
annotated target: genetic transformation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: knockin evidence used in manual assertion
annotated property: definition
annotated target: A type of knockin evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

knockout evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: knockout phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: knockout phenotypic evidence
subclass of: genetic transformation evidence used in manual assertion
has GO evidence code: IMP
definition: A type of knockout evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:51:31Z
has_obo_namespace: eco
id: ECO:0001225

Axiom
annotated source: knockout evidence used in manual assertion
annotated property: subClassOf
annotated target: genetic transformation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: knockout evidence used in manual assertion
annotated property: definition
annotated target: A type of knockout evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

lipid binding assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: lipid binding assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: physical interaction evidence used in manual assertion
subclass of: lipid binding assay evidence
has GO evidence code: IPI
definition: A type of lipid binding assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:52:19Z
has_obo_namespace: eco
id: ECO:0001226

Axiom
annotated source: lipid binding assay evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: lipid binding assay evidence used in manual assertion
annotated property: definition
annotated target: A type of lipid binding assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

luminescence-based mammalian interactome mapping assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: luminescence-based mammalian interactome mapping assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: physical interaction evidence used in manual assertion
subclass of: luminescence-based mammalian interactome mapping assay evidence
has GO evidence code: IPI
definition: A type of LUMIER assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:55:16Z
has_broad_synonym: LUMIER assay evidence
has_obo_namespace: eco
id: ECO:0001227

Axiom
annotated source: luminescence-based mammalian interactome mapping assay evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: luminescence-based mammalian interactome mapping assay evidence used in manual assertion
annotated property: definition
annotated target: A type of LUMIER assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

macroscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: macroscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: macroscopy evidence
has GO evidence code: EXP
definition: A type of macroscopy evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:56:21Z
has_obo_namespace: eco
id: ECO:0001228

Axiom
annotated source: macroscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: macroscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of macroscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

mammalian 2-hybrid assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: mammalian 2-hybrid assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mammalian 2-hybrid assay evidence
subclass of: bait-prey hybrid interaction evidence used in manual assertion
has GO evidence code: IPI
definition: A type of mammalian 2-hybrid assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:57:25Z
has_obo_namespace: eco
id: ECO:0001229

Axiom
annotated source: mammalian 2-hybrid assay evidence used in manual assertion
annotated property: subClassOf
annotated target: bait-prey hybrid interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: mammalian 2-hybrid assay evidence used in manual assertion
annotated property: definition
annotated target: A type of mammalian 2-hybrid assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

mass spectrometry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: mass spectrometry evidence
has GO evidence code: EXP
definition: A type of mass spectrometry evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T18:59:50Z
has_obo_namespace: eco
id: ECO:0001230

Axiom
annotated source: mass spectrometry evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: mass spectrometry evidence used in manual assertion
annotated property: definition
annotated target: A type of mass spectrometry evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

medical imaging evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: medical imaging evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: medical imaging evidence
subclass of: imaging assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of medical imaging evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:04:43Z
has_obo_namespace: eco
id: ECO:0001231

Axiom
annotated source: medical imaging evidence used in manual assertion
annotated property: subClassOf
annotated target: imaging assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: medical imaging evidence used in manual assertion
annotated property: definition
annotated target: A type of medical imaging evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: microscopy evidence
subclass of: imaging assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of microscopy evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:05:37Z
has_obo_namespace: eco
id: ECO:0001232

Axiom
annotated source: microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: imaging assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: microscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of microscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

motility wound healing assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: motility wound healing assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: motility wound healing assay evidence
has GO evidence code: IDA
definition: A type of motility wound healing assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:08:13Z
has_alternative_id: ECO:0001262
has_broad_synonym: wound healing assay evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0001233

Axiom
annotated source: motility wound healing assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: motility wound healing assay evidence used in manual assertion
annotated property: definition
annotated target: A type of motility wound healing assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

MTS assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: MTS assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: MTS assay evidence
has GO evidence code: IDA
definition: A type of MTS assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:08:51Z
has_obo_namespace: eco
has_related_synonym: 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium
id: ECO:0001234

Axiom
annotated source: MTS assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: MTS assay evidence used in manual assertion
annotated property: definition
annotated target: A type of MTS assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

MTT assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: MTT assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: MTT assay evidence
has GO evidence code: IDA
definition: A type of MTT assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:13:17Z
has_obo_namespace: eco
has_related_synonym: 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
id: ECO:0001235

Axiom
annotated source: MTT assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: MTT assay evidence used in manual assertion
annotated property: definition
annotated target: A type of MTT assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

multiplex bead-based immunoassay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: multiplex bead-based immunoassay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: multiplex bead-based immunoassay evidence
has GO evidence code: EXP
definition: A type of multiplex bead-based immunoassay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:14:03Z
has_obo_namespace: eco
id: ECO:0001236

Axiom
annotated source: multiplex bead-based immunoassay evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: multiplex bead-based immunoassay evidence used in manual assertion
annotated property: definition
annotated target: A type of multiplex bead-based immunoassay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

natural variation mutant evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: natural variation mutant evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: natural variation mutant evidence
subclass of: ECO_0007634
has GO evidence code: EXP
definition: A type of natural variation mutant evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:15:48Z
has_obo_namespace: eco
id: ECO:0001237

Axiom
annotated source: natural variation mutant evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: natural variation mutant evidence used in manual assertion
annotated property: definition
annotated target: A type of natural variation mutant evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

nuclear magnetic resonance evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: nuclear magnetic resonance evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: nuclear magnetic resonance evidence
subclass of: magnetic resonance evidence used in manual assertion
has GO evidence code: EXP
definition: A type of nuclear magnetic resonance evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:18:50Z
has_obo_namespace: eco
id: ECO:0001238

Axiom
annotated source: nuclear magnetic resonance evidence used in manual assertion
annotated property: subClassOf
annotated target: magnetic resonance evidence used in manual assertion
is_inferred: true

Axiom
annotated source: nuclear magnetic resonance evidence used in manual assertion
annotated property: definition
annotated target: A type of nuclear magnetic resonance evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

nuclear fragmentation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: nuclear fragmentation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: nuclear fragmentation evidence
has GO evidence code: IDA
definition: A type of nuclear fragmentation evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:19:55Z
has_obo_namespace: eco
id: ECO:0001239

Axiom
annotated source: nuclear fragmentation evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: nuclear fragmentation evidence used in manual assertion
annotated property: definition
annotated target: A type of nuclear fragmentation evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

nuclease protection assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: nuclease protection assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: nuclease protection assay evidence
has GO evidence code: EXP
definition: A type of nuclease protection assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:23:41Z
has_obo_namespace: eco
id: ECO:0001240

Axiom
annotated source: nuclease protection assay evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: nuclease protection assay evidence used in manual assertion
annotated property: definition
annotated target: A type of nuclease protection assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

nucleotide analog incorporation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: nucleotide analog incorporation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: nucleotide analog incorporation assay evidence
has GO evidence code: IDA
definition: A type of nucleotide analog incorporation assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:25:17Z
has_obo_namespace: eco
id: ECO:0001241

Axiom
annotated source: nucleotide analog incorporation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: nucleotide analog incorporation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of nucleotide analog incorporation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

phage display evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: phage display evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: phage display evidence
subclass of: protein binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of phage display evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:27:17Z
has_obo_namespace: eco
id: ECO:0001242

Axiom
annotated source: phage display evidence used in manual assertion
annotated property: subClassOf
annotated target: protein binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: phage display evidence used in manual assertion
annotated property: definition
annotated target: A type of phage display evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

phosphoamino acid analysis evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: phosphoamino acid analysis evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: phosphoamino acid analysis evidence
has GO evidence code: IDA
definition: A type of phosphoamino acid analysis evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:28:59Z
has_obo_namespace: eco
id: ECO:0001243

Axiom
annotated source: phosphoamino acid analysis evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: phosphoamino acid analysis evidence used in manual assertion
annotated property: definition
annotated target: A type of phosphoamino acid analysis evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

peptide affinity enrichment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: peptide affinity enrichment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: peptide affinity enrichment evidence
subclass of: affinity evidence used in manual assertion
has GO evidence code: IPI
definition: A type of peptide affinity enrichment evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T19:30:13Z
has_obo_namespace: eco
has_related_synonym: phosphopeptide affinity enrichment evidence
id: ECO:0001244

Axiom
annotated source: peptide affinity enrichment evidence used in manual assertion
annotated property: subClassOf
annotated target: affinity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: peptide affinity enrichment evidence used in manual assertion
annotated property: definition
annotated target: A type of peptide affinity enrichment evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

peptide array evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: peptide array evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: peptide array evidence
subclass of: protein binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of peptide array evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:16:45Z
has_obo_namespace: eco
has_related_synonym: phosphopeptide array evidence
id: ECO:0001245

Axiom
annotated source: peptide array evidence used in manual assertion
annotated property: subClassOf
annotated target: protein binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: peptide array evidence used in manual assertion
annotated property: definition
annotated target: A type of peptide array evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

physical examination evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: physical examination evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: physical examination evidence
has GO evidence code: IDA
definition: A type of physical examination evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:17:27Z
has_obo_namespace: eco
id: ECO:0001246

Axiom
annotated source: physical examination evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: physical examination evidence used in manual assertion
annotated property: definition
annotated target: A type of physical examination evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

point mutation phenotypic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: point mutation phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mutant phenotype evidence used in manual assertion
subclass of: point mutation phenotypic evidence
has GO evidence code: IMP
definition: A type of point mutation phenotypic evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:18:10Z
has_exact_synonym: point mutation evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0001247

Axiom
annotated source: point mutation phenotypic evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

Axiom
annotated source: point mutation phenotypic evidence used in manual assertion
annotated property: definition
annotated target: A type of point mutation phenotypic evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

propidium iodide staining evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: propidium iodide staining evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: propidium iodide staining evidence
has GO evidence code: IDA
definition: A type of propidium iodide staining evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:18:58Z
has_obo_namespace: eco
id: ECO:0001248

Axiom
annotated source: propidium iodide staining evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: propidium iodide staining evidence used in manual assertion
annotated property: definition
annotated target: A type of propidium iodide staining evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

fluorescence evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: fluorescence evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: fluorescence evidence
has GO evidence code: IDA
definition: A type of protein detection by fluorescence evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:19:35Z
has_obo_namespace: eco
id: ECO:0001249

Axiom
annotated source: fluorescence evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: fluorescence evidence used in manual assertion
annotated property: definition
annotated target: A type of protein detection by fluorescence evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

protein dot blot assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein dot blot assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: protein dot blot assay evidence
has GO evidence code: EXP
definition: A type of protein dot blot assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:20:30Z
has_obo_namespace: eco
id: ECO:0001250

Axiom
annotated source: protein dot blot assay evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: protein dot blot assay evidence used in manual assertion
annotated property: definition
annotated target: A type of protein dot blot assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

protein microarray evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein microarray evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: protein microarray evidence
has GO evidence code: EXP
definition: A type of protein microarray evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:21:11Z
has_obo_namespace: eco
id: ECO:0001251

Axiom
annotated source: protein microarray evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: protein microarray evidence used in manual assertion
annotated property: definition
annotated target: A type of protein microarray evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

protein sequencing assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein sequencing assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: protein sequencing assay evidence
has GO evidence code: EXP
definition: A type of protein sequencing assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:22:08Z
has_obo_namespace: eco
id: ECO:0001252

Axiom
annotated source: protein sequencing assay evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: protein sequencing assay evidence used in manual assertion
annotated property: definition
annotated target: A type of protein sequencing assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

quantitative mass spectrometry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: quantitative mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: quantitative mass spectrometry evidence
subclass of: mass spectrometry evidence used in manual assertion
has GO evidence code: EXP
definition: A type of quantitative mass spectrometry evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:23:15Z
has_obo_namespace: eco
id: ECO:0001253

Axiom
annotated source: quantitative mass spectrometry evidence used in manual assertion
annotated property: subClassOf
annotated target: mass spectrometry evidence used in manual assertion
is_inferred: true

Axiom
annotated source: quantitative mass spectrometry evidence used in manual assertion
annotated property: definition
annotated target: A type of quantitative mass spectrometry evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

radioisotope assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: radioisotope assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: radioisotope assay evidence
has GO evidence code: IDA
definition: A type of radioisotope assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:27:05Z
has_broad_synonym: radioassay evidence
has_broad_synonym: radioisotopic assay evidence
has_obo_namespace: eco
id: ECO:0001254

Axiom
annotated source: radioisotope assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: radioisotope assay evidence used in manual assertion
annotated property: definition
annotated target: A type of radioisotope assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

radioimmunoassay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: radioimmunoassay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: radioimmunoassay evidence
has GO evidence code: EXP
definition: A type of radioimmunoassay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:28:04Z
has_obo_namespace: eco
id: ECO:0001255

Axiom
annotated source: radioimmunoassay evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: radioimmunoassay evidence used in manual assertion
annotated property: definition
annotated target: A type of radioimmunoassay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

imaging assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: imaging assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: imaging assay evidence
has GO evidence code: IDA
definition: A type of imaging assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:00Z
has_obo_namespace: eco
has_related_synonym: radiologic test evidence
id: ECO:0001256

Axiom
annotated source: imaging assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: imaging assay evidence used in manual assertion
annotated property: definition
annotated target: A type of imaging assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

restriction fragment detection evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: restriction fragment detection evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: restriction fragment detection evidence
has GO evidence code: EXP
definition: A type of restriction fragment detection evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:05Z
has_obo_namespace: eco
id: ECO:0001257

Axiom
annotated source: restriction fragment detection evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: restriction fragment detection evidence used in manual assertion
annotated property: definition
annotated target: A type of restriction fragment detection evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

spectrophotometry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: spectrophotometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: spectrophotometry evidence
has GO evidence code: EXP
definition: A type of spectrophotometry evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:09Z
has_obo_namespace: eco
id: ECO:0001258

Axiom
annotated source: spectrophotometry evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: spectrophotometry evidence used in manual assertion
annotated property: definition
annotated target: A type of spectrophotometry evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

syngeneic transplantation experiment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: syngeneic transplantation experiment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: syngeneic transplantation experiment evidence
subclass of: ECO_0007634
has GO evidence code: EXP
definition: A type of syngeneic transplantation experiment evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:13Z
has_obo_namespace: eco
id: ECO:0001259

Axiom
annotated source: syngeneic transplantation experiment evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: syngeneic transplantation experiment evidence used in manual assertion
annotated property: definition
annotated target: A type of syngeneic transplantation experiment evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

xenotransplantation phenotypic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: xenotransplantation phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: xenotransplantation phenotypic evidence
subclass of: ECO_0007634
has GO evidence code: EXP
definition: A type of xenotransplantation phenotypic evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:18Z
has_broad_synonym: xenograft transplantation evidence
has_broad_synonym: xenografting evidence
has_broad_synonym: xenotransplantation evidence
has_exact_synonym: xenotransplantation experiment evidence used in manual assertion
has_obo_namespace: eco
has_related_synonym: tissue grafting
id: ECO:0001260

Axiom
annotated source: xenotransplantation phenotypic evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: xenotransplantation phenotypic evidence used in manual assertion
annotated property: definition
annotated target: A type of xenotransplantation phenotypic evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

WST-1 assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: WST-1 assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: WST-1 assay evidence
has GO evidence code: IDA
definition: A type of WST-1 assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:22Z
has_broad_synonym: metabolic cell proliferation assay evidence
has_obo_namespace: eco
id: ECO:0001261

Axiom
annotated source: WST-1 assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: WST-1 assay evidence used in manual assertion
annotated property: definition
annotated target: A type of WST-1 assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

urine test evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: urine test evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: urine test evidence
has GO evidence code: IDA
definition: A type of urine test evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:30Z
has_obo_namespace: eco
id: ECO:0001263

Axiom
annotated source: urine test evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: urine test evidence used in manual assertion
annotated property: definition
annotated target: A type of urine test evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence
has GO evidence code: IDA
definition: A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:34Z
has_broad_synonym: TUNEL assay evidence
has_broad_synonym: TdT-mediated dUTP-biotin nick end labeling assay evidence
has_broad_synonym: terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence
has_obo_namespace: eco
id: ECO:0001264

Axiom
annotated source: terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion
annotated property: definition
annotated target: A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

tryptic phosphopeptide mapping assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: tryptic phosphopeptide mapping assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: tryptic phosphopeptide mapping assay evidence
subclass of: mass spectrometry evidence used in manual assertion
has GO evidence code: EXP
definition: A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:38Z
has_obo_namespace: eco
id: ECO:0001265

Axiom
annotated source: tryptic phosphopeptide mapping assay evidence used in manual assertion
annotated property: subClassOf
annotated target: mass spectrometry evidence used in manual assertion
is_inferred: true

Axiom
annotated source: tryptic phosphopeptide mapping assay evidence used in manual assertion
annotated property: definition
annotated target: A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

transgenic organism evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: transgenic organism evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: transgenic organism evidence
subclass of: genetic transformation evidence used in manual assertion
has GO evidence code: IMP
definition: A type of transgenic organism evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:41Z
has_obo_namespace: eco
id: ECO:0001266

Axiom
annotated source: transgenic organism evidence used in manual assertion
annotated property: subClassOf
annotated target: genetic transformation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: transgenic organism evidence used in manual assertion
annotated property: definition
annotated target: A type of transgenic organism evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

tissue microarray evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: tissue microarray evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: tissue microarray evidence
subclass of: cytochemistry evidence used in manual assertion
has GO evidence code: IDA
definition: A type of tissue microarray evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:45Z
has_obo_namespace: eco
id: ECO:0001267

Axiom
annotated source: tissue microarray evidence used in manual assertion
annotated property: subClassOf
annotated target: cytochemistry evidence used in manual assertion
is_inferred: true

Axiom
annotated source: tissue microarray evidence used in manual assertion
annotated property: definition
annotated target: A type of tissue microarray evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

TACE activity assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: TACE activity assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: TACE activity assay evidence
subclass of: enzymatic activity assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of TACE activity assay evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:49Z
has_broad_synonym: Tumor necrosis factor - alpha converting enzyme activity assay evidence
has_obo_namespace: eco
id: ECO:0001268

Axiom
annotated source: TACE activity assay evidence used in manual assertion
annotated property: subClassOf
annotated target: enzymatic activity assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: TACE activity assay evidence used in manual assertion
annotated property: definition
annotated target: A type of TACE activity assay evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

surface plasmon resonance evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: surface plasmon resonance evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: physical interaction evidence used in manual assertion
subclass of: surface plasmon resonance evidence
has GO evidence code: IPI
definition: A type of surface plasmon resonance evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:54Z
has_broad_synonym: SPR evidence
has_obo_namespace: eco
id: ECO:0001269

Axiom
annotated source: surface plasmon resonance evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: surface plasmon resonance evidence used in manual assertion
annotated property: definition
annotated target: A type of surface plasmon resonance evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

restriction landmark genomic scanning evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: restriction landmark genomic scanning evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: restriction landmark genomic scanning evidence
subclass of: experimental evidence used in manual assertion
has GO evidence code: EXP
definition: A type of restriction landmark genome scanning evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:29:58Z
has_broad_synonym: RLGS evidence
has_broad_synonym: restriction landmark genome scanning evidence
has_obo_namespace: eco
id: ECO:0001270

Axiom
annotated source: restriction landmark genomic scanning evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: restriction landmark genomic scanning evidence used in manual assertion
annotated property: definition
annotated target: A type of restriction landmark genome scanning evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

resonant mirror biosensor evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: resonant mirror biosensor evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: resonant mirror biosensor evidence
has GO evidence code: IDA
definition: A type of resonant mirror biosensor evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T20:30:02Z
has_obo_namespace: eco
id: ECO:0001271

Axiom
annotated source: resonant mirror biosensor evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: resonant mirror biosensor evidence used in manual assertion
annotated property: definition
annotated target: A type of resonant mirror biosensor evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

high-performance liquid chromatography evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: high-performance liquid chromatography evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: high-performance liquid chromatography evidence
subclass of: ECO_0007680
has GO evidence code: EXP
definition: A type of high-performance liquid chromatography evidence that is used in a manual assertion.
created_by: mchibucos
creation_date: 2014-03-16T20:49:54Z
has_broad_synonym: HPLC evidence
has_obo_namespace: eco
id: ECO:0001272

Axiom
annotated source: high-performance liquid chromatography evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007680
is_inferred: true

Axiom
annotated source: high-performance liquid chromatography evidence used in manual assertion
annotated property: definition
annotated target: A type of high-performance liquid chromatography evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

ectopic expression evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: ectopic expression evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: ectopic expression evidence
subclass of: ECO_0007634
has GO evidence code: EXP
definition: A type of ectopic expression evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: mchibucos
creation_date: 2014-03-17T22:34:56Z
has_obo_namespace: eco
has_related_synonym: analysis of overexpression/ectopic expression phenotype
id: ECO:0001273

Axiom
annotated source: ectopic expression evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: ectopic expression evidence used in manual assertion
annotated property: definition
annotated target: A type of ectopic expression evidence that is used in a manual assertion.
database_cross_reference: ECO:MCC

small molecule detection assay evidence
type: Class
subclass of: molecule detection assay evidence
definition: A type of molecule detection assay evidence resulting from the detection and quantification of a small molecule (a low molecular weight (typically < 900 daltons) organic compound), such as lipids, sugars, animo acids, drugs, etc.
ontology term requester: CollecTF
created_by: jbmunro
date: 2018-11-09T12:00:00Z
has_narrow_synonym: metabolite detection assay evidence
has_obo_namespace: eco
id: ECO:0001522

localization evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence in which the sub-cellular location of a protein or nucleic acid sequence is determined.
ontology term requester: ECO_ExpGenomicCleanup
created_by: jbmunro
creation_date: 2018-05-17T12:00:00Z
has_obo_namespace: eco
id: ECO:0001533

nucleic acid localization evidence
type: Class
subclass of: localization evidence
definition: 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.
ontology term requester: ECO_ExpGenomicCleanup
created_by: jbmunro
creation_date: 2018-05-17T12:00:00Z
has_obo_namespace: eco
id: ECO:0001534

acetylation assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where acetylated residues are detected in a protein.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001546

Axiom
annotated source: acetylation assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where acetylated residues are detected in a protein.
database_cross_reference: SIB:PG
database_cross_reference: url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml

cleavage assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where the cleavage of a protein into protein fragments by a protease is detected.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001547

Axiom
annotated source: cleavage assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where the cleavage of a protein into protein fragments by a protease is detected.
database_cross_reference: PMID:21121091
database_cross_reference: PMID:22154596

deacetylation assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where the removal of acetyl groups are detected in a protein.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001548

Axiom
annotated source: deacetylation assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where the removal of acetyl groups are detected in a protein.
database_cross_reference: SIB:PG
database_cross_reference: url:http://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml

defarnesylation assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where the removal of farnesyl groups from a protein is detected.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001549

Axiom
annotated source: defarnesylation assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where the removal of farnesyl groups from a protein is detected.
database_cross_reference: PMID:15556768
database_cross_reference: PMID:16126733
database_cross_reference: PMID:16507103
database_cross_reference: SIB:PG

demethylation assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where the removal of methyl groups from a substrate (RNA/DNA or protein) is detected.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001550

Axiom
annotated source: demethylation assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where the removal of methyl groups from a substrate (RNA/DNA or protein) is detected.
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Demethylation

desumoylation assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where the removal of sumo groups from a protein is detected.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001551

Axiom
annotated source: desumoylation assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where the removal of sumo groups from a protein is detected.
database_cross_reference: SIB:PG
database_cross_reference: url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/

deubiquitination assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where the removal of ubiquitin groups from a protein is detected.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001552

Axiom
annotated source: deubiquitination assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where the removal of ubiquitin groups from a protein is detected.
database_cross_reference: PMID:19692941
database_cross_reference: SIB:PG

farnesylation assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where farnesylated residues in proteins are detected.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001553

Axiom
annotated source: farnesylation assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where farnesylated residues in proteins are detected.
database_cross_reference: PMID:9030603
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Farnesyltransferase

methylation assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where methylated residues of a substarte (RNA/DNA or protein) are detected.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001554

Axiom
annotated source: methylation assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where methylated residues of a substarte (RNA/DNA or protein) are detected.
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Methylation

palmitoylation assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where palmitoylated residues in a protein are detected.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001555

Axiom
annotated source: palmitoylation assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where palmitoylated residues in a protein are detected.
database_cross_reference: PMID:10329400
database_cross_reference: PMID:17077383
database_cross_reference: SIB:PG

phosphatase assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where the removal of phosphatase groups from a protein is detected.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001556

Axiom
annotated source: phosphatase assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where the removal of phosphatase groups from a protein is detected.
database_cross_reference: SIB:PG
database_cross_reference: url:http://en.wikipedia.org/wiki/Phosphatase

polyADP-ribosylation assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where ADP-ribosylated residues in proteins are detected.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001557

Axiom
annotated source: polyADP-ribosylation assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where ADP-ribosylated residues in proteins are detected.
database_cross_reference: PMID:21870253
database_cross_reference: PMID:2820766
database_cross_reference: SIB:PG

protein kinase assay evidence
type: Class
subclass of: enzymatic activity assay evidence
definition: A type of enzymatic activity assay evidence that measures transfer of a phosphate to a peptide or protein substrate by a protein kinase.
ontology term requester: ECO_AssayCleanup
created_by: jbmunro
created_by: mchibucos
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001558

Axiom
annotated source: protein kinase assay evidence
annotated property: definition
annotated target: A type of enzymatic activity assay evidence that measures transfer of a phosphate to a peptide or protein substrate by a protein kinase.
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/books/NBK91991/

sumoylation assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where sumoylated residues on a protein are detected.
ontology term requester: ECO_AssayCleanup
created_by: jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001559

Axiom
annotated source: sumoylation assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where sumoylated residues on a protein are detected.
database_cross_reference: SIB:PG
database_cross_reference: url:http://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/

single-cell RNA-sequencing evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: single-cell RNA-sequencing evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: single-cell RNA-sequencing evidence
subclass of: RNA-sequencing evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of single cell RNA-sequencing evidence that is used in automatic assertion.
created_by: jbmunro
creation_date: 2019-01-02T12:00:00Z
has_obo_namespace: eco
id: ECO:000156

Axiom
annotated source: single-cell RNA-sequencing evidence used in automatic assertion
annotated property: subClassOf
annotated target: RNA-sequencing evidence used in automatic assertion
is_inferred: true

single-cell RNA-sequencing evidence
type: Class
subclass of: RNA-sequencing evidence
definition: A type of RNA-sequencing evidence that uses a single cell as the source of the RNA.
ontology term requester: Bgee
created_by: jbmunro
creation_date: 2019-01-02T12:00:00Z
has_exact_synonym: scRNA-seq evidence
has_obo_namespace: eco
id: ECO:0001560

translation assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where de novo protein synthesis is detected.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001561

Axiom
annotated source: translation assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where de novo protein synthesis is detected.
database_cross_reference: PMID:18230759
database_cross_reference: PMID:24901308
database_cross_reference: SIB:PG

ubiquitination assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where ubiquitinated residues on a protein are detected.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001562

Axiom
annotated source: ubiquitination assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where ubiquitinated residues on a protein are detected.
database_cross_reference: PMID:19692941
database_cross_reference: SIB:PG

cell growth assay evidence
type: Class
subclass of: cell-based assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0016049
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    union of: OBI_0000964
    union of: OBI_0000978
example of usage: However, as shown in Fig. 5A, the recombinant mycobacterial cells became sensitive to the anti-TB drugs isoniazid and streptomycin, as evidenced by their inhibited growth in the presence of 25 mug/mL of isoniazid or 0.5 mug/mL of streptomycin in the medium.
example of usage: Similar growth profiles of these strains were observed in liquid media with the corresponding inducers (data not shown). These indicate that the expression of vapC10 alone led to growth arrest of E. coli, and the simultaneous expression of vapB10 could neutralize this growth-inhibition effect, suggesting that vapC10 encodes a TA toxin and vapB10 encodes the cognate antitoxin.
definition: A type of direct assay evidence where biological cell development, i.e. an increase in cell mass and size are measured.
ontology term requester: ECO_AssayCleanup
created_by: mchibucos / jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001563

Axiom
annotated source: cell growth assay evidence
annotated property: example of usage
annotated target: However, as shown in Fig. 5A, the recombinant mycobacterial cells became sensitive to the anti-TB drugs isoniazid and streptomycin, as evidenced by their inhibited growth in the presence of 25 mug/mL of isoniazid or 0.5 mug/mL of streptomycin in the medium.
database_cross_reference: PMID:20843371

Axiom
annotated source: cell growth assay evidence
annotated property: example of usage
annotated target: Similar growth profiles of these strains were observed in liquid media with the corresponding inducers (data not shown). These indicate that the expression of vapC10 alone led to growth arrest of E. coli, and the simultaneous expression of vapB10 could neutralize this growth-inhibition effect, suggesting that vapC10 encodes a TA toxin and vapB10 encodes the cognate antitoxin.
database_cross_reference: PMID:24260461

Axiom
annotated source: cell growth assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where biological cell development, i.e. an increase in cell mass and size are measured.
database_cross_reference: GO:0016049
database_cross_reference: PMID:11057898

cell-based assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence resulting from the study of cells.
created_by: jbmunro
creation_date: 2017-11-30T14:00:00Z
has_obo_namespace: eco
id: ECO:0001565

quantitative reverse transcription polymerase chain reaction evidence
type: Class
subclass of: reverse transcription polymerase chain reaction evidence
example of usage: The real-time RT-PCR validated that Zur repressed the first gene of each of the three operons, znuA, znuCB and ykgM-rpmJ2 (Additional file 5).
definition: 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.
created_by: jbmunro
creation_date: 2018-07-07T12:00:00Z
has_exact_synonym: RRT-PCR evidence
has_exact_synonym: RT-qPCR evidence
has_exact_synonym: qRT-PCR evidence
has_exact_synonym: quantitative RT-PCR evidence
has_exact_synonym: quantitative real-time RT-PCR evidence
has_exact_synonym: rRT-PCR evidence
has_exact_synonym: real-time RT-PCR evidence
has_exact_synonym: real-time qRT-PCR evidence
has_exact_synonym: real-time quantitative reverse transcription PCR evidence
has_exact_synonym: real-time reverse transcription polymerase chain reaction evidence
has_obo_namespace: eco
id: ECO:0001566

Axiom
annotated source: quantitative reverse transcription polymerase chain reaction evidence
annotated property: example of usage
annotated target: The real-time RT-PCR validated that Zur repressed the first gene of each of the three operons, znuA, znuCB and ykgM-rpmJ2 (Additional file 5).
database_cross_reference: PMID:19552825

quantitative reverse transcription polymerase chain reaction evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: quantitative reverse transcription polymerase chain reaction evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: quantitative reverse transcription polymerase chain reaction evidence
subclass of: reverse transcription polymerase chain reaction evidence used in manual assertion
has GO evidence code: EXP
definition: A type of quantitative reverse transcription polymerase chain reaction evidence used in manual assertion.
created_by: jbmunro
creation_date: 2018-07-07T12:00:00Z
has_obo_namespace: eco
id: ECO:0001567

Axiom
annotated source: quantitative reverse transcription polymerase chain reaction evidence used in manual assertion
annotated property: subClassOf
annotated target: reverse transcription polymerase chain reaction evidence used in manual assertion
is_inferred: true

quantitative reverse transcription polymerase chain reaction evidence used in automatic assertion.
type: Class
equivalent class: Class
  intersection of: quantitative reverse transcription polymerase chain reaction evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: quantitative reverse transcription polymerase chain reaction evidence
subclass of: ECO_0007475
has GO evidence code: IEA
definition: A type of quantitative reverse transcription polymerase chain reaction evidence used in automatic assertion.
created_by: jbmunro
creation_date: 2018-07-07T12:00:00Z
has_alternative_id: ECO:000156
has_obo_namespace: eco
id: ECO:0001568

Axiom
annotated source: quantitative reverse transcription polymerase chain reaction evidence used in automatic assertion.
annotated property: subClassOf
annotated target: ECO_0007475
is_inferred: true

colony diameter phenotype evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: colony diameter phenotype evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: colony diameter phenotype evidence
subclass of: ECO_0007082
has GO evidence code: EXP
definition: A type of colony diameter phenotype evidence that is used in manual assertion.
created_by: jbmunro
creation_date: 2019-01-03T12:00:00Z
has_obo_namespace: eco
id: ECO:000157

Axiom
annotated source: colony diameter phenotype evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007082
is_inferred: true

single-cell RNA-sequencing evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: single-cell RNA-sequencing evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: single-cell RNA-sequencing evidence
subclass of: RNA-sequencing evidence used in manual assertion
has GO evidence code: IEP
definition: A type of single cell RNA-sequencing evidence that is used in manual assertion.
created_by: jbmunro
creation_date: 2019-01-02T12:00:00Z
has_obo_namespace: eco
id: ECO:0001570

Axiom
annotated source: single-cell RNA-sequencing evidence used in manual assertion
annotated property: subClassOf
annotated target: RNA-sequencing evidence used in manual assertion
is_inferred: true

colony diameter phenotype evidence
type: Class
subclass of: ECO_0007081
definition: A type of colony size phenotypic evidence resulting from measurement of a microbial colony's diameter.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-01-03T12:00:00Z
has_obo_namespace: eco
id: ECO:0001571

colony diameter phenotype evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: colony diameter phenotype evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: colony diameter phenotype evidence
subclass of: ECO_0007627
has GO evidence code: IEA
definition: A type of colony diameter phenotype evidence that is used in automatic assertion
created_by: jbmunro
creation_date: 2019-01-03T12:00:00Z
has_obo_namespace: eco
id: ECO:0001572

Axiom
annotated source: colony diameter phenotype evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007627
is_inferred: true

membrane fusion assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence in which a broad variety of physiological processes are measured when two separate membranes merge into a single contiguous membrane.
created_by: jbmunro
creation_date: 2019-03-01T12:00:00Z
has_obo_namespace: eco
id: ECO:0001574
comment: Measurements can include but are not limited to: synaptic transmission, fertilization, and viral entry.

Axiom
annotated source: membrane fusion assay evidence
annotated property: definition
annotated target: A type of direct assay evidence in which a broad variety of physiological processes are measured when two separate membranes merge into a single contiguous membrane.
database_cross_reference: PMID:1836993

membrane fusion assay evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: membrane fusion assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: membrane fusion assay evidence
subclass of: ECO_0007307
has GO evidence code: IEA
definition: A type of membrane fusion assay evidence that is used in automatic assertion.
created_by: jbmunro
creation_date: 2019-03-01T12:00:00Z
has_obo_namespace: eco
id: ECO:0001575

Axiom
annotated source: membrane fusion assay evidence used in automatic assertion
annotated property: subClassOf
annotated target: membrane fusion assay evidence
is_inferred: true

Axiom
annotated source: membrane fusion assay evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007307
is_inferred: true

membrane fusion assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: membrane fusion assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: membrane fusion assay evidence
has GO evidence code: IDA
definition: A type of membrane fusion assay evidence that is used in manual assertion.
created_by: jbmunro
creation_date: 2019-03-01T12:00:00Z
has_obo_namespace: eco
id: ECO:0001576

Axiom
annotated source: membrane fusion assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: membrane fusion assay evidence used in manual assertion
annotated property: subClassOf
annotated target: membrane fusion assay evidence
is_inferred: true

spheroplast fusion assay evidence
type: Class
subclass of: membrane fusion assay evidence
definition: A type of membrane fusion assay evidence based on the fusion of spheroplasts.
created_by: jbmunro
creation_date: 2019-03-01T12:00:00Z
has_obo_namespace: eco
id: ECO:0001577
comment: A spheroplast is a Gram-negative bacterium cell in which the cell wall has been almost completely removed.

Axiom
annotated source: spheroplast fusion assay evidence
annotated property: comment
annotated target: A spheroplast is a Gram-negative bacterium cell in which the cell wall has been almost completely removed.
database_cross_reference: PMID:25870259

spheroplast fusion assay evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: spheroplast fusion assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: membrane fusion assay evidence used in automatic assertion
subclass of: spheroplast fusion assay evidence
has GO evidence code: IEA
definition: A type of spheroplast fusion assay evidence used in automatic assertion.
created_by: jbmunro
creation_date: 2019-03-01T12:00:00Z
has_obo_namespace: eco
id: ECO:0001578

Axiom
annotated source: spheroplast fusion assay evidence used in automatic assertion
annotated property: subClassOf
annotated target: membrane fusion assay evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: spheroplast fusion assay evidence used in automatic assertion
annotated property: subClassOf
annotated target: spheroplast fusion assay evidence
is_inferred: true

spheroplast fusion assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: spheroplast fusion assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: membrane fusion assay evidence used in manual assertion
subclass of: spheroplast fusion assay evidence
has GO evidence code: IDA
definition: A type of spheroplast fusion assay evidence that is used in manual assertion.
created_by: jbmunro
creation_date: 2019-03-01T12:00:00Z
has_obo_namespace: eco
id: ECO:0001579

Axiom
annotated source: spheroplast fusion assay evidence used in manual assertion
annotated property: subClassOf
annotated target: membrane fusion assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: spheroplast fusion assay evidence used in manual assertion
annotated property: subClassOf
annotated target: spheroplast fusion assay evidence
is_inferred: true

liquid chromatography coupled with tandem mass spectrometry evidence
type: Class
subclass of: mass spectrometry evidence
definition: A type of mass spectrometry evidence where liquid chromatography is used to separate particles in solution, followed by fragmentation and measurement of the mass-to-charge ratio of the resulting particles to identify the amount and type of material entities present in a sample.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-03-26T12:00:00Z
has_obo_namespace: eco
id: ECO:0001580

liquid chromatography coupled with tandem mass spectrometry evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: liquid chromatography coupled with tandem mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: liquid chromatography coupled with tandem mass spectrometry evidence
subclass of: ECO_0007433
has GO evidence code: IEA
definition: A type of liquid chromatography coupled with tandem mass spectrometry evidence that is used in an automatic assertion.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-03-26T12:00:00Z
has_obo_namespace: eco
id: ECO:0001581

Axiom
annotated source: liquid chromatography coupled with tandem mass spectrometry evidence used in automatic assertion
annotated property: subClassOf
annotated target: liquid chromatography coupled with tandem mass spectrometry evidence
is_inferred: true

Axiom
annotated source: liquid chromatography coupled with tandem mass spectrometry evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007433
is_inferred: true

liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: liquid chromatography coupled with tandem mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mass spectrometry evidence used in manual assertion
subclass of: liquid chromatography coupled with tandem mass spectrometry evidence
has GO evidence code: EXP
definition: A type of liquid chromatography coupled with tandem mass spectrometry evidence that is used in a manual assertion.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-03-26T12:00:00Z
id: ECO:0001582

Axiom
annotated source: liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion
annotated property: subClassOf
annotated target: mass spectrometry evidence used in manual assertion
is_inferred: true

Axiom
annotated source: liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion
annotated property: subClassOf
annotated target: liquid chromatography coupled with tandem mass spectrometry evidence
is_inferred: true

small interfering RNA knockdown evidence
type: Class
subclass of: anti-sense experiment evidence
definition: A type of anti-sense experiment evidence where gene expression is disrupted through the introduction of double-stranded RNA molecules, 20-25 base pairs in length, which operate within the RNA interference pathway.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-04-03T12:00:00Z
has_exact_synonym: short interfering RNA
has_exact_synonym: siRNA
has_exact_synonym: silencing RNA
has_obo_namespace: eco
id: ECO:0001583

small interfering RNA knockdown evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: small interfering RNA knockdown evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: small interfering RNA knockdown evidence
subclass of: ECO_0007556
has GO evidence code: IEA
definition: A type of small interfering RNA knockdown evidence that is used in an automatic assertion.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-04-03T12:00:00Z
has_obo_namespace: eco
id: ECO:0001584

Axiom
annotated source: small interfering RNA knockdown evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007556
is_inferred: true

small interfering RNA knockdown evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: small interfering RNA knockdown evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: small interfering RNA knockdown evidence
subclass of: anti-sense experiment evidence used in manual assertion
has GO evidence code: IMP
definition: A type of small interfering RNA knockdown evidence that is used in a manual assertion.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-04-03T12:00:00Z
has_obo_namespace: eco
id: ECO:0001585

Axiom
annotated source: small interfering RNA knockdown evidence used in manual assertion
annotated property: subClassOf
annotated target: anti-sense experiment evidence used in manual assertion
is_inferred: true

ion trap mass spectrometry evidence
type: Class
subclass of: mass spectrometry evidence
definition: A type of mass spectrometry evidence where a combination of magnetic and/or electric fields are utilized to capture charged particles in tandem with mass spectrometry.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-04-15T12:00:00Z
has_obo_namespace: eco
id: ECO:0001586

Axiom
annotated source: ion trap mass spectrometry evidence
annotated property: definition
annotated target: A type of mass spectrometry evidence where a combination of magnetic and/or electric fields are utilized to capture charged particles in tandem with mass spectrometry.
database_cross_reference: PMID:1561330

ion trap mass spectrometry evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: ion trap mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: ion trap mass spectrometry evidence
subclass of: ECO_0007433
has GO evidence code: IEA
definition: A type of ion trap mass spectrometry evidence that is used in an automatic assertion.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-04-15T12:00:00Z
has_obo_namespace: eco
id: ECO:0001587

Axiom
annotated source: ion trap mass spectrometry evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007433
is_inferred: true

ion trap mass spectrometry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: ion trap mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mass spectrometry evidence used in manual assertion
subclass of: ion trap mass spectrometry evidence
has GO evidence code: EXP
definition: A type of ion trap mass spectrometry evidence that is used in a manual assertion.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-04-15T12:00:00Z
has_obo_namespace: eco
id: ECO:0001588

Axiom
annotated source: ion trap mass spectrometry evidence used in manual assertion
annotated property: subClassOf
annotated target: mass spectrometry evidence used in manual assertion
is_inferred: true

atomic force microscopy evidence
type: Class
subclass of: microscopy evidence
example of usage: AFM revealed loop structures stabilized by multiple EspR dimer of dimers suggesting the presence of several distant EspR binding sites in the espACD upstream region.
definition: A type of microscopy evidence where a mechanical probe is applied to a sample (i.e. a type of scanning probe microscopy) which can result in production of an image (with resolution in the order of fractions of a nanometer), force measurement, or sample manipulation.
ontology term requester: CollecTF
created_by: jbmunro
creation_date: 2019-04-15T12:00:00Z
has_exact_synonym: AFM
has_exact_synonym: SFM
has_exact_synonym: scanning force microscopy
has_obo_namespace: eco
id: ECO:0001589
comment: Atomic force microscopy can be used for force measurement (force spectroscopy), imaging (rendering a three-dimensional shape (topography), and manipulation of the sample.

Axiom
annotated source: atomic force microscopy evidence
annotated property: example of usage
annotated target: AFM revealed loop structures stabilized by multiple EspR dimer of dimers suggesting the presence of several distant EspR binding sites in the espACD upstream region.
database_cross_reference: PMID:22479184

atomic force microscopy evidence used in automatic assertion
type: Class
subclass of: atomic force microscopy evidence
definition: A type of atomic force microscopy evidence that is used in an automatic assertion.
ontology term requester: CollecTF
created_by: jbmunro
creation_date: 2019-04-15T12:00:00Z
has_obo_namespace: eco
id: ECO:0001590

atomic force microscopy evidence used in manual assertion
type: Class
subclass of: atomic force microscopy evidence
definition: A type of atomic force microscopy evidence that is used in a manual assertion.
ontology term requester: CollecTF
created_by: jbmunro
creation_date: 2019-04-15T12:00:00Z
has_obo_namespace: eco
id: ECO:0001591

polysome profiling evidence
type: Class
subclass of: experimental evidence
definition: A type of experimental evidence employed to study the associations between multiple ribosomes and mRNA that utilizes density gradient centrifugation to separate out the lysate of cells of interest with the objective of isolating polysomes/polyribosomes which are complexes of an mRNA molecule and two or more ribosomes that act to translate mRNA. The optical density of the fractions is then determined.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-04-15T12:00:00Z
has_obo_namespace: eco
id: ECO:0001592
comment: Once isolated, gel electrophoresis, immunoblot, and other protein profiling techniques can be applied to garner more information.

Axiom
annotated source: polysome profiling evidence
annotated property: definition
annotated target: A type of experimental evidence employed to study the associations between multiple ribosomes and mRNA that utilizes density gradient centrifugation to separate out the lysate of cells of interest with the objective of isolating polysomes/polyribosomes which are complexes of an mRNA molecule and two or more ribosomes that act to translate mRNA. The optical density of the fractions is then determined.
database_cross_reference: PMID:30545912

polysome profiling evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: polysome profiling evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: polysome profiling evidence
subclass of: ECO_0007297
has GO evidence code: IEA
definition: A type of polysome profiling evidence that is used in an automatic assertion.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-04-15T12:00:00Z
has_obo_namespace: eco
id: ECO:0001593

Axiom
annotated source: polysome profiling evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007297
is_inferred: true

polysome profiling evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: polysome profiling evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: polysome profiling evidence
has GO evidence code: EXP
definition: A type of polysome profiling evidence that is used in a manual assertion.
ontology term requester: OMP
created_by: jbmunro
creation_date: 2019-04-15T12:00:00Z
has_obo_namespace: eco
id: ECO:0001594

Axiom
annotated source: polysome profiling evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

multilocus sequence typing evidence
type: Class
subclass of: nucleotide sequencing assay evidence
definition: A type of nucleotide sequencing assay evidence in which DNA sequence variations within a specific set of genes (typically housekeeping genes) are used to characterizes strains by their unique allelic profiles.
ontology term requester: CollecTF
created_by: jbmunro
creation_date: 2019-05-06T12:00:00Z
has_exact_synonym: MLST
has_obo_namespace: eco
id: ECO:0001598
comment: See PMID:24713082 for use example.

Axiom
annotated source: multilocus sequence typing evidence
annotated property: definition
annotated target: A type of nucleotide sequencing assay evidence in which DNA sequence variations within a specific set of genes (typically housekeeping genes) are used to characterizes strains by their unique allelic profiles.
database_cross_reference: PMID:9501229

multilocus sequence typing evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: multilocus sequence typing evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: multilocus sequence typing evidence
subclass of: ECO_0007813
has GO evidence code: IEA
definition: A type of multilocus sequence typing evidence that is used in an automatic assertion.
ontology term requester: CollecTF
created_by: jbmunro
creation_date: 2019-05-06T12:00:00Z
has_obo_namespace: eco
id: ECO:0001599

Axiom
annotated source: multilocus sequence typing evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007813
is_inferred: true

multilocus sequence typing evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: multilocus sequence typing evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: multilocus sequence typing evidence
has GO evidence code: EXP
definition: A type of multilocus sequence typing evidence that is used in a manual assertion
ontology term requester: CollecTF
created_by: jbmunro
creation_date: 2019-05-06T12:00:00Z
has_obo_namespace: eco
id: ECO:0001600

Axiom
annotated source: multilocus sequence typing evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

protein-oligonucleotide microarray binding evidence
type: Class
subclass of: protein binding evidence
subclass of: nucleic acid binding evidence
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: GO_0003676
    intersection of: Restriction
      on property: has participant
      some values from: PR_000000001
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001318
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001425
definition: A type of protein-binding evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
created_by: swolfish
creation_date: 2015-06-05T14:36:00Z
has_exact_synonym: PBM evidence
has_obo_namespace: eco
id: ECO:0001601

Axiom
annotated source: protein-oligonucleotide microarray binding evidence
annotated property: definition
annotated target: A type of protein-binding evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
database_cross_reference: PMID:22146299

cell staining evidence
type: Class
subclass of: cell-based assay evidence
definition: 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.
created_by: swolfish
creation_date: 2015-06-08T11:51:37Z
has_obo_namespace: eco
has_related_synonym: vital staining evidence
id: ECO:0001603

Axiom
annotated source: cell staining evidence
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:MAH

Axiom
annotated source: cell staining evidence
annotated property: has_related_synonym
annotated target: vital staining evidence
database_cross_reference: GOC:MAH

alkaline phosphatase reporter gene assay evidence
type: Class
subclass of: reporter gene assay evidence
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-10-29T15:53:45Z
has_obo_namespace: eco
has_related_synonym: SEAP reporter assay
has_related_synonym: Secreted Embryonic Alkaline Phosphatase reporter assay
id: ECO:0001801
comment: Alkaline phosphatase reporter assay produces a hybrid protein with alkaline phosphatase activity following transportation across the cellular membrane.

Axiom
annotated source: alkaline phosphatase reporter gene assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:11823238

beta-galactosidase reporter gene assay evidence
type: Class
subclass of: reporter gene assay evidence
example of usage: For each of the three genes, there was a significant increase of beta-galactosidase activity in Deltazur compared to WT when they grew in TMH with the addition of zinc. Thus, Zur repressed the promoter activities of znuC, znuA and ykgM.
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-10-29T15:57:10Z
has_alternative_id: ECO:0000297
has_exact_synonym: LacZ transcript localization evidence
has_exact_synonym: beta-gal reporter gene assay
has_exact_synonym: beta-galactosidase assay evidence
has_obo_namespace: eco
has_related_synonym: lacZ reporter gene assay
id: ECO:0001802
comment: The assay is often performed using a plasmid borne construction on a lacZ strain.

Axiom
annotated source: beta-galactosidase reporter gene assay evidence
annotated property: example of usage
annotated target: For each of the three genes, there was a significant increase of beta-galactosidase activity in Deltazur compared to WT when they grew in TMH with the addition of zinc. Thus, Zur repressed the promoter activities of znuC, znuA and ykgM.
database_cross_reference: PMID:19552825

Axiom
annotated source: beta-galactosidase reporter gene assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:20439410

chloramphenicol acetyltransferase reporter gene assay evidence
type: Class
subclass of: reporter gene assay evidence
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-10-29T16:06:42Z
has_exact_synonym: CAT reporter gene assay
has_obo_namespace: eco
id: ECO:0001803
comment: The amount of acetylated chloramphenicol is directly proportional to the amount of CAT enzyme present.

Axiom
annotated source: chloramphenicol acetyltransferase reporter gene assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:1630936

Axiom
annotated source: chloramphenicol acetyltransferase reporter gene assay evidence
annotated property: has_exact_synonym
annotated target: CAT reporter gene assay
database_cross_reference: PMID:1630936

beta-glucuronidase reporter gene assay evidence
type: Class
subclass of: reporter gene assay evidence
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-10-29T16:11:02Z
has_exact_synonym: GUS reporter gene assay
has_obo_namespace: eco
id: ECO:0001804

Axiom
annotated source: beta-glucuronidase reporter gene assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW

luciferase reporter gene assay evidence
type: Class
subclass of: reporter gene assay evidence
definition: A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-10-29T16:15:39Z
has_obo_namespace: eco
id: ECO:0001805

Axiom
annotated source: luciferase reporter gene assay evidence
annotated property: definition
annotated target: A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence.
database_cross_reference: ECO:SW
database_cross_reference: PMID:17623934

chromatin immunoprecipitation- exonuclease evidence
type: Class
subclass of: chromatin immunoprecipitation evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001925
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-10-29T16:37:36Z
has_exact_synonym: ChIP-exo
has_obo_namespace: eco
id: ECO:0001806

Axiom
annotated source: chromatin immunoprecipitation- exonuclease evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:25249628

Axiom
annotated source: chromatin immunoprecipitation- exonuclease evidence
annotated property: has_exact_synonym
annotated target: ChIP-exo
database_cross_reference: PMID:25249628

electrophoretic mobility shift assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: electrophoretic mobility shift assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: electrophoretic mobility shift assay evidence
subclass of: physical interaction evidence used in manual assertion
has GO evidence code: IPI
definition: A type of electrophoretic mobility shift that is used in a manual assertion.
created_by: swolfish
creation_date: 2015-11-03T12:13:17Z
has_broad_synonym: EMSA evidence
has_broad_synonym: electrophoretic mobility shift assay
has_obo_namespace: eco
has_related_synonym: gel retardation assay
id: ECO:0001807

Axiom
annotated source: electrophoretic mobility shift assay evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: electrophoretic mobility shift assay evidence used in manual assertion
annotated property: definition
annotated target: A type of electrophoretic mobility shift that is used in a manual assertion.
database_cross_reference: ECO:SW

reverse transcription polymerase chain reaction evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: reverse transcription polymerase chain reaction evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: reverse transcription polymerase chain reaction evidence
subclass of: experimental evidence used in manual assertion
has GO evidence code: EXP
definition: A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion.
created_by: swolfish
creation_date: 2015-11-03T12:22:46Z
has_obo_namespace: eco
id: ECO:0001808

Axiom
annotated source: reverse transcription polymerase chain reaction evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: reverse transcription polymerase chain reaction evidence used in manual assertion
annotated property: definition
annotated target: A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion.
database_cross_reference: ECO:SW

DNA affinity chromatography evidence
type: Class
subclass of: chromatography evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: Class
        intersection of: OBI_0600046
        intersection of: Class
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-03T13:48:49Z
has_obo_namespace: eco
has_related_synonym: DNA affinity purification
id: ECO:0001809
comment: 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.

Axiom
annotated source: DNA affinity chromatography evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:11694305
database_cross_reference: PMID:11725488

DNAse footprinting evidence
type: Class
subclass of: nucleic acid binding evidence
example of usage: Subsequent DNase I footprinting experiments (Fig. 5d) indicated that His-PhoP protected a single region located from 102 to 47 bp upstream of rovA. This footprint was considered the PhoP site.
example of usage: The subsequent DNase I footprinting experiments (Figure 3a) showed that His-OmpR-P protected a single region within the ompR promoter. Therefore, OmpR stimulated its own gene at the transcriptional level, which was mediated through the binding of OmpR-P to its own promoter.
example of usage: To precisely determine the PhoP-binding sites of target genes, DNase I footprinting assay was performed on 17 PhoP-dependent promoter DNA regions (both coding and noncoding strands) (Additional file 6). DNase I footprinting results confirmed the direct binding of His-PhoP to these promoter regions in vitro.
example of usage: We therefore pursued DNase I footprinting assays on several of the Crp-associated sequences that gave an unusual downshift in our initial EMSA trials, in an effort to identify a consensus binding sequence (see Fig. S2 in the supplemental material). We mapped sites upstream of crp itself, SCO4561 and SCO2977, and identified a consensus binding sequence [GTG(N)6GNCAC]; derivatives of this motif could be found in all of the secondary metabolism-associated target sequences, although notably, one-half of the palindrome seemed to be better conserved than the other [GTG(N)6GNGAN] (Fig. 2C; Table 1).
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-03T13:55:15Z
has_obo_namespace: eco
has_related_synonym: DNase protection
id: ECO:0001810
comment: 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.

Axiom
annotated source: DNAse footprinting evidence
annotated property: example of usage
annotated target: Subsequent DNase I footprinting experiments (Fig. 5d) indicated that His-PhoP protected a single region located from 102 to 47 bp upstream of rovA. This footprint was considered the PhoP site.
database_cross_reference: PMID:21966533

Axiom
annotated source: DNAse footprinting evidence
annotated property: example of usage
annotated target: The subsequent DNase I footprinting experiments (Figure 3a) showed that His-OmpR-P protected a single region within the ompR promoter. Therefore, OmpR stimulated its own gene at the transcriptional level, which was mediated through the binding of OmpR-P to its own promoter.
database_cross_reference: PMID:21345178

Axiom
annotated source: DNAse footprinting evidence
annotated property: example of usage
annotated target: To precisely determine the PhoP-binding sites of target genes, DNase I footprinting assay was performed on 17 PhoP-dependent promoter DNA regions (both coding and noncoding strands) (Additional file 6). DNase I footprinting results confirmed the direct binding of His-PhoP to these promoter regions in vitro.
database_cross_reference: PMID:18366809

Axiom
annotated source: DNAse footprinting evidence
annotated property: example of usage
annotated target: We therefore pursued DNase I footprinting assays on several of the Crp-associated sequences that gave an unusual downshift in our initial EMSA trials, in an effort to identify a consensus binding sequence (see Fig. S2 in the supplemental material). We mapped sites upstream of crp itself, SCO4561 and SCO2977, and identified a consensus binding sequence [GTG(N)6GNCAC]; derivatives of this motif could be found in all of the secondary metabolism-associated target sequences, although notably, one-half of the palindrome seemed to be better conserved than the other [GTG(N)6GNGAN] (Fig. 2C; Table 1).
database_cross_reference: PMID:23232715

Axiom
annotated source: DNAse footprinting evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:212715
database_cross_reference: PMID:22194258

fluorescence anisotropy evidence
type: Class
subclass of: fluorescence evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001025
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0002590
example of usage: Since these FA analyses are conducted with 300 nM scOhrR, this suggests that oxidation leads to at least a 100-fold reduction in DNA-binding affinity.
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-03T14:01:36Z
has_exact_synonym: FA
has_obo_namespace: eco
has_related_synonym: FP
has_related_synonym: Fluorescence polarization
id: ECO:0001811
comment: 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.

Axiom
annotated source: fluorescence anisotropy evidence
annotated property: example of usage
annotated target: Since these FA analyses are conducted with 300 nM scOhrR, this suggests that oxidation leads to at least a 100-fold reduction in DNA-binding affinity.
database_cross_reference: PMID:19129220

Axiom
annotated source: fluorescence anisotropy evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:20232898

Axiom
annotated source: fluorescence anisotropy evidence
annotated property: has_related_synonym
annotated target: FP
database_cross_reference: PMCID:3277431
database_cross_reference: PMID:20232898

Axiom
annotated source: fluorescence anisotropy evidence
annotated property: has_related_synonym
annotated target: Fluorescence polarization
database_cross_reference: PMCID:3277431
database_cross_reference: PMID:20232898

genomic systematic evolution of ligands by exponential amplification evidence
type: Class
subclass of: systematic evolution of ligands by exponential amplification evidence
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-03T14:05:37Z
has_exact_synonym: genomic SELEX
has_obo_namespace: eco
id: ECO:0001812
comment: The reported sequences should always be verified for presence in the genome sequence.

Axiom
annotated source: genomic systematic evolution of ligands by exponential amplification evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:20541015
database_cross_reference: PMID:21720957

Axiom
annotated source: genomic systematic evolution of ligands by exponential amplification evidence
annotated property: has_exact_synonym
annotated target: genomic SELEX
database_cross_reference: PMID:20541015

heteronuclear single quantum coherence spectroscopy evidence
type: Class
subclass of: nuclear magnetic resonance spectroscopy evidence
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-03T14:11:06Z
has_exact_synonym: HSQC
has_obo_namespace: eco
id: ECO:0001813
comment: 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.

Axiom
annotated source: heteronuclear single quantum coherence spectroscopy evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:19856946

Axiom
annotated source: heteronuclear single quantum coherence spectroscopy evidence
annotated property: has_exact_synonym
annotated target: HSQC
database_cross_reference: PMID:19856946

methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
type: Class
subclass of: nucleic acid binding evidence
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-03T14:24:04Z
has_obo_namespace: eco
has_related_synonym: MPE Fe(II) footprinting
has_related_synonym: MPE-EDTA Fe(II) footprinting
has_related_synonym: Methidiumpropyl-EDTA Fe(II) footprinting
id: ECO:0001814

Axiom
annotated source: methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:6225070

Axiom
annotated source: methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
annotated property: has_related_synonym
annotated target: MPE Fe(II) footprinting
database_cross_reference: PMID:6225070

Axiom
annotated source: methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
annotated property: has_related_synonym
annotated target: MPE-EDTA Fe(II) footprinting
database_cross_reference: PMID:6225070

Axiom
annotated source: methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
annotated property: has_related_synonym
annotated target: Methidiumpropyl-EDTA Fe(II) footprinting
database_cross_reference: PMID:6225070

copper-phenanthroline footprinting evidence
type: Class
subclass of: nucleic acid binding evidence
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-04T08:37:51Z
has_exact_synonym: 1,10-Phenanthroline-copper footprinting
has_obo_namespace: eco
has_related_synonym: OP-Cu Complex
id: ECO:0001815

Axiom
annotated source: copper-phenanthroline footprinting evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:11691942

Axiom
annotated source: copper-phenanthroline footprinting evidence
annotated property: has_exact_synonym
annotated target: 1,10-Phenanthroline-copper footprinting
database_cross_reference: PMID:1384472

Axiom
annotated source: copper-phenanthroline footprinting evidence
annotated property: has_related_synonym
annotated target: OP-Cu Complex
database_cross_reference: PMID:1384472

green fluorescent protein reporter gene assay evidence
type: Class
subclass of: reporter gene assay evidence
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-04T08:58:42Z
has_alternative_id: ECO:0000296
has_exact_synonym: GFP reporter gene assay
has_exact_synonym: green fluorescent protein transcript localization evidence
has_obo_namespace: eco
has_related_synonym: GFP promoter fusion
has_related_synonym: green fluorescent protein promoter fusion
id: ECO:0001816

Axiom
annotated source: green fluorescent protein reporter gene assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:11989662

Axiom
annotated source: green fluorescent protein reporter gene assay evidence
annotated property: has_exact_synonym
annotated target: GFP reporter gene assay
database_cross_reference: PMID:11989662

glutathione S-transferase pull-down assay evidence
type: Class
subclass of: bait-prey hybrid interaction evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001700
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0001149
definition: A type of bait-prey hybrid interaction 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-04T09:05:56Z
has_exact_synonym: GST pull-down assay
has_obo_namespace: eco
id: ECO:0001817
comment: The recombinant protein can also be eluted following the pull-down and analyzed further with qPCR or sequencing.

Axiom
annotated source: glutathione S-transferase pull-down assay evidence
annotated property: definition
annotated target: A type of bait-prey hybrid interaction 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:26096507

Axiom
annotated source: glutathione S-transferase pull-down assay evidence
annotated property: has_exact_synonym
annotated target: GST pull-down assay
database_cross_reference: PMID:26096507

hydroxyl-radical footprinting evidence
type: Class
subclass of: nucleic acid binding evidence
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-04T09:20:26Z
has_obo_namespace: eco
id: ECO:0001818

Axiom
annotated source: hydroxyl-radical footprinting evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:18546600
database_cross_reference: PMID:19378159
database_cross_reference: PMID:3090544

primer extension assay evidence
type: Class
subclass of: transcript expression evidence
example of usage: The primer extension assay (Fig. 6a) defined the transcription start sites the three sRNA genes qrr2 - 4, and this assay also indicated that the promoter activity of all the thee qrr genes was under the positive control of OpaR.
example of usage: The primer extension assay detected two transcriptional start sites located at 343 and 78 bp upstream of rovA (Fig. 2); therefore, two promoters (named P2 and P1, respectively) were transcribed for rovA.
definition: A type of transcript expression evidence used to determine expression levels of mRNA where a labeled synthetic oligonucleotide primer is annealed to mRNA downstream of the presumed transcription start site of a gene. The mRNA is extended with reverse transcriptase, producing cDNA which is electrophoresed, and the band size is enables determination of the 5' end of the mRNA (i.e. the transcription start site).
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-04T09:33:18Z
has_obo_namespace: eco
id: ECO:0001819
comment: The most commonly used radiolabel is 32P.

Axiom
annotated source: primer extension assay evidence
annotated property: example of usage
annotated target: The primer extension assay (Fig. 6a) defined the transcription start sites the three sRNA genes qrr2 - 4, and this assay also indicated that the promoter activity of all the thee qrr genes was under the positive control of OpaR.
database_cross_reference: PMID:22506036

Axiom
annotated source: primer extension assay evidence
annotated property: example of usage
annotated target: The primer extension assay detected two transcriptional start sites located at 343 and 78 bp upstream of rovA (Fig. 2); therefore, two promoters (named P2 and P1, respectively) were transcribed for rovA.
database_cross_reference: PMID:21966533

Axiom
annotated source: primer extension assay evidence
annotated property: definition
annotated target: A type of transcript expression evidence used to determine expression levels of mRNA where a labeled synthetic oligonucleotide primer is annealed to mRNA downstream of the presumed transcription start site of a gene. The mRNA is extended with reverse transcriptase, producing cDNA which is electrophoresed, and the band size is enables determination of the 5' end of the mRNA (i.e. the transcription start site).
database_cross_reference: ECO:SW
database_cross_reference: PMID:23378648

rapid amplification of cDNA ends polymerase chain reaction evidence
type: Class
subclass of: nucleotide sequencing assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0002090
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001285
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
example of usage: 5' RACE analysis was employed to localize the espR promoter using RNA extracted from Mtb H37Rv grown to mid-log phase. The espR transcript starts with a poly-G (7) sequence 144 bp upstream of the translational start codon.
example of usage: The 5'-end of the espA mRNA was located 66 bp upstream of the translation start codon using 5' RACE (Fig. S3).
example of usage: Using 5' rapid amplification of cDNA ends (RACE), we mapped the transcriptional start sites of rpoQ and VF_A1016 (Fig. 4A). Neither start site was detected in the DeltarpoQ mutant, supporting the idea that transcription of rpoQ and VF_A1016 requires RpoQ (data not shown).
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-04T09:48:38Z
has_exact_synonym: 3’ RACE-PCR
has_exact_synonym: 5’ RACE-PCR
has_exact_synonym: RACE PCR
has_obo_namespace: eco
id: ECO:0001820
comment: 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.
comment: RACE PCR is frequently used to verify transcription start sites relevant to the function of transcription factor binding sites such as repression.

Axiom
annotated source: rapid amplification of cDNA ends polymerase chain reaction evidence
annotated property: example of usage
annotated target: 5' RACE analysis was employed to localize the espR promoter using RNA extracted from Mtb H37Rv grown to mid-log phase. The espR transcript starts with a poly-G (7) sequence 144 bp upstream of the translational start codon.
database_cross_reference: PMID:22479184

Axiom
annotated source: rapid amplification of cDNA ends polymerase chain reaction evidence
annotated property: example of usage
annotated target: The 5'-end of the espA mRNA was located 66 bp upstream of the translation start codon using 5' RACE (Fig. S3).
database_cross_reference: PMID:22479184

Axiom
annotated source: rapid amplification of cDNA ends polymerase chain reaction evidence
annotated property: example of usage
annotated target: Using 5' rapid amplification of cDNA ends (RACE), we mapped the transcriptional start sites of rpoQ and VF_A1016 (Fig. 4A). Neither start site was detected in the DeltarpoQ mutant, supporting the idea that transcription of rpoQ and VF_A1016 requires RpoQ (data not shown).
database_cross_reference: PMID:22233679

Axiom
annotated source: rapid amplification of cDNA ends polymerase chain reaction evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:17498297
database_cross_reference: PMID:7685466

Axiom
annotated source: rapid amplification of cDNA ends polymerase chain reaction evidence
annotated property: has_exact_synonym
annotated target: RACE PCR
database_cross_reference: PMI:17498297

RNA sequencing assay evidence
type: Class
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-04T10:15:57Z
has_obo_namespace: eco
id: ECO:0001821
comment: Use ECO:0000295 (RNA-seq evidence) in place of this term.
deprecated: true

survival rate analysis evidence
type: Class
subclass of: knockout phenotypic evidence
subclass of: Restriction
  on property: is about
  some values from: OBI_0600054
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000699
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-04T10:48:59Z
has_obo_namespace: eco
id: ECO:0001822

Axiom
annotated source: survival rate analysis evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW

x-ray crystallography evidence
type: Class
subclass of: crystallography evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000912
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-04T10:56:22Z
has_obo_namespace: eco
id: ECO:0001823
comment: 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.

Axiom
annotated source: x-ray crystallography evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:23135450
database_cross_reference: PMID:24648090

DNA adenine methyltransferase identification evidence
type: Class
subclass of: affinity evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0008104
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001425
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001146
    intersection of: Restriction
      on property: has part
      some values from: Class
        intersection of: OBI_0000652
        intersection of: Restriction
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-05T15:56:13Z
has_exact_synonym: DamID
has_obo_namespace: eco
id: ECO:0001824
comment: The methylation tag is detected with methylation-sensitive restriction enzymes, DpnI and DpnII.

Axiom
annotated source: DNA adenine methyltransferase identification evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:16938559
database_cross_reference: PMID:17545983
database_cross_reference: PMID:19588092

Axiom
annotated source: DNA adenine methyltransferase identification evidence
annotated property: has_exact_synonym
annotated target: DamID
database_cross_reference: PMID:19588092

isothermal titration calorimetry evidence
type: Class
subclass of: affinity evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001634
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-05T16:06:20Z
has_exact_synonym: ITC
has_obo_namespace: eco
id: ECO:0001825
comment: 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)).

Axiom
annotated source: isothermal titration calorimetry evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:10527727

Axiom
annotated source: isothermal titration calorimetry evidence
annotated property: has_exact_synonym
annotated target: ITC
database_cross_reference: PMID:10527727

ultraviolet light footprinting evidence
type: Class
subclass of: nucleic acid binding evidence
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-05T16:13:36Z
has_obo_namespace: eco
has_related_synonym: UV footprinting
has_related_synonym: ultraviolet footprinting
id: ECO:0001826

Axiom
annotated source: ultraviolet light footprinting evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:2842760
database_cross_reference: PMID:7602584

methylation interference footprinting evidence
type: Class
subclass of: nucleic acid binding evidence
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-05T16:16:27Z
has_exact_synonym: methylation interference footprinting evidence
has_obo_namespace: eco
id: ECO:0001827

Axiom
annotated source: methylation interference footprinting evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:1583685

inference of sequence features from visual inspection used in manual assertion
type: Class
equivalent class: Class
  intersection of: ECO_0007850
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: ECO_0007751
subclass of: ECO_0007850
definition: A type of inference of sequence features from visual inspection that is used in a manual assertion.
created_by: swolfish
creation_date: 2015-11-10T14:40:16Z
has_broad_synonym: visual sequence inspection evidence
has_obo_namespace: eco
id: ECO:0001828

Axiom
annotated source: inference of sequence features from visual inspection used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007751
is_inferred: true

Axiom
annotated source: inference of sequence features from visual inspection used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007850
is_inferred: true

Axiom
annotated source: inference of sequence features from visual inspection used in manual assertion
annotated property: definition
annotated target: A type of inference of sequence features from visual inspection that is used in a manual assertion.
database_cross_reference: ECO:RCJ

ferric uptake regulator titration assay evidence
type: Class
subclass of: reporter gene assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000913
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: 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.
ontology term requester: CollecTF
created_by: swolfish
creation_date: 2015-11-10T14:55:36Z
has_exact_synonym: FURTA
has_obo_namespace: eco
has_related_synonym: Fluorescence polarization
id: ECO:0001829

Axiom
annotated source: ferric uptake regulator titration assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:10713425
database_cross_reference: PMID:7642488
database_cross_reference: PMID:8107138

Axiom
annotated source: ferric uptake regulator titration assay evidence
annotated property: has_exact_synonym
annotated target: FURTA
database_cross_reference: PMID:10713425

Axiom
annotated source: ferric uptake regulator titration assay evidence
annotated property: has_related_synonym
annotated target: Fluorescence polarization
database_cross_reference: PMID:15689115

host colonization assay evidence
type: Class
subclass of: experimental evidence
definition: A type of experimental evidence in which the colonization or adhesion capacity is measured.
ontology term requester: CollecTF
created_by: jbmunro
creation_date: 2019-05-06T12:00:00Z
has_exact_synonym: adhesion assay evidence
has_obo_namespace: eco
id: ECO:0001830
comment: Has to do with the ability of the bacterium or virus to bind to a host.

host colonization assay evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: host colonization assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: host colonization assay evidence
subclass of: ECO_0007297
has GO evidence code: IEA
definition: A type of host colonization assay evidence that is used in an automatic assertion.
ontology term requester: CollecTF
created_by: jbmunro
creation_date: 2019-05-06T12:00:00Z
has_obo_namespace: eco
id: ECO:0001831

Axiom
annotated source: host colonization assay evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007297
is_inferred: true

host colonization assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: host colonization assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: host colonization assay evidence
has GO evidence code: EXP
definition: A type of host colonization assay evidence that is used in a manual assertion.
ontology term requester: CollecTF
created_by: jbmunro
creation_date: 2019-05-06T12:00:00Z
has_obo_namespace: eco
id: ECO:0001832

Axiom
annotated source: host colonization assay evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

infection assay evidence
type: Class
subclass of: host colonization assay evidence
definition: A type of host colonization assay evidence in which the infection capacity is measured by assessing changes in the host.
ontology term requester: CollecTF
created_by: jbmunro
creation_date: 2019-05-06T12:00:00Z
has_obo_namespace: eco
id: ECO:0001833
comment: Has to do with the outcome of a bacterial or viral / host interaction, be it a measure of cell death, cytotoxicity, invasion, etc.

infection assay evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: infection assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: host colonization assay evidence used in automatic assertion
subclass of: infection assay evidence
has GO evidence code: IEA
definition: A type of infection assay evidence that is used in an automatic assertion.
ontology term requester: CollecTF
created_by: jbmunro
creation_date: 2019-05-06T12:00:00Z
has_obo_namespace: eco
id: ECO:0001834

Axiom
annotated source: infection assay evidence used in automatic assertion
annotated property: subClassOf
annotated target: host colonization assay evidence used in automatic assertion
is_inferred: true

infection assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: infection assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: host colonization assay evidence used in manual assertion
subclass of: infection assay evidence
has GO evidence code: EXP
definition: A type of infection assay evidence that is used in a manual assertion.
ontology term requester: CollecTF
created_by: jbmunro
creation_date: 2019-05-06T12:00:00Z
has_obo_namespace: eco
id: ECO:0001835

Axiom
annotated source: infection assay evidence used in manual assertion
annotated property: subClassOf
annotated target: host colonization assay evidence used in manual assertion
is_inferred: true

in situ hybridization evidence
type: Class
subclass of: expression pattern evidence
definition: A type of expression pattern evidence in which single-stranded DNA or RNA (probe) are annealed to complementary DNA or RNA in a portion or section of tissue.
ontology term requester: planarian anatomy ontology (PLANA)
created_by: jbmunro
creation_date: 2019-09-26T12:00:00Z
has_obo_namespace: eco
id: ECO:0001836

in situ hybridization evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: in situ hybridization evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: in situ hybridization evidence
subclass of: ECO_0007298
has GO evidence code: IEA
definition: A type of in situ hybridization evidence that is used in an automatic assertion.
created_by: jbmunro
creation_date: 2019-09-26T12:00:00Z
has_obo_namespace: eco
id: ECO:0001837

Axiom
annotated source: in situ hybridization evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007298
is_inferred: true

in situ hybridization evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in situ hybridization evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence used in manual assertion
subclass of: in situ hybridization evidence
has GO evidence code: IEP
definition: A type of in situ hybridization evidence that is used in a manual assertion.
created_by: jbmunro
creation_date: 2019-09-26T12:00:00Z
has_obo_namespace: eco
id: ECO:0001838

Axiom
annotated source: in situ hybridization evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

colorimetric in situ hybridization evidence
type: Class
subclass of: in situ hybridization evidence
definition: A type of nucleic acid localization evidence and in situ hybridization evidence resulting from the use of colorimetric probes to detect complementary sequences of nucleic acids.
ontology term requester: planarian anatomy ontology (PLANA)
created_by: jbmunro
creation_date: 2019-09-26T12:00:00Z
has_obo_namespace: eco
id: ECO:0001839

Axiom
annotated source: colorimetric in situ hybridization evidence
annotated property: definition
annotated target: A type of nucleic acid localization evidence and in situ hybridization evidence resulting from the use of colorimetric probes to detect complementary sequences of nucleic acids.
database_cross_reference: PMID:23497040

colorimetric in situ hybridization evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: colorimetric in situ hybridization evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: in situ hybridization evidence used in automatic assertion
subclass of: colorimetric in situ hybridization evidence
has GO evidence code: IEA
definition: A type of colorimetric in situ hybridization evidence that is used in an automatic assertion.
created_by: jbmunro
creation_date: 2019-09-26T12:00:00Z
has_obo_namespace: eco
id: ECO:0001840

Axiom
annotated source: colorimetric in situ hybridization evidence used in automatic assertion
annotated property: subClassOf
annotated target: in situ hybridization evidence used in automatic assertion
is_inferred: true

colorimetric in situ hybridization evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: colorimetric in situ hybridization evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: in situ hybridization evidence used in manual assertion
subclass of: colorimetric in situ hybridization evidence
has GO evidence code: IEP
definition: A type of colorimetric in situ hybridization evidence that is used in a manual assertion.
created_by: jbmunro
creation_date: 2019-09-26T12:00:00Z
has_obo_namespace: eco
id: ECO:0001841

Axiom
annotated source: colorimetric in situ hybridization evidence used in manual assertion
annotated property: subClassOf
annotated target: in situ hybridization evidence used in manual assertion
is_inferred: true

random mutagenesis of specific target DNA evidence
type: Class
subclass of: random mutagenesis phenotypic evidence
definition: A type of random mutagenesis phenotypic evidence resulting from the random mutation of a specifically targeted region of DNA.
ontology term requester: ECO
created_by: jbmunro
creation_date: 2019-12-09T12:00:00Z
has_obo_namespace: eco
id: ECO:0001842

random mutagenesis of specific target DNA evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: random mutagenesis of specific target DNA evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: random mutagenesis of specific target DNA evidence
subclass of: ECO_0007478
has GO evidence code: IEA
definition: A type of random mutagenesis of specific target DNA evidence that is used in an automatic assertion.
ontology term requester: ECO
created_by: jbmunro
creation_date: 2019-12-09T12:00:00Z
has_obo_namespace: eco
id: ECO:0001843

Axiom
annotated source: random mutagenesis of specific target DNA evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007478
is_inferred: true

random mutagenesis of specific target DNA evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: random mutagenesis of specific target DNA evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: random mutagenesis of specific target DNA evidence
subclass of: random mutagenesis evidence used in manual assertion
has GO evidence code: IMP
definition: A type of random mutagenesis of specific target DNA evidence that is used in a manual assertion.
ontology term requester: ECO
created_by: jbmunro
creation_date: 2019-12-09T12:00:00Z
has_obo_namespace: eco
id: ECO:0001844

Axiom
annotated source: random mutagenesis of specific target DNA evidence used in manual assertion
annotated property: subClassOf
annotated target: random mutagenesis evidence used in manual assertion
is_inferred: true

cell population optical density evidence
type: Class
subclass of: cell-based assay evidence
definition: A type of cell-based assay evidence in which optical density is used to measure some aspect of a population of cells. Examples of aspects that can affect optical density measurements include, but are not limited to, cell number and cell shape.
ontology term requester: CACAO
created_by: jbmunro
creation_date: 2020-01-28T12:00:00Z
has_obo_namespace: eco
id: ECO:0001845

cell population optical density evidence used in automatic assertion
type: Class
subclass of: cell population optical density evidence
definition: A type of cell population optical density evidence that is used in an automatic assertion.
ontology term requester: CACAO
created_by: jbmunro
creation_date: 2020-01-28T12:00:00Z
has_obo_namespace: eco
id: ECO:0001846

cell population optical density evidence used in manual assertion
type: Class
subclass of: cell population optical density evidence
definition: A type of cell population optical density evidence that is used in a manual assertion.
ontology term requester: CACAO
created_by: jbmunro
creation_date: 2020-01-28T12:00:00Z
has_obo_namespace: eco
id: ECO:0001847

cell viability assay evidence
type: Class
subclass of: cell-based assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0009987
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001977
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000699
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: A type of cell-based assay evidence resulting from analyzing the ability of cells to survive or live successfully.
created_by: snadendla
creation_date: 2015-02-13T12:08:01Z
has_obo_namespace: eco
id: ECO:0005004

Axiom
annotated source: cell viability assay evidence
annotated property: definition
annotated target: A type of cell-based assay evidence resulting from analyzing the ability of cells to survive or live successfully.
database_cross_reference: NBK:144065

cell proliferation assay evidence
type: Class
subclass of: cell-based assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0008283
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000891
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: 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.
created_by: snadendla
creation_date: 2015-02-11T16:27:13Z
has_obo_namespace: eco
id: ECO:0005007

Axiom
annotated source: cell proliferation assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT
comment: GO:0008283
comment: PMID:11057898

DNA synthesis cell proliferation assay evidence
type: Class
subclass of: cell proliferation assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0090592
definition: A type of cell proliferation assay evidence resulting from the measure of DNA synthesis in the presece of a label.
created_by: snadendla
creation_date: 2015-02-11T16:30:10Z
has_obo_namespace: eco
id: ECO:0005008

Axiom
annotated source: DNA synthesis cell proliferation assay evidence
annotated property: definition
annotated target: A type of cell proliferation assay evidence resulting from the measure of DNA synthesis in the presece of a label.
database_cross_reference: PMC:3908118

ATP bioluminescence assay evidence
type: Class
subclass of: cell viability assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002175
definition: 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.
created_by: snadendla
creation_date: 2015-02-11T16:47:30Z
has_obo_namespace: eco
id: ECO:0005011

Axiom
annotated source: ATP bioluminescence assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:15344559

cytotoxicity assay evidence
type: Class
subclass of: cell-based assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0009636
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001977
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: 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.
created_by: snadendla
creation_date: 2015-02-12T11:39:35Z
has_obo_namespace: eco
id: ECO:0005012

in vitro cell based assay evidence
type: Class
created_by: snadendla
creation_date: 2015-02-12T13:26:55Z
has_obo_namespace: eco
id: ECO:0005014
comment: Use children of ECO:0001565 (cell-based assay evidence) in place of this term.
deprecated: true

staining evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000185
    intersection of: Restriction
      on property: has part
      some values from: OBI_0302887
definition: A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image.
created_by: snadendla
creation_date: 2015-02-19T11:48:57Z
has_obo_namespace: eco
id: ECO:0005019

Axiom
annotated source: staining evidence
annotated property: definition
annotated target: A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image.
database_cross_reference: ECO:RCT

chemotaxis assay evidence
type: Class
subclass of: cell-based assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0006935
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000978
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000807
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001396
definition: 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.
created_by: snadendla
creation_date: 2015-02-19T13:10:20Z
has_obo_namespace: eco
id: ECO:0005021

Axiom
annotated source: chemotaxis assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMC:3667641

genetic transformation evidence
type: Class
subclass of: mutant phenotype evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600043
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001460
definition: A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA.
created_by: snadendla
creation_date: 2015-03-16T15:33:50Z
has_obo_namespace: eco
id: ECO:0005027

Axiom
annotated source: genetic transformation evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA.
database_cross_reference: ECO:RCT

structure determination evidence
type: Class
subclass of: experimental evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
example of usage: The secondary structure of VapC10 (Figure S2), predicted with the 3DJIGSAW prediction tool [36] and the DALI server [37], exhibited homology with several well studied VapC toxins, such as the first PIN domain structure for the protein PAE2754 from the archae bacterium Pyrobaculum aerophilum (30).
definition: A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures.
created_by: snadendla
creation_date: 2015-03-20T12:16:17Z
has_obo_namespace: eco
id: ECO:0005031

Axiom
annotated source: structure determination evidence
annotated property: example of usage
annotated target: The secondary structure of VapC10 (Figure S2), predicted with the 3DJIGSAW prediction tool [36] and the DALI server [37], exhibited homology with several well studied VapC toxins, such as the first PIN domain structure for the protein PAE2754 from the archae bacterium Pyrobaculum aerophilum (30).
database_cross_reference: PMID:24260461

Axiom
annotated source: structure determination evidence
annotated property: definition
annotated target: A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures.
database_cross_reference: ECO:RCT

electron microscopy evidence
type: Class
subclass of: microscopy evidence
subclass of: structure determination evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001631
example of usage: Electron micrographs showed that all the cells are rod-shaped and those of the parent strain Ye9 and the envZ mutant strain EZ10 are flagellated, but the ompR mutant cells lack flagella.
definition: A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image.
created_by: snadendla
creation_date: 2015-03-20T12:21:48Z
has_obo_namespace: eco
id: ECO:0005033

Axiom
annotated source: electron microscopy evidence
annotated property: example of usage
annotated target: Electron micrographs showed that all the cells are rod-shaped and those of the parent strain Ye9 and the envZ mutant strain EZ10 are flagellated, but the ompR mutant cells lack flagella.
database_cross_reference: PMID:20830609

Axiom
annotated source: electron microscopy evidence
annotated property: definition
annotated target: A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image.
database_cross_reference: ECO:RCT

apoptotic assay evidence
type: Class
subclass of: cell-based assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0006915
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0001977
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001365
definition: A type of cell-based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis.
created_by: snadendla
creation_date: 2015-04-07T21:58:24Z
has_obo_namespace: eco
id: ECO:0005034

Axiom
annotated source: apoptotic assay evidence
annotated property: definition
annotated target: A type of cell-based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis.
database_cross_reference: ECO:RCT

in vivo polyADP-ribosylation assay evidence
type: Class
subclass of: polyADP-ribosylation assay evidence
definition: A type of polyADP-ribosylation assay evidence used in an in vivo experiment.
created_by: snadendla
creation_date: 2015-06-15T15:35:05Z
has_obo_namespace: eco
id: ECO:0005500

Axiom
annotated source: in vivo polyADP-ribosylation assay evidence
annotated property: definition
annotated target: A type of polyADP-ribosylation assay evidence used in an in vivo experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:2820766
database_cross_reference: SIB:PG

in vivo polyADP-ribosylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: in vivo polyADP-ribosylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: in vivo polyADP-ribosylation assay evidence
has GO evidence code: IDA
definition: A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2015-06-15T15:37:23Z
has_obo_namespace: eco
id: ECO:0005501

Axiom
annotated source: in vivo polyADP-ribosylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: in vivo polyADP-ribosylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

ex vivo assay evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000964
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001211
definition: 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.
created_by: snadendla
creation_date: 2015-06-26T11:46:15Z
has_obo_namespace: eco
id: ECO:0005502

Axiom
annotated source: ex vivo assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:16305312
database_cross_reference: url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf

two-dimensional polyacrylamide gel electrophoresis evidence
type: Class
subclass of: gel electrophoresis evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: OBI_0001121
        intersection of: Restriction
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-10-01T16:23:20Z
has_exact_synonym: 2D PAGE
has_exact_synonym: 2D-PAGE
has_obo_namespace: eco
id: ECO:0005503
comment: Two-dimensional polyacrylamide gel electrophoresis is commonly employed to establish a proteome for an organism and demonstrate expression changes.

Axiom
annotated source: two-dimensional polyacrylamide gel electrophoresis evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: url:http://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html

spectrometry evidence
type: Class
subclass of: experimental evidence
definition: A type of experimental evidence resulting from the use of a spectrometer.
created_by: snadendla
creation_date: 2015-08-14T15:48:08Z
has_obo_namespace: eco
id: ECO:0005504

Axiom
annotated source: spectrometry evidence
annotated property: definition
annotated target: A type of experimental evidence resulting from the use of a spectrometer.
database_cross_reference: ECO:RCT

regular expression motif search evidence
type: Class
subclass of: motif similarity evidence
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-10-09T13:51:52Z
has_obo_namespace: eco
id: ECO:0005505
comment: 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).

Axiom
annotated source: regular expression motif search evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:17337630

missense mutation phenotypic evidence
type: Class
subclass of: point mutation phenotypic evidence
definition: A type of point mutation phenotypic evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another.
created_by: snadendla
creation_date: 2015-09-18T16:52:34Z
has_exact_synonym: missense mutation evidence
has_obo_namespace: eco
id: ECO:0005506

Axiom
annotated source: missense mutation phenotypic evidence
annotated property: definition
annotated target: A type of point mutation phenotypic evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another.
database_cross_reference: SO:0001583

nonsense mutation phenotypic evidence
type: Class
subclass of: point mutation phenotypic evidence
definition: A type of point mutation phenotypic evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon.
created_by: snadendla
creation_date: 2015-09-18T16:55:32Z
has_exact_synonym: nonsense mutation evidence
has_obo_namespace: eco
id: ECO:0005507

Axiom
annotated source: nonsense mutation phenotypic evidence
annotated property: definition
annotated target: A type of point mutation phenotypic evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon.
database_cross_reference: url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations

silent mutation evidence
type: Class
subclass of: point mutation phenotypic evidence
definition: A type of point mutation phenotypic evidence resulting from the change of a DNA nucleotide that does not cause any changes in the amino acid sequence.
created_by: snadendla
creation_date: 2015-09-18T17:01:12Z
has_obo_namespace: eco
id: ECO:0005508

Axiom
annotated source: silent mutation evidence
annotated property: definition
annotated target: A type of point mutation phenotypic evidence resulting from the change of a DNA nucleotide that does not cause any changes in the amino acid sequence.
database_cross_reference: url:http://www.sciencemag.org/news/2006/12/sound-silent-mutation

insertion mutation phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
definition: A type of mutant phenotype evidence resulting from a mutation in which there is an insertion of one or more contiguous nucleotides.
created_by: snadendla
creation_date: 2015-09-18T17:02:03Z
has_exact_synonym: insertion mutation evidence
has_obo_namespace: eco
id: ECO:0005509

Axiom
annotated source: insertion mutation phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from a mutation in which there is an insertion of one or more contiguous nucleotides.
database_cross_reference: GO:0070705

duplication mutation evidence
type: Class
subclass of: experimental phenotypic evidence
definition: 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.
created_by: snadendla
creation_date: 2015-09-18T17:03:25Z
has_obo_namespace: eco
id: ECO:0005511

Axiom
annotated source: duplication mutation evidence
annotated property: definition
annotated target: 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.
database_cross_reference: SO:1000035

frameshift mutation phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
definition: A type of mutant phenotype evidence resulting from any mutation that causes an insertion or deletion of nucleotides in a DNA sequence that is not divisible by three and therefore changes the codon reading frame and the translated amino acids.
created_by: snadendla
creation_date: 2015-09-18T17:05:49Z
has_exact_synonym: frameshift mutation evidence
has_obo_namespace: eco
id: ECO:0005512

Axiom
annotated source: frameshift mutation phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from any mutation that causes an insertion or deletion of nucleotides in a DNA sequence that is not divisible by three and therefore changes the codon reading frame and the translated amino acids.
database_cross_reference: url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations

repeat expansion mutation phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
definition: A type of mutant phenotype evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated.
created_by: snadendla
creation_date: 2015-09-18T17:06:34Z
has_exact_synonym: repeat expansion mutation evidence
has_obo_namespace: eco
id: ECO:0005513

Axiom
annotated source: repeat expansion mutation phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated.
database_cross_reference: PMID:9397685
database_cross_reference: url:https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations

splice site mutation phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
definition: A type of mutant phenotype evidence resulting from a mutation in which there is a change in nucleotides at a splice site.
created_by: snadendla
creation_date: 2015-09-18T17:07:29Z
has_exact_synonym: splice site mutation evidence
has_obo_namespace: eco
id: ECO:0005514

Axiom
annotated source: splice site mutation phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from a mutation in which there is a change in nucleotides at a splice site.
database_cross_reference: ECO:RCT

translocation mutation phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
definition: A type of mutant phenotype evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome.
created_by: snadendla
creation_date: 2015-09-18T17:08:01Z
has_exact_synonym: translocation mutation evidence
has_obo_namespace: eco
id: ECO:0005515

Axiom
annotated source: translocation mutation phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome.
database_cross_reference: ECO:RCT

molecule detection assay evidence
type: Class
subclass of: experimental evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600017
definition: A type of experimental evidence resulting from the detection and analysis of molecular markers.
created_by: snadendla
creation_date: 2015-09-24T15:54:21Z
has_obo_namespace: eco
id: ECO:0005516

Axiom
annotated source: molecule detection assay evidence
annotated property: definition
annotated target: A type of experimental evidence resulting from the detection and analysis of molecular markers.
database_cross_reference: ECO:RCT

protein detection assay evidence
type: Class
subclass of: molecule detection assay evidence
definition: A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins.
created_by: snadendla
creation_date: 2015-09-25T14:27:40Z
has_obo_namespace: eco
id: ECO:0005517

Axiom
annotated source: protein detection assay evidence
annotated property: definition
annotated target: A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins.
database_cross_reference: ECO:RCT

RNA detection assay evidence
type: Class
subclass of: molecule detection assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0010467
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001430
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000424
    intersection of: OBI_0600025
definition: A type of molecule detection assay evidence resulting from the detection of specific RNAs.
created_by: snadendla
creation_date: 2015-09-25T14:43:53Z
has_obo_namespace: eco
id: ECO:0005518

Axiom
annotated source: RNA detection assay evidence
annotated property: definition
annotated target: A type of molecule detection assay evidence resulting from the detection of specific RNAs.
database_cross_reference: ECO:RCT

DNA detection assay evidence
type: Class
subclass of: molecule detection assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0600025
    intersection of: Restriction
      on property: has participant
      some values from: Class
        intersection of: deoxyribonucleic acid
        intersection of: Restriction
definition: A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA.
created_by: snadendla
creation_date: 2015-09-25T19:33:25Z
has_obo_namespace: eco
id: ECO:0005519

Axiom
annotated source: DNA detection assay evidence
annotated property: definition
annotated target: A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA.
database_cross_reference: ECO:RCT

interferometric reflectance imaging sensor evidence
type: Class
subclass of: molecule detection assay evidence
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-09-28T16:01:01Z
has_exact_synonym: IRIS
has_exact_synonym: SRIB
has_exact_synonym: Spectral Reflectance Imaging Biosensor
has_obo_namespace: eco
id: ECO:0005520
comment: 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.

Axiom
annotated source: interferometric reflectance imaging sensor evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:21587155
database_cross_reference: PMID:24271115

S1 nuclease protection assay evidence
type: Class
subclass of: nuclease protection assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001670
    intersection of: Restriction
      on property: has participant
      some values from: PR_000025471
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-09-28T17:16:56Z
has_obo_namespace: eco
id: ECO:0005521

Axiom
annotated source: S1 nuclease protection assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:21390683

DNA dot blot assay evidence
type: Class
subclass of: DNA detection assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0302903
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001430
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0002171
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0001051
definition: 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.
created_by: snadendla
creation_date: 2015-09-30T10:03:03Z
has_obo_namespace: eco
id: ECO:0005522

Axiom
annotated source: DNA dot blot assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18265189

DNA dot blot assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: DNA dot blot assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: DNA dot blot assay evidence
has GO evidence code: EXP
definition: A type of DNA dot blot assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2015-09-30T10:04:00Z
has_obo_namespace: eco
id: ECO:0005523

Axiom
annotated source: DNA dot blot assay evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: DNA dot blot assay evidence used in manual assertion
annotated property: definition
annotated target: A type of DNA dot blot assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN
database_cross_reference: ECO:SW

matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence
type: Class
subclass of: protein detection assay evidence
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-09-30T10:51:56Z
has_exact_synonym: MALDI-TOF Mass Spectrometry
has_exact_synonym: MALDI-TOF-MS
has_obo_namespace: eco
id: ECO:0005526
comment: 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.

Axiom
annotated source: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:21964792
database_cross_reference: PMID:25354905

matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence
has GO evidence code: EXP
definition: A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2015-09-30T10:58:51Z
has_broad_synonym: MALDI-TOF mass spectrometry evidence
has_broad_synonym: MALDI-TOF-MS evidence
has_obo_namespace: eco
id: ECO:0005527

Axiom
annotated source: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
annotated property: definition
annotated target: A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion.
database_cross_reference: ECO:SN
database_cross_reference: ECO:SW

site-directed mutagenesis phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0002619
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001460
example of usage: If the AGAA sequence is mutated CTCC (Pxyn2aM, see Table 1), no DNA-protein complex is formed under either repressing or inducing conditions (Figure 1). This result indicates that this part of the xyn2 promoter is essential for binding a transcription factor under repressing conditions.
example of usage: To identify key residues required for specific GlnR binding we mutated the highly conserved AC-n9-AC and AT-n9-AC DNA binding motifs. Figure 4 shows that the highly conserved adenosine residues in the motif are critical as GlnR binding is abolished when these residues are mutated.
example of usage: We also tested a hyaS promoter in which one (highest score) of the three putative AdpA-binding sites was mutated (at position -134 to -129, see Additional file 3: Figure S1a): the affinity of AdpA for this promoter region was reduced and one protein-DNA complex disappeared (Additional file 3: Figure S1b). These results suggest that one dimer of AdpA binds the adjacent sites -129 and -123 of S. lividans hyaS promoter and another dimer binds the -100 site resulting in the formation of the two DNA-AdpA complexes depicted in Figure 2.
definition: A type of mutant phenotype phenotype 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-09-30T11:34:41Z
has_exact_synonym: site directed mutagenesis
has_exact_synonym: site-directed mutagenesis evidence
has_obo_namespace: eco
id: ECO:0005528
comment: 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.

Axiom
annotated source: site-directed mutagenesis phenotypic evidence
annotated property: example of usage
annotated target: If the AGAA sequence is mutated CTCC (Pxyn2aM, see Table 1), no DNA-protein complex is formed under either repressing or inducing conditions (Figure 1). This result indicates that this part of the xyn2 promoter is essential for binding a transcription factor under repressing conditions.
database_cross_reference: PMID:21087492

Axiom
annotated source: site-directed mutagenesis phenotypic evidence
annotated property: example of usage
annotated target: To identify key residues required for specific GlnR binding we mutated the highly conserved AC-n9-AC and AT-n9-AC DNA binding motifs. Figure 4 shows that the highly conserved adenosine residues in the motif are critical as GlnR binding is abolished when these residues are mutated.
database_cross_reference: PMID:23642041

Axiom
annotated source: site-directed mutagenesis phenotypic evidence
annotated property: example of usage
annotated target: We also tested a hyaS promoter in which one (highest score) of the three putative AdpA-binding sites was mutated (at position -134 to -129, see Additional file 3: Figure S1a): the affinity of AdpA for this promoter region was reduced and one protein-DNA complex disappeared (Additional file 3: Figure S1b). These results suggest that one dimer of AdpA binds the adjacent sites -129 and -123 of S. lividans hyaS promoter and another dimer binds the -100 site resulting in the formation of the two DNA-AdpA complexes depicted in Figure 2.
database_cross_reference: PMID:24694298

Axiom
annotated source: site-directed mutagenesis phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype phenotype 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:21204030
database_cross_reference: PMID:24011050
database_cross_reference: PMID:3541892

random mutagenesis phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0002620
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001460
definition: A type of mutant phenotype evidence where a mutagenic product or process is used to alter the nucleotide sequence and thus induce genetic mutation. Examples include, but are not limited to mutagenic compounds, irradiation, PCR w/ degenerate primers, etc.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-09-30T11:55:03Z
has_narrow_synonym: random mutagenesis evidence
has_obo_namespace: eco
id: ECO:0005529
comment: 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.

Axiom
annotated source: random mutagenesis phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence where a mutagenic product or process is used to alter the nucleotide sequence and thus induce genetic mutation. Examples include, but are not limited to mutagenic compounds, irradiation, PCR w/ degenerate primers, etc.
database_cross_reference: ECO:SW
database_cross_reference: PMID:15153637
database_cross_reference: PMID:18265275

random mutagenesis evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: random mutagenesis phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mutant phenotype evidence used in manual assertion
subclass of: random mutagenesis phenotypic evidence
has GO evidence code: IMP
definition: A type of random mutagenesis phenotypic evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2015-09-30T11:57:00Z
has_obo_namespace: eco
id: ECO:0005530

Axiom
annotated source: random mutagenesis evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

motif discovery evidence
type: Class
subclass of: multiple sequence alignment evidence
example of usage: A sequence alignment of the phlA gene promoter region from strain 2P24 with other well-studied 2,4-DAPG producing Pseudomonas strains revealed a very well conserved palindromic sequence GAAACN5GTTTC (Fig. S1).
example of usage: In order to identify a potential regulatory motif for KstR2, we used the promoter regions of the kstR2 orthologues as a training set for the motif identification program MEME (Bailey & Elkan, 1994). This identified a potential regulatory sequence that contains a 14 bp inverted palindromic motif AnCAAGnnCTTGnT (Fig. 2).
example of usage: We mapped sites upstream of crp itself, SCO4561 and SCO2977, and identified a consensus binding sequence [GTG(N)6GNCAC]; derivatives of this motif could be found in all of the secondary metabolism-associated target sequences, although notably, one-half of the palindrome seemed to be better conserved than the other [GTG(N)6GNGAN] (Fig. 2C; Table 1).
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-09-30T15:04:45Z
has_obo_namespace: eco
id: ECO:0005531
comment: 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.

Axiom
annotated source: motif discovery evidence
annotated property: example of usage
annotated target: A sequence alignment of the phlA gene promoter region from strain 2P24 with other well-studied 2,4-DAPG producing Pseudomonas strains revealed a very well conserved palindromic sequence GAAACN5GTTTC (Fig. S1).
database_cross_reference: PMID:23209661

Axiom
annotated source: motif discovery evidence
annotated property: example of usage
annotated target: In order to identify a potential regulatory motif for KstR2, we used the promoter regions of the kstR2 orthologues as a training set for the motif identification program MEME (Bailey & Elkan, 1994). This identified a potential regulatory sequence that contains a 14 bp inverted palindromic motif AnCAAGnnCTTGnT (Fig. 2).
database_cross_reference: PMID:20167624

Axiom
annotated source: motif discovery evidence
annotated property: example of usage
annotated target: We mapped sites upstream of crp itself, SCO4561 and SCO2977, and identified a consensus binding sequence [GTG(N)6GNCAC]; derivatives of this motif could be found in all of the secondary metabolism-associated target sequences, although notably, one-half of the palindrome seemed to be better conserved than the other [GTG(N)6GNGAN] (Fig. 2C; Table 1).
database_cross_reference: PMID:23232715

Axiom
annotated source: motif discovery evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:10812473
database_cross_reference: PMID:16845028
database_cross_reference: PMID:8211139

Axiom
annotated source: motif discovery evidence
annotated property: comment
annotated target: 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.
database_cross_reference: PMID:19892760
database_cross_reference: PMID:23032607

consensus search evidence
type: Class
subclass of: motif similarity evidence
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-10-09T14:12:54Z
has_obo_namespace: eco
id: ECO:0005532
comment: 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.

Axiom
annotated source: consensus search evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:15130839

phylogenetic footprinting evidence
type: Class
subclass of: motif discovery evidence
definition: 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'.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-09-30T16:23:02Z
has_obo_namespace: eco
id: ECO:0005533
comment: 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).

Axiom
annotated source: phylogenetic footprinting evidence
annotated property: definition
annotated target: 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'.
database_cross_reference: ECO:SW
database_cross_reference: PMID:16477324
database_cross_reference: PMID:3199442

comparative genomics motif search evidence
type: Class
subclass of: motif similarity evidence
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-10-09T14:30:38Z
has_obo_namespace: eco
id: ECO:0005534
comment: 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.

Axiom
annotated source: comparative genomics motif search evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:10854408

machine learning prediction of motif instance evidence
type: Class
subclass of: match to sequence model evidence
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-10-01T11:58:36Z
has_obo_namespace: eco
id: ECO:0005535
comment: 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).

Axiom
annotated source: machine learning prediction of motif instance evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:17117497
database_cross_reference: PMID:2014171

position-specific scoring matrix motif search evidence
type: Class
subclass of: motif similarity evidence
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-10-09T15:04:35Z
has_exact_synonym: PSSM motif search
has_narrow_synonym: PSSM
has_obo_namespace: eco
id: ECO:0005536
comment: This technique is used to predict transcription factor binding sites in gene promoter regions by using a position weight matrix approach. (PMID: 15604457).

Axiom
annotated source: position-specific scoring matrix motif search evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:10812473

xylE reporter gene assay evidence
type: Class
subclass of: reporter gene assay evidence
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2015-10-28T15:31:28Z
has_obo_namespace: eco
id: ECO:0005537

Axiom
annotated source: xylE reporter gene assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SW
database_cross_reference: PMID:2592344

computationally derived logical inference
type: Class
created_by: snadendla
creation_date: 2015-11-17T15:15:50Z
has_obo_namespace: eco
id: ECO:0005538
deprecated: true

computationally derived logical inference used in automatic assertion
type: Class
created_by: snadendla
creation_date: 2015-11-17T15:17:47Z
has_obo_namespace: eco
id: ECO:0005539
deprecated: true

computationally derived logical inference from automatic assertion used in automatic assertion
type: Class
created_by: snadendla
creation_date: 2015-11-17T15:24:42Z
has_obo_namespace: eco
id: ECO:0005540
deprecated: true

computationally derived logical inference from manual assertion used in automatic assertion
type: Class
created_by: snadendla
creation_date: 2015-11-17T15:32:03Z
has_obo_namespace: eco
id: ECO:0005541
deprecated: true

biological system reconstruction evidence by experimental evidence from single species used in manual assertion
type: Class
equivalent class: Class
  intersection of: biological system reconstruction evidence by experimental evidence from single species
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: evidence used in manual assertion
subclass of: biological system reconstruction evidence by experimental evidence from single species
definition: A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion.
created_by: snadendla
creation_date: 2015-12-16T15:32:41Z
has_obo_namespace: eco
id: ECO:0005542
comment: Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof.

Axiom
annotated source: biological system reconstruction evidence by experimental evidence from single species used in manual assertion
annotated property: subClassOf
annotated target: evidence used in manual assertion
is_inferred: true

Axiom
annotated source: biological system reconstruction evidence by experimental evidence from single species used in manual assertion
annotated property: definition
annotated target: A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion.
database_cross_reference: ECO:SN
database_cross_reference: PMID:19450514

biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion
type: Class
equivalent class: Class
  intersection of: biological system reconstruction evidence by experimental evidence from mixed species
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: evidence used in manual assertion
subclass of: biological system reconstruction evidence by experimental evidence from mixed species
definition: A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion.
created_by: snadendla
creation_date: 2015-12-16T15:45:01Z
has_obo_namespace: eco
id: ECO:0005543
comment: 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.

Axiom
annotated source: biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion
annotated property: subClassOf
annotated target: evidence used in manual assertion
is_inferred: true

Axiom
annotated source: biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion
annotated property: definition
annotated target: A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion.
database_cross_reference: ECO:SN
database_cross_reference: PMID:22232657

biological system reconstruction evidence based on orthology evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: biological system reconstruction evidence based on orthology evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: biological system reconstruction evidence based on orthology evidence
subclass of: biological system reconstruction evidence based on homology evidence used in manual assertion
definition: A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2015-12-18T16:20:49Z
has_obo_namespace: eco
id: ECO:0005544
comment: 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.

Axiom
annotated source: biological system reconstruction evidence based on orthology evidence used in manual assertion
annotated property: definition
annotated target: A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

biological system reconstruction evidence based on orthology evidence
type: Class
subclass of: biological system reconstruction evidence based on homology evidence
definition: 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.
created_by: snadendla
creation_date: 2015-12-16T15:57:37Z
has_obo_namespace: eco
id: ECO:0005545
comment: 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.

Axiom
annotated source: biological system reconstruction evidence based on orthology evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:15660128

biological system reconstruction evidence based on paralogy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: biological system reconstruction evidence based on paralogy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: biological system reconstruction evidence based on paralogy evidence
subclass of: biological system reconstruction evidence based on homology evidence used in manual assertion
definition: A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2015-12-16T16:05:15Z
has_obo_namespace: eco
id: ECO:0005546
comment: 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.

Axiom
annotated source: biological system reconstruction evidence based on paralogy evidence used in manual assertion
annotated property: definition
annotated target: A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion.
database_cross_reference: ECO:SN
database_cross_reference: PMID:15660128

biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion
type: Class
equivalent class: Class
  intersection of: biological system reconstruction evidence based on inference from background scientific knowledge
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: evidence used in manual assertion
subclass of: biological system reconstruction evidence based on inference from background scientific knowledge
definition: A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion.
created_by: snadendla
creation_date: 2015-12-16T16:07:42Z
has_obo_namespace: eco
id: ECO:0005547
comment: 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.

Axiom
annotated source: biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion
annotated property: subClassOf
annotated target: evidence used in manual assertion
is_inferred: true

Axiom
annotated source: biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion
annotated property: definition
annotated target: A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion.
database_cross_reference: ECO:SN
database_cross_reference: PMID:17876790

biological system reconstruction evidence based on inference from background scientific knowledge
type: Class
subclass of: biological system reconstruction evidence
definition: A type of biological system reconstruction based solely on background scientific knowledge of that biological system.
created_by: snadendla
creation_date: 2015-12-18T15:32:15Z
has_obo_namespace: eco
id: ECO:0005548
comment: 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.

Axiom
annotated source: biological system reconstruction evidence based on inference from background scientific knowledge
annotated property: definition
annotated target: A type of biological system reconstruction based solely on background scientific knowledge of that biological system.
database_cross_reference: ECO:SN
database_cross_reference: PMID:17876790

biological system reconstruction evidence based on homology evidence
type: Class
subclass of: biological system reconstruction evidence
definition: 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.
created_by: snadendla
creation_date: 2015-12-18T15:49:46Z
has_obo_namespace: eco
id: ECO:0005549
comment: 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.

Axiom
annotated source: biological system reconstruction evidence based on homology evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:15660128

biological system reconstruction evidence based on paralogy evidence
type: Class
subclass of: biological system reconstruction evidence based on homology evidence
definition: 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.
created_by: snadendla
creation_date: 2015-12-18T16:24:08Z
has_obo_namespace: eco
id: ECO:0005550
comment: 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.

Axiom
annotated source: biological system reconstruction evidence based on paralogy evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:15660128

biological system reconstruction evidence by experimental evidence
type: Class
subclass of: biological system reconstruction evidence
definition: A type of biological system reconstruction evidence that uses experimental evidence as support.
created_by: snadendla
creation_date: 2015-12-18T16:34:13Z
has_obo_namespace: eco
id: ECO:0005551

Axiom
annotated source: biological system reconstruction evidence by experimental evidence
annotated property: definition
annotated target: A type of biological system reconstruction evidence that uses experimental evidence as support.
database_cross_reference: ECO:SN
database_cross_reference: PMID:19450514
database_cross_reference: PMID:22232657

biological system reconstruction evidence by experimental evidence from mixed species
type: Class
subclass of: biological system reconstruction evidence by experimental evidence
definition: A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment.
created_by: snadendla
creation_date: 2015-12-18T16:35:13Z
has_obo_namespace: eco
id: ECO:0005552
comment: 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.

Axiom
annotated source: biological system reconstruction evidence by experimental evidence from mixed species
annotated property: definition
annotated target: A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment.
database_cross_reference: ECO:SN
database_cross_reference: PMID:22232657

biological system reconstruction evidence by experimental evidence from single species
type: Class
subclass of: biological system reconstruction evidence by experimental evidence
definition: A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species.
created_by: snadendla
creation_date: 2015-12-18T16:36:44Z
has_obo_namespace: eco
id: ECO:0005553
comment: Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof.

Axiom
annotated source: biological system reconstruction evidence by experimental evidence from single species
annotated property: definition
annotated target: A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species.
database_cross_reference: ECO:SN

pairwise sequence alignment evidence
type: Class
subclass of: sequence alignment evidence
definition: 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).
created_by: snadendla
creation_date: 2016-02-08T14:30:46Z
has_obo_namespace: eco
id: ECO:0005554

Axiom
annotated source: pairwise sequence alignment evidence
annotated property: definition
annotated target: 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).
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.ebi.ac.uk/Tools/psa/

multiple sequence alignment evidence
type: Class
subclass of: sequence alignment evidence
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2016-02-08T14:31:24Z
has_obo_namespace: eco
id: ECO:0005555

Axiom
annotated source: multiple sequence alignment evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.ebi.ac.uk/Tools/msa/

multiple sequence alignment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: multiple sequence alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: sequence alignment evidence used in manual assertion
subclass of: multiple sequence alignment evidence
has GO evidence code: ISA
definition: A type of multiple sequence alignment evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-02-08T14:59:18Z
has_obo_namespace: eco
id: ECO:0005556

Axiom
annotated source: multiple sequence alignment evidence used in manual assertion
annotated property: subClassOf
annotated target: sequence alignment evidence used in manual assertion
is_inferred: true

Axiom
annotated source: multiple sequence alignment evidence used in manual assertion
annotated property: definition
annotated target: A type of multiple sequence alignment evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

multiple sequence alignment evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: multiple sequence alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: sequence alignment evidence used in automatic assertion
subclass of: multiple sequence alignment evidence
has GO evidence code: IEA
definition: A type of multiple sequence alignment evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-02-08T15:00:50Z
has_obo_namespace: eco
id: ECO:0005557

Axiom
annotated source: multiple sequence alignment evidence used in automatic assertion
annotated property: subClassOf
annotated target: sequence alignment evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: multiple sequence alignment evidence used in automatic assertion
annotated property: definition
annotated target: A type of multiple sequence alignment evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

motif discovery evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: motif discovery evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: motif discovery evidence
subclass of: multiple sequence alignment evidence used in manual assertion
has GO evidence code: ISA
definition: A type of motif discovery evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-02-08T15:07:47Z
has_obo_namespace: eco
id: ECO:0005558

Axiom
annotated source: motif discovery evidence used in manual assertion
annotated property: subClassOf
annotated target: multiple sequence alignment evidence used in manual assertion
is_inferred: true

Axiom
annotated source: motif discovery evidence used in manual assertion
annotated property: definition
annotated target: A type of motif discovery evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

motif discovery evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: motif discovery evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: motif discovery evidence
subclass of: multiple sequence alignment evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of motif discovery evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-02-08T15:08:19Z
has_obo_namespace: eco
id: ECO:0005559

Axiom
annotated source: motif discovery evidence used in automatic assertion
annotated property: subClassOf
annotated target: multiple sequence alignment evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: motif discovery evidence used in automatic assertion
annotated property: definition
annotated target: A type of motif discovery evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

pairwise sequence alignment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: pairwise sequence alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: sequence alignment evidence used in manual assertion
subclass of: pairwise sequence alignment evidence
has GO evidence code: ISA
definition: A type of pairwise sequence alignment evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-02-08T15:17:05Z
has_obo_namespace: eco
id: ECO:0005560

Axiom
annotated source: pairwise sequence alignment evidence used in manual assertion
annotated property: subClassOf
annotated target: sequence alignment evidence used in manual assertion
is_inferred: true

Axiom
annotated source: pairwise sequence alignment evidence used in manual assertion
annotated property: definition
annotated target: A type of pairwise sequence alignment evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

pairwise sequence alignment evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: pairwise sequence alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: sequence alignment evidence used in automatic assertion
subclass of: pairwise sequence alignment evidence
has GO evidence code: IEA
definition: A type of pairwise sequence alignment evidence that is used in an automatic evidence.
created_by: snadendla
creation_date: 2016-02-08T15:17:52Z
has_obo_namespace: eco
id: ECO:0005561

Axiom
annotated source: pairwise sequence alignment evidence used in automatic assertion
annotated property: subClassOf
annotated target: sequence alignment evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: pairwise sequence alignment evidence used in automatic assertion
annotated property: definition
annotated target: A type of pairwise sequence alignment evidence that is used in an automatic evidence.
database_cross_reference: ECO:SN

in-gel protein kinase assay evidence
type: Class
subclass of: protein kinase assay evidence
definition: A type of protein kinase assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated kinase substrate.
created_by: snadendla
creation_date: 2016-02-09T12:05:29Z
has_obo_namespace: eco
id: ECO:0005562

Axiom
annotated source: in-gel protein kinase assay evidence
annotated property: definition
annotated target: A type of protein kinase assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated kinase substrate.
database_cross_reference: PMID:12372853

macroscopic current trace evidence
type: Class
subclass of: voltage clamp recording evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0005216
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000447
definition: 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.
created_by: snadendla
creation_date: 2016-02-09T12:40:03Z
has_obo_namespace: eco
id: ECO:0005563

Axiom
annotated source: macroscopic current trace evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:17938230
database_cross_reference: url:http://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch03.pdf

current density evidence
type: Class
subclass of: electrophysiology assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0005216
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000447
definition: A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane.
created_by: snadendla
creation_date: 2016-02-09T12:43:07Z
has_obo_namespace: eco
id: ECO:0005564

Axiom
annotated source: current density evidence
annotated property: definition
annotated target: A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane.
database_cross_reference: ECO:SN
database_cross_reference: url:http://circres.ahajournals.org/content/102/11/1298.full
database_cross_reference: url:http://www.bem.fi/book/04/04.htm

single channel conductance evidence
type: Class
created_by: snadendla
creation_date: 2016-02-09T12:45:42Z
has_obo_namespace: eco
id: ECO:0005565
deprecated: true

sustained current evidence
type: Class
subclass of: electrophysiology assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0005216
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000447
definition: 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.
created_by: snadendla
creation_date: 2016-02-09T12:46:54Z
has_obo_namespace: eco
id: ECO:0005566

Axiom
annotated source: sustained current evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.nature.com/ncomms/journal/v3/n2/full/ncomms1717.html

steady state activation curve evidence
type: Class
created_by: snadendla
creation_date: 2016-02-09T12:48:17Z
has_obo_namespace: eco
id: ECO:0005567
deprecated: true

steady state inactivation curve evidence
type: Class
created_by: snadendla
creation_date: 2016-02-09T12:50:45Z
has_obo_namespace: eco
id: ECO:0005568
deprecated: true

window current trace evidence
type: Class
created_by: snadendla
creation_date: 2016-02-09T12:57:16Z
has_obo_namespace: eco
id: ECO:0005569
deprecated: true

use dependence of inactivation evidence
type: Class
subclass of: electrophysiology assay evidence
definition: 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.
created_by: snadendla
creation_date: 2016-02-09T12:58:18Z
has_obo_namespace: eco
id: ECO:0005570

Axiom
annotated source: use dependence of inactivation evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://circres.ahajournals.org/content/89/8/700.full

current clamp recording evidence
type: Class
subclass of: electrophysiology assay evidence
definition: A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell.
created_by: snadendla
creation_date: 2016-02-12T13:58:32Z
database_cross_reference: birnlex:2278
has_exact_synonym: current clamp voltage recording evidence
has_obo_namespace: eco
id: ECO:0005571

Axiom
annotated source: current clamp recording evidence
annotated property: definition
annotated target: A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell.
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.nature.com/nprot/journal/v4/n8/full/nprot.2009.91.html

current clamp voltage recording protocol
type: Axiom
annotated source: current clamp recording evidence
annotated property: database_cross_reference
annotated target: birnlex:2278

whole-cell voltage clamp recording evidence
type: Class
subclass of: voltage clamp recording evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0005216
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000447
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0001129
definition: 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.
created_by: snadendla
creation_date: 2016-02-12T14:06:40Z
database_cross_reference: birnlex:2281
has_obo_namespace: eco
id: ECO:0005572

Axiom
annotated source: whole-cell voltage clamp recording evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://circres.ahajournals.org/content/72/1/91.full.pdf

whole-cell voltage clamp recording protocol
type: Axiom
annotated source: whole-cell voltage clamp recording evidence
annotated property: database_cross_reference
annotated target: birnlex:2281

cell-attached single-channel recording evidence
type: Class
subclass of: patch-clamp recording evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002179
definition: 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.
created_by: snadendla
creation_date: 2016-02-12T14:07:39Z
database_cross_reference: birnlex:2283
has_exact_synonym: cell-attached patch-clamp recording evidence
has_obo_namespace: eco
id: ECO:0005573

Axiom
annotated source: cell-attached single-channel recording evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch04.pdf

cell-attached single-channel recording protocol
type: Axiom
annotated source: cell-attached single-channel recording evidence
annotated property: database_cross_reference
annotated target: birnlex:2283

cell-detached inside-out single-channel recording evidence
type: Class
subclass of: patch-clamp recording evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002180
definition: 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.
created_by: snadendla
creation_date: 2016-02-12T14:16:53Z
database_cross_reference: birnlex:2286
has_exact_synonym: cell-detached inside-out patch-clamp recording evidence
has_obo_namespace: eco
id: ECO:0005574

Axiom
annotated source: cell-detached inside-out single-channel recording evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.acnp.org/g4/GN401000005/CH005.html

cell-detached inside-out single-channel recording protocol
type: Axiom
annotated source: cell-detached inside-out single-channel recording evidence
annotated property: database_cross_reference
annotated target: birnlex:2286

reconstituted bilayer single-channel patch recording evidence
type: Class
subclass of: patch-clamp recording evidence
definition: 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.
created_by: snadendla
creation_date: 2016-02-12T14:17:46Z
database_cross_reference: birnlex:2287
has_obo_namespace: eco
id: ECO:0005575

Axiom
annotated source: reconstituted bilayer single-channel patch recording evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://nanion.de/images/stories/papers/Bilayers_lab-on-a-chip08.pdf

reconstituted bilayer single-channel patch recording protocol
type: Axiom
annotated source: reconstituted bilayer single-channel patch recording evidence
annotated property: database_cross_reference
annotated target: birnlex:2287

voltage clamp recording evidence
type: Class
subclass of: electrophysiology assay evidence
definition: 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.
created_by: snadendla
creation_date: 2016-02-12T14:18:36Z
database_cross_reference: birnlex:2279
has_exact_synonym: voltage clamp current recording evidence
has_obo_namespace: eco
id: ECO:0005576

Axiom
annotated source: voltage clamp recording evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://neurobio.drexelmed.edu/GaoWeb/Resources/Recording%20_Techniques.pdf
database_cross_reference: url:http://www.acnp.org/g4/GN401000005/CH005.html

voltage clamp current recording protocol
type: Axiom
annotated source: voltage clamp recording evidence
annotated property: database_cross_reference
annotated target: birnlex:2279

electroencephalography recording evidence
type: Class
subclass of: electrophysiology assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0005216
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002186
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
definition: 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.
created_by: snadendla
creation_date: 2016-02-12T14:19:21Z
database_cross_reference: birnlex:2293
has_obo_namespace: eco
id: ECO:0005577

Axiom
annotated source: electroencephalography recording evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.jove.com/science-education/5420/electro-encephalography-eeg

electroencephalography recording protocol
type: Axiom
annotated source: electroencephalography recording evidence
annotated property: database_cross_reference
annotated target: birnlex:2293

super-resolution microscopy evidence
type: Class
subclass of: microscopy evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: light microscopy
definition: 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.
created_by: snadendla
creation_date: 2016-02-12T15:20:47Z
has_obo_namespace: eco
id: ECO:0005578

Axiom
annotated source: super-resolution microscopy evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://journal.frontiersin.org/article/10.3389/fncel.2015.00007/full

immunogold labelling evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunogold labelling evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: immunogold labelling evidence
subclass of: immunolocalization evidence used in manual assertion
has GO evidence code: IDA
definition: A type of immunogold labelling evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-02-12T15:38:03Z
has_broad_synonym: immunogold labelling
has_obo_namespace: eco
id: ECO:0005579

Axiom
annotated source: immunogold labelling evidence used in manual assertion
annotated property: subClassOf
annotated target: immunolocalization evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunogold labelling evidence used in manual assertion
annotated property: definition
annotated target: A type of immunogold labelling evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

flow cytometry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: flow cytometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: flow cytometry evidence
subclass of: direct assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of flow cytometry evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-02-12T16:04:23Z
has_broad_synonym: FCM
has_obo_namespace: eco
id: ECO:0005580

Axiom
annotated source: flow cytometry evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: flow cytometry evidence used in manual assertion
annotated property: definition
annotated target: A type of flow cytometry evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

enzyme-linked immunoabsorbent assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: enzyme-linked immunoabsorbent assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: enzyme-linked immunoabsorbent assay evidence
subclass of: experimental evidence used in manual assertion
has GO evidence code: EXP
definition: A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-02-12T16:23:38Z
has_broad_synonym: ELISA evidence|enzyme-linked immunosorbent assay evidence
has_obo_namespace: eco
id: ECO:0005581

Axiom
annotated source: enzyme-linked immunoabsorbent assay evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: enzyme-linked immunoabsorbent assay evidence used in manual assertion
annotated property: definition
annotated target: A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

cell-detached outside-out single-channel recording evidence
type: Class
subclass of: patch-clamp recording evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002181
definition: 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).
created_by: snadendla
creation_date: 2016-03-02T10:47:25Z
has_exact_synonym: cell-detached outside-out patch-clamp evidence
has_obo_namespace: eco
id: ECO:0005582

Axiom
annotated source: cell-detached outside-out single-channel recording evidence
annotated property: definition
annotated target: 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).
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.nature.com/nprot/journal/v2/n11/full/nprot.2007.403.html

cut-open oocyte voltage clamp recording evidence
type: Class
subclass of: voltage clamp recording evidence
definition: 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.
created_by: snadendla
creation_date: 2016-03-02T11:29:32Z
has_obo_namespace: eco
id: ECO:0005583

Axiom
annotated source: cut-open oocyte voltage clamp recording evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:9711615

macropatch voltage clamp recording evidence
type: Class
subclass of: voltage clamp recording evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0005216
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000447
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0001129
definition: 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).
created_by: snadendla
creation_date: 2016-03-02T11:33:48Z
has_obo_namespace: eco
id: ECO:0005584

Axiom
annotated source: macropatch voltage clamp recording evidence
annotated property: definition
annotated target: 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).
database_cross_reference: ECO:SN
database_cross_reference: url:http://jxb.oxfordjournals.org/content/50/Special_Issue/1037.full.pdf

high throughput mass spectrometry evidence
type: Class
subclass of: mass spectrometry evidence
definition: 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.
created_by: snadendla
creation_date: 2016-03-02T12:33:07Z
has_obo_namespace: eco
id: ECO:0005585
comment: 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.

Axiom
annotated source: high throughput mass spectrometry evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:20805795

high throughput mass spectrometry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: high throughput mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mass spectrometry evidence used in manual assertion
subclass of: high throughput mass spectrometry evidence
has GO evidence code: EXP
definition: A type of high throughput mass spectrometry evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-03-02T12:50:02Z
has_obo_namespace: eco
id: ECO:0005586

Axiom
annotated source: high throughput mass spectrometry evidence used in manual assertion
annotated property: subClassOf
annotated target: mass spectrometry evidence used in manual assertion
is_inferred: true

Axiom
annotated source: high throughput mass spectrometry evidence used in manual assertion
annotated property: definition
annotated target: A type of high throughput mass spectrometry evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

confocal microscopy evidence
type: Class
subclass of: microscopy evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000185
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0001079
definition: 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.
created_by: snadendla
creation_date: 2016-03-17T12:29:45Z
has_obo_namespace: eco
id: ECO:0005587

Axiom
annotated source: confocal microscopy evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.physics.emory.edu/faculty/weeks//lab/papers/ebbe05.pdf

wide-field microscopy evidence
type: Class
subclass of: microscopy evidence
definition: 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.
created_by: snadendla
creation_date: 2016-03-17T12:30:27Z
has_obo_namespace: eco
id: ECO:0005588

Axiom
annotated source: wide-field microscopy evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://jcb.rupress.org/content/172/1/9.full
database_cross_reference: url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048960/
database_cross_reference: url:http://zeiss-campus.magnet.fsu.edu/articles/livecellimaging/techniques.html

confocal microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: confocal microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: microscopy evidence used in manual assertion
subclass of: confocal microscopy evidence
has GO evidence code: IDA
definition: A type confocal microscopy evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-03-17T12:32:24Z
has_obo_namespace: eco
id: ECO:0005589

Axiom
annotated source: confocal microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: confocal microscopy evidence used in manual assertion
annotated property: definition
annotated target: A type confocal microscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

wide-field microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: wide-field microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: microscopy evidence used in manual assertion
subclass of: wide-field microscopy evidence
has GO evidence code: IDA
definition: A type of wide-field microscopy evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-03-17T12:34:42Z
has_obo_namespace: eco
id: ECO:0005590

Axiom
annotated source: wide-field microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: wide-field microscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of wide-field microscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

immunogold labelling electron microscopy assay evidence
type: Class
subclass of: immunogold labelling evidence
subclass of: electron microscopy evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001631
    intersection of: Class
      intersection of: Restriction
        on property: has part
        some values from: GO_0003823
      intersection of: Restriction
        on property: has part
        some values from: OBI_0600038
definition: A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles.
created_by: snadendla
creation_date: 2016-03-17T15:43:00Z
has_obo_namespace: eco
id: ECO:0005591

Axiom
annotated source: immunogold labelling electron microscopy assay evidence
annotated property: definition
annotated target: A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles.
database_cross_reference: ECO:SN
database_cross_reference: PMID:4110101

immunogold labelling electron microscopy assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunogold labelling electron microscopy assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: immunogold labelling evidence used in manual assertion
subclass of: immunogold labelling electron microscopy assay evidence
subclass of: electron microscopy evidence used in manual assertion
has GO evidence code: IDA
definition: A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-03-17T16:39:37Z
has_obo_namespace: eco
id: ECO:0005592

Axiom
annotated source: immunogold labelling electron microscopy assay evidence used in manual assertion
annotated property: subClassOf
annotated target: immunogold labelling evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunogold labelling electron microscopy assay evidence used in manual assertion
annotated property: subClassOf
annotated target: electron microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunogold labelling electron microscopy assay evidence used in manual assertion
annotated property: definition
annotated target: A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

immunodetection assay evidence
type: Class
subclass of: direct assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0003823
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0600025
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: Class
        intersection of: OBI_0600038
        intersection of: Restriction
definition: A type of direct assay evidence that involves the use of antibodies to detect biomolecules.
created_by: snadendla
creation_date: 2016-03-17T17:07:33Z
has_obo_namespace: eco
id: ECO:0005593

Axiom
annotated source: immunodetection assay evidence
annotated property: definition
annotated target: A type of direct assay evidence that involves the use of antibodies to detect biomolecules.
database_cross_reference: ECO:SN

immunoperoxidase immunolocalization evidence
type: Class
subclass of: immunolocalization evidence
definition: A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody.
created_by: snadendla
creation_date: 2016-03-17T17:11:34Z
has_obo_namespace: eco
id: ECO:0005594

Axiom
annotated source: immunoperoxidase immunolocalization evidence
annotated property: definition
annotated target: A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody.
database_cross_reference: ECO:SN

immunoperoxidase immunolocalization evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunoperoxidase immunolocalization evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: immunoperoxidase immunolocalization evidence
subclass of: immunolocalization evidence used in manual assertion
has GO evidence code: IDA
definition: A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-03-17T17:14:05Z
has_obo_namespace: eco
id: ECO:0005595

Axiom
annotated source: immunoperoxidase immunolocalization evidence used in manual assertion
annotated property: subClassOf
annotated target: immunolocalization evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunoperoxidase immunolocalization evidence used in manual assertion
annotated property: definition
annotated target: A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

immunoperoxidase immunolocalization electron microscopy evidence
type: Class
subclass of: electron microscopy evidence
subclass of: immunoperoxidase immunolocalization evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001631
    intersection of: OBI_0001632
definition: A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody.
created_by: snadendla
creation_date: 2016-03-17T17:16:38Z
has_exact_synonym: Immunoperoxidase labelling electron microscopy
has_obo_namespace: eco
id: ECO:0005596

Axiom
annotated source: immunoperoxidase immunolocalization electron microscopy evidence
annotated property: definition
annotated target: A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody.
database_cross_reference: ECO:SN

immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunoperoxidase immunolocalization electron microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: immunoperoxidase immunolocalization evidence used in manual assertion
subclass of: immunoperoxidase immunolocalization electron microscopy evidence
subclass of: electron microscopy evidence used in manual assertion
has GO evidence code: IDA
definition: A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-03-17T17:23:56Z
has_broad_synonym: immunoperoxidase labelling electron microscopy evidence
has_obo_namespace: eco
id: ECO:0005597

Axiom
annotated source: immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: immunoperoxidase immunolocalization evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: electron microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

wide-field fluorescence microscopy evidence
type: Class
subclass of: wide-field microscopy evidence
definition: 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.
created_by: snadendla
creation_date: 2016-03-18T11:53:56Z
has_obo_namespace: eco
id: ECO:0005598
comment: 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.

Axiom
annotated source: wide-field fluorescence microscopy evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.bristol.ac.uk/synaptic/research/techniques/widefield.html

immunofluorescence wide-field microscopy evidence
type: Class
subclass of: immunofluorescence evidence
subclass of: wide-field fluorescence microscopy evidence
definition: A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
created_by: snadendla
creation_date: 2016-03-18T11:55:40Z
has_exact_synonym: wide-field epifluorescence microscopy
has_obo_namespace: eco
id: ECO:0005599

Axiom
annotated source: immunofluorescence wide-field microscopy evidence
annotated property: definition
annotated target: A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
database_cross_reference: ECO:SN
database_cross_reference: url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057135

immunofluorescence confocal microscopy evidence
type: Class
subclass of: immunofluorescence evidence
subclass of: confocal microscopy evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001635
    intersection of: Class
      intersection of: OBI_0000185
      intersection of: Restriction
        on property: has participant
        some values from: OBI_0001079
example of usage: The endogenous protein expression and localization for WalR and WalK was also checked using confocal immunofluorescence microscopy. WalR could be localized to the cytoplasm of B. anthracis but WalK could not be detected once again (data not shown).
definition: 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.
created_by: snadendla
creation_date: 2016-03-18T12:48:42Z
has_obo_namespace: eco
id: ECO:0005600
comment: This allows visualization of sub cellular distribution of biomolecules of interest.

Axiom
annotated source: immunofluorescence confocal microscopy evidence
annotated property: example of usage
annotated target: The endogenous protein expression and localization for WalR and WalK was also checked using confocal immunofluorescence microscopy. WalR could be localized to the cytoplasm of B. anthracis but WalK could not be detected once again (data not shown).
database_cross_reference: PMID:24490131

Axiom
annotated source: immunofluorescence confocal microscopy evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.physics.emory.edu/faculty/weeks/confocal/
database_cross_reference: url:https://www.hycultbiotech.com/media/wysiwyg/protocol_Immunofluorescence.pdf

immunofluorescence confocal microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunofluorescence confocal microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: confocal microscopy evidence used in manual assertion
subclass of: immunofluorescence confocal microscopy evidence
subclass of: immunofluorescence evidence used in manual assertion
has GO evidence code: IDA
definition: A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-03-18T12:52:04Z
has_obo_namespace: eco
id: ECO:0005601

Axiom
annotated source: immunofluorescence confocal microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: confocal microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunofluorescence confocal microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: immunofluorescence evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunofluorescence confocal microscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

protein mass spectrometry evidence
type: Class
subclass of: mass spectrometry evidence
definition: A type of mass spectrometry evidence where one or more protein analyses are performed.
created_by: snadendla
creation_date: 2016-03-18T13:11:37Z
has_obo_namespace: eco
id: ECO:0005603

Axiom
annotated source: protein mass spectrometry evidence
annotated property: definition
annotated target: A type of mass spectrometry evidence where one or more protein analyses are performed.
database_cross_reference: ECO:SN

cross-streak test evidence
type: Class
subclass of: cell proliferation assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0009607
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000978
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0000153
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001285
definition: 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.
created_by: snadendla
creation_date: 2016-03-29T15:40:54Z
has_obo_namespace: eco
id: ECO:0005604

Axiom
annotated source: cross-streak test evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:www.jstor.org/stable/3792785

disk diffusion test evidence
type: Class
subclass of: ECO_0007083
subclass of: Restriction
  on property: is about
  some values from: GO_0046677
example of usage: Disk diffusion assays were used to determine if ohr and ohrR mutations affected resistance to ROS. The ohr mutant was less resistant than its parental strain when challenged with organic peroxides as shown by the zones of growth inhibition: 4.1 +- 0.2 cm for CuOOH and 3.1 +- 0.1 cm for tBOOH versus to 2.3 +- 0.2 and 2.5 +- 0.3 cm for wild type strain.
definition: 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.
created_by: snadendla
creation_date: 2016-03-29T16:02:22Z
has_obo_namespace: eco
id: ECO:0005605

Axiom
annotated source: disk diffusion test evidence
annotated property: example of usage
annotated target: Disk diffusion assays were used to determine if ohr and ohrR mutations affected resistance to ROS. The ohr mutant was less resistant than its parental strain when challenged with organic peroxides as shown by the zones of growth inhibition: 4.1 +- 0.2 cm for CuOOH and 3.1 +- 0.1 cm for tBOOH versus to 2.3 +- 0.2 and 2.5 +- 0.3 cm for wild type strain.
database_cross_reference: PMID:21569462

Axiom
annotated source: disk diffusion test evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.cdc.gov/nczved/resources/cholera/ch9.pdf

cell transfection experiment evidence
type: Class
subclass of: experimental evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0050789
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0001152
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001460
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000964
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0001151
definition: 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.
created_by: snadendla
creation_date: 2016-03-29T16:59:17Z
has_obo_namespace: eco
id: ECO:0005606

Axiom
annotated source: cell transfection experiment evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://ch.promega.com/resources/product-guides-and-selectors/protocols-and-applications-guide/transfection/
database_cross_reference: url:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911531/

tethered cell assay evidence
type: Class
subclass of: chemotaxis assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0060326
definition: 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.
created_by: snadendla
creation_date: 2016-03-31T15:51:10Z
has_obo_namespace: eco
id: ECO:0005607

Axiom
annotated source: tethered cell assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:1103143

tumble frequency assay evidence
type: Class
subclass of: chemotaxis assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0060326
definition: 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.
created_by: snadendla
creation_date: 2016-03-31T16:42:35Z
has_exact_synonym: Temporal assay
has_obo_namespace: eco
id: ECO:0005608

Axiom
annotated source: tumble frequency assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:4576832

capillary assay evidence
type: Class
subclass of: chemotaxis assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0060326
definition: 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.
created_by: snadendla
creation_date: 2016-03-31T16:45:29Z
has_obo_namespace: eco
id: ECO:0005609
comment: 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.
comment: 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.

Axiom
annotated source: capillary assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:4632978

biological system reconstruction evidence based on homology evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: biological system reconstruction evidence based on homology evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: evidence used in manual assertion
subclass of: biological system reconstruction evidence based on homology evidence
definition: A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-03-31T17:00:03Z
has_obo_namespace: eco
id: ECO:0005610
comment: 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.

Axiom
annotated source: biological system reconstruction evidence based on homology evidence used in manual assertion
annotated property: subClassOf
annotated target: evidence used in manual assertion
is_inferred: true

Axiom
annotated source: biological system reconstruction evidence based on homology evidence used in manual assertion
annotated property: definition
annotated target: A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

inference from experimental data evidence
type: Class
definition: 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.
created_by: snadendla
creation_date: 2016-04-12T16:55:16Z
has_exact_synonym: IED
has_exact_synonym: inferred from experimental data
has_obo_namespace: eco
id: ECO:0005611
deprecated: true

Axiom
annotated source: inference from experimental data evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN

inference from phenotype manipulation evidence
type: Class
definition: 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.
created_by: snadendla
creation_date: 2016-04-12T17:09:43Z
has_exact_synonym: IPM
has_exact_synonym: inferred from phenotype manipulation
has_obo_namespace: eco
id: ECO:0005612
comment: 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.
deprecated: true

Axiom
annotated source: inference from phenotype manipulation evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN

inference by association of genotype from phenotype
type: Class
subclass of: natural variation mutant evidence used in manual assertion
has GO evidence code: EXP
definition: 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.
created_by: snadendla
creation_date: 2016-04-12T17:24:00Z
has_exact_synonym: IAGP
has_exact_synonym: inferred by association of genotype from phenotype
has_obo_namespace: eco
id: ECO:0005613
comment: 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.

Axiom
annotated source: inference by association of genotype from phenotype
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN

two-dimensional polyacrylamide gel electrophoresis evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: two-dimensional polyacrylamide gel electrophoresis evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: two-dimensional polyacrylamide gel electrophoresis evidence
has GO evidence code: IDA
definition: A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T11:03:08Z
has_broad_synonym: 2D-PAGE evidence
has_obo_namespace: eco
id: ECO:0005614

Axiom
annotated source: two-dimensional polyacrylamide gel electrophoresis evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: two-dimensional polyacrylamide gel electrophoresis evidence used in manual assertion
annotated property: definition
annotated target: A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

alkaline phosphatase reporter gene assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: alkaline phosphatase reporter gene assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence used in manual assertion
subclass of: alkaline phosphatase reporter gene assay evidence
has GO evidence code: IEP
definition: A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T11:05:59Z
has_obo_namespace: eco
has_related_synonym: SEAP reporter assay
has_related_synonym: secreted embryonic alkaline phosphatase reporter assay
id: ECO:0005615

Axiom
annotated source: alkaline phosphatase reporter gene assay evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

Axiom
annotated source: alkaline phosphatase reporter gene assay evidence used in manual assertion
annotated property: definition
annotated target: A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

beta-galactosidase reporter gene assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: beta-galactosidase reporter gene assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence used in manual assertion
subclass of: beta-galactosidase reporter gene assay evidence
has GO evidence code: IEP
definition: A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T11:08:57Z
has_broad_synonym: beta-gal reporter gene assay evidence
has_exact_synonym: LacZ transcript localization evidence used in manual assertion
has_obo_namespace: eco
has_related_synonym: lacZ reporter gene assay
id: ECO:0005616

Axiom
annotated source: beta-galactosidase reporter gene assay evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

Axiom
annotated source: beta-galactosidase reporter gene assay evidence used in manual assertion
annotated property: definition
annotated target: A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

chloramphenicol acetyltransferase reporter gene assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: chloramphenicol acetyltransferase reporter gene assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence used in manual assertion
subclass of: chloramphenicol acetyltransferase reporter gene assay evidence
has GO evidence code: IEP
definition: A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T11:11:07Z
has_broad_synonym: CAT reporter gene assay evidence
has_obo_namespace: eco
id: ECO:0005617

Axiom
annotated source: chloramphenicol acetyltransferase reporter gene assay evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

Axiom
annotated source: chloramphenicol acetyltransferase reporter gene assay evidence used in manual assertion
annotated property: definition
annotated target: A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

chromatin immunoprecipitation-chip evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: chromatin immunoprecipitation-chip evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: chromatin immunoprecipitation-chip evidence
subclass of: ECO_0007786
has GO evidence code: IEA
definition: A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T11:17:04Z
has_broad_synonym: ChIP-chip evidence
has_broad_synonym: ChIP-on-chip evidence
has_obo_namespace: eco
id: ECO:0005618

Axiom
annotated source: chromatin immunoprecipitation-chip evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007786
is_inferred: true

Axiom
annotated source: chromatin immunoprecipitation-chip evidence used in automatic assertion
annotated property: definition
annotated target: A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

chromatin immunoprecipitation- exonuclease evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: chromatin immunoprecipitation- exonuclease evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: chromatin immunoprecipitation- exonuclease evidence
subclass of: ECO_0007786
has GO evidence code: IEA
definition: A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T11:22:25Z
has_broad_synonym: ChIP-exo evidence
has_obo_namespace: eco
id: ECO:0005619

Axiom
annotated source: chromatin immunoprecipitation- exonuclease evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007786
is_inferred: true

Axiom
annotated source: chromatin immunoprecipitation- exonuclease evidence used in automatic assertion
annotated property: definition
annotated target: A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

chromatin immunoprecipitation-PCR evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: chromatin immunoprecipitation-PCR evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: chromatin immunoprecipitation-PCR evidence
subclass of: immunoprecipitation evidence used in manual assertion
has GO evidence code: IPI
definition: A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T11:25:01Z
has_broad_synonym: ChIP-PCR evidence
has_obo_namespace: eco
id: ECO:0005620

Axiom
annotated source: chromatin immunoprecipitation-PCR evidence used in manual assertion
annotated property: subClassOf
annotated target: immunoprecipitation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: chromatin immunoprecipitation-PCR evidence used in manual assertion
annotated property: definition
annotated target: A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

chromatin immunoprecipitation-seq evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: chromatin immunoprecipitation-seq evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: chromatin immunoprecipitation-seq evidence
subclass of: ECO_0007786
has GO evidence code: IEA
definition: A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T11:29:13Z
has_broad_synonym: ChIP-SEQ evidence
has_broad_synonym: ChIP-seq evidence
has_obo_namespace: eco
id: ECO:0005621

Axiom
annotated source: chromatin immunoprecipitation-seq evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007786
is_inferred: true

Axiom
annotated source: chromatin immunoprecipitation-seq evidence used in automatic assertion
annotated property: definition
annotated target: A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

comparative genomics motif search evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: comparative genomics motif search evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: motif similarity evidence used in manual assertion
subclass of: comparative genomics motif search evidence
has GO evidence code: ISM
definition: A type of comparative genomics motif search evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T14:49:36Z
has_obo_namespace: eco
id: ECO:0005622

Axiom
annotated source: comparative genomics motif search evidence used in manual assertion
annotated property: subClassOf
annotated target: motif similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: comparative genomics motif search evidence used in manual assertion
annotated property: definition
annotated target: A type of comparative genomics motif search evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

comparative genomics motif search evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: comparative genomics motif search evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: motif similarity evidence used in automatic assertion
subclass of: comparative genomics motif search evidence
has GO evidence code: IEA
definition: A type of comparative genomics motif search evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T14:52:21Z
has_obo_namespace: eco
id: ECO:0005623

Axiom
annotated source: comparative genomics motif search evidence used in automatic assertion
annotated property: subClassOf
annotated target: motif similarity evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: comparative genomics motif search evidence used in automatic assertion
annotated property: definition
annotated target: A type of comparative genomics motif search evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

consensus search evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: consensus search evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: motif similarity evidence used in manual assertion
subclass of: consensus search evidence
has GO evidence code: ISM
definition: A type of consensus search evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T14:54:53Z
has_obo_namespace: eco
id: ECO:0005624

Axiom
annotated source: consensus search evidence used in manual assertion
annotated property: subClassOf
annotated target: motif similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: consensus search evidence used in manual assertion
annotated property: definition
annotated target: A type of consensus search evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

consensus search evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: consensus search evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: motif similarity evidence used in automatic assertion
subclass of: consensus search evidence
has GO evidence code: IEA
definition: A type of consensus search evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T14:58:22Z
has_obo_namespace: eco
id: ECO:0005625

Axiom
annotated source: consensus search evidence used in automatic assertion
annotated property: subClassOf
annotated target: motif similarity evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: consensus search evidence used in automatic assertion
annotated property: definition
annotated target: A type of consensus search evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

copper-phenanthroline footprinting evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: copper-phenanthroline footprinting evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: copper-phenanthroline footprinting evidence
subclass of: nucleic acid binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of copper-phenanthroline footprinting evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T15:01:25Z
has_broad_synonym: 1,10-phenanthroline-copper footprinting evidence
has_obo_namespace: eco
has_related_synonym: OP-Cu Complex
id: ECO:0005626

Axiom
annotated source: copper-phenanthroline footprinting evidence used in manual assertion
annotated property: subClassOf
annotated target: nucleic acid binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: copper-phenanthroline footprinting evidence used in manual assertion
annotated property: definition
annotated target: A type of copper-phenanthroline footprinting evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

DNA adenine methyltransferase identification evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: DNA adenine methyltransferase identification evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: DNA adenine methyltransferase identification evidence
subclass of: affinity evidence used in manual assertion
has GO evidence code: IPI
definition: A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T15:05:14Z
has_broad_synonym: DamID evidence
has_obo_namespace: eco
id: ECO:0005627

Axiom
annotated source: DNA adenine methyltransferase identification evidence used in manual assertion
annotated property: subClassOf
annotated target: affinity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: DNA adenine methyltransferase identification evidence used in manual assertion
annotated property: definition
annotated target: A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

DNA adenine methyltransferase identification evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: DNA adenine methyltransferase identification evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: DNA adenine methyltransferase identification evidence
subclass of: ECO_0007384
has GO evidence code: IEA
definition: A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T15:06:46Z
has_broad_synonym: DamID evidence
has_obo_namespace: eco
id: ECO:0005628

Axiom
annotated source: DNA adenine methyltransferase identification evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007384
is_inferred: true

Axiom
annotated source: DNA adenine methyltransferase identification evidence used in automatic assertion
annotated property: definition
annotated target: A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

DNA affinity chromatography evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: DNA affinity chromatography evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: DNA affinity chromatography evidence
subclass of: ECO_0007680
has GO evidence code: EXP
definition: A type of DNA affinity chromatography evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T15:08:40Z
has_broad_synonym: DNA affinity purification evidence
has_obo_namespace: eco
id: ECO:0005629

Axiom
annotated source: DNA affinity chromatography evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007680
is_inferred: true

Axiom
annotated source: DNA affinity chromatography evidence used in manual assertion
annotated property: definition
annotated target: A type of DNA affinity chromatography evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

cDNA to DNA expression microarray evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: cDNA to DNA expression microarray evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: cDNA to DNA expression microarray evidence
subclass of: ECO_0007301
has GO evidence code: IEA
definition: A type of cDNA to DNA expression microarray evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T15:31:51Z
has_broad_synonym: DNA microarray evidence
has_broad_synonym: RNA microarray evidence
has_obo_namespace: eco
id: ECO:0005630

Axiom
annotated source: cDNA to DNA expression microarray evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007301
is_inferred: true

Axiom
annotated source: cDNA to DNA expression microarray evidence used in automatic assertion
annotated property: definition
annotated target: A type of cDNA to DNA expression microarray evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

DNAse footprinting evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: DNAse footprinting evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: DNAse footprinting evidence
subclass of: nucleic acid binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of DNAse footprinting evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T15:35:41Z
has_broad_synonym: DNase protection evidence
has_obo_namespace: eco
id: ECO:0005631

Axiom
annotated source: DNAse footprinting evidence used in manual assertion
annotated property: subClassOf
annotated target: nucleic acid binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: DNAse footprinting evidence used in manual assertion
annotated property: definition
annotated target: A type of DNAse footprinting evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

fluorescence anisotropy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: fluorescence anisotropy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: fluorescence evidence used in manual assertion
subclass of: fluorescence anisotropy evidence
has GO evidence code: IDA
definition: A type of fluorescence anisotropy evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T15:45:40Z
has_broad_synonym: FA evidence
has_obo_namespace: eco
has_related_synonym: FP
has_related_synonym: fluorescence polarization
id: ECO:0005632

Axiom
annotated source: fluorescence anisotropy evidence used in manual assertion
annotated property: subClassOf
annotated target: fluorescence evidence used in manual assertion
is_inferred: true

Axiom
annotated source: fluorescence anisotropy evidence used in manual assertion
annotated property: definition
annotated target: A type of fluorescence anisotropy evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

ferric uptake regulator titration assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: ferric uptake regulator titration assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence used in manual assertion
subclass of: ferric uptake regulator titration assay evidence
has GO evidence code: IEP
definition: A type of ferric uptake regulator titration assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T15:49:18Z
has_broad_synonym: FURTA evidence
has_obo_namespace: eco
id: ECO:0005633

Axiom
annotated source: ferric uptake regulator titration assay evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

Axiom
annotated source: ferric uptake regulator titration assay evidence used in manual assertion
annotated property: definition
annotated target: A type of ferric uptake regulator titration assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

genomic systematic evolution of ligands by exponential amplification evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: genomic systematic evolution of ligands by exponential amplification evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: genomic systematic evolution of ligands by exponential amplification evidence
subclass of: systematic evolution of ligands by exponential amplification evidence used in manual assertion
has GO evidence code: IPI
definition: A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T16:41:30Z
has_broad_synonym: genomic SELEX evidence
has_obo_namespace: eco
id: ECO:0005634

Axiom
annotated source: genomic systematic evolution of ligands by exponential amplification evidence used in manual assertion
annotated property: subClassOf
annotated target: systematic evolution of ligands by exponential amplification evidence used in manual assertion
is_inferred: true

Axiom
annotated source: genomic systematic evolution of ligands by exponential amplification evidence used in manual assertion
annotated property: definition
annotated target: A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

genomic systematic evolution of ligands by exponential amplification evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: genomic systematic evolution of ligands by exponential amplification evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: genomic systematic evolution of ligands by exponential amplification evidence
subclass of: ECO_0007510
has GO evidence code: IEA
definition: A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T16:43:03Z
has_broad_synonym: genomic SELEX evidence
has_obo_namespace: eco
id: ECO:0005635

Axiom
annotated source: genomic systematic evolution of ligands by exponential amplification evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007510
is_inferred: true

Axiom
annotated source: genomic systematic evolution of ligands by exponential amplification evidence used in automatic assertion
annotated property: definition
annotated target: A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

green fluorescent protein reporter gene assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: green fluorescent protein reporter gene assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence used in manual assertion
subclass of: green fluorescent protein reporter gene assay evidence
has GO evidence code: IEP
definition: A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T16:46:32Z
has_broad_synonym: GFP reporter gene assay evidence
has_exact_synonym: green fluorescent protein transcript localization evidence used in manual assertion
has_obo_namespace: eco
has_related_synonym: GFP promoter fusion
has_related_synonym: green fluorescent protein promoter fusion
id: ECO:0005636

Axiom
annotated source: green fluorescent protein reporter gene assay evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

Axiom
annotated source: green fluorescent protein reporter gene assay evidence used in manual assertion
annotated property: definition
annotated target: A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

green fluorescent protein reporter gene assay evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: green fluorescent protein reporter gene assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: green fluorescent protein reporter gene assay evidence
subclass of: ECO_0007765
has GO evidence code: IEA
definition: A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T16:48:29Z
has_broad_synonym: GFP reporter gene assay evidence
has_exact_synonym: green fluorescent protein transcript localization evidence used in automatic assertion
has_obo_namespace: eco
has_related_synonym: GFP promoter fusion
has_related_synonym: green fluorescent protein promoter fusion
id: ECO:0005637

Axiom
annotated source: green fluorescent protein reporter gene assay evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007765
is_inferred: true

Axiom
annotated source: green fluorescent protein reporter gene assay evidence used in automatic assertion
annotated property: definition
annotated target: A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

cell growth regulation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cell growth regulation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: cell growth regulation assay evidence
subclass of: direct assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of cell growth regulation assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T16:52:15Z
has_obo_namespace: eco
has_related_synonym: growth curve analysis
id: ECO:0005638

Axiom
annotated source: cell growth regulation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cell growth regulation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of cell growth regulation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

cell growth regulation assay evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: cell growth regulation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: cell growth regulation assay evidence
subclass of: ECO_0007778
has GO evidence code: IEA
definition: A type of cell growth regulation assay evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T16:53:28Z
has_obo_namespace: eco
has_related_synonym: growth curve analysis
id: ECO:0005639

Axiom
annotated source: cell growth regulation assay evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007778
is_inferred: true

Axiom
annotated source: cell growth regulation assay evidence used in automatic assertion
annotated property: definition
annotated target: A type of cell growth regulation assay evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

glutathione S-transferase pull-down assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: glutathione S-transferase pull-down assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: glutathione S-transferase pull-down assay evidence
subclass of: bait-prey hybrid interaction evidence used in manual assertion
has GO evidence code: IPI
definition: A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T16:56:39Z
has_broad_synonym: GST pull-down assay evidence
has_obo_namespace: eco
id: ECO:0005640

Axiom
annotated source: glutathione S-transferase pull-down assay evidence used in manual assertion
annotated property: subClassOf
annotated target: bait-prey hybrid interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: glutathione S-transferase pull-down assay evidence used in manual assertion
annotated property: definition
annotated target: A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

beta-glucuronidase reporter gene assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: beta-glucuronidase reporter gene assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence used in manual assertion
subclass of: beta-glucuronidase reporter gene assay evidence
has GO evidence code: IEP
definition: A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T16:58:29Z
has_broad_synonym: GUS reporter gene assay evidence
has_obo_namespace: eco
id: ECO:0005641

Axiom
annotated source: beta-glucuronidase reporter gene assay evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

Axiom
annotated source: beta-glucuronidase reporter gene assay evidence used in manual assertion
annotated property: definition
annotated target: A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: heteronuclear single quantum coherence spectroscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: heteronuclear single quantum coherence spectroscopy evidence
subclass of: nuclear magnetic resonance spectroscopy evidence used in manual assertion
has GO evidence code: EXP
definition: A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T23:10:13Z
has_broad_synonym: HSQC evidence
has_obo_namespace: eco
id: ECO:0005642

Axiom
annotated source: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: nuclear magnetic resonance spectroscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

hydroxyl-radical footprinting evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: hydroxyl-radical footprinting evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: hydroxyl-radical footprinting evidence
subclass of: nucleic acid binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of hydroxyl-radical footprinting evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T23:14:48Z
has_obo_namespace: eco
id: ECO:0005643

Axiom
annotated source: hydroxyl-radical footprinting evidence used in manual assertion
annotated property: subClassOf
annotated target: nucleic acid binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: hydroxyl-radical footprinting evidence used in manual assertion
annotated property: definition
annotated target: A type of hydroxyl-radical footprinting evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

immunoprecipitation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunoprecipitation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: immunoprecipitation evidence
subclass of: protein binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of immunoprecipitation evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T23:20:49Z
has_broad_synonym: immunoprecipitation
has_obo_namespace: eco
id: ECO:0005644

Axiom
annotated source: immunoprecipitation evidence used in manual assertion
annotated property: subClassOf
annotated target: protein binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunoprecipitation evidence used in manual assertion
annotated property: definition
annotated target: A type of immunoprecipitation evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

interferometric reflectance imaging sensor evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: interferometric reflectance imaging sensor evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: interferometric reflectance imaging sensor evidence
has GO evidence code: EXP
definition: A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T23:27:58Z
has_broad_synonym: IRIS evidence
has_broad_synonym: SRIB evidence
has_broad_synonym: spectral reflectance imaging biosensor evidence
has_obo_namespace: eco
id: ECO:0005645

Axiom
annotated source: interferometric reflectance imaging sensor evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: interferometric reflectance imaging sensor evidence used in manual assertion
annotated property: definition
annotated target: A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

interferometric reflectance imaging sensor evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: interferometric reflectance imaging sensor evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: interferometric reflectance imaging sensor evidence
subclass of: ECO_0007816
has GO evidence code: IEA
definition: A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T23:29:23Z
has_broad_synonym: IRIS evidence
has_broad_synonym: SRIB evidence
has_broad_synonym: spectral reflectance imaging biosensor evidence
has_obo_namespace: eco
id: ECO:0005646

Axiom
annotated source: interferometric reflectance imaging sensor evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007816
is_inferred: true

Axiom
annotated source: interferometric reflectance imaging sensor evidence used in automatic assertion
annotated property: definition
annotated target: A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

isothermal titration calorimetry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: isothermal titration calorimetry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: isothermal titration calorimetry evidence
subclass of: affinity evidence used in manual assertion
has GO evidence code: IPI
definition: A type of isothermal titration calorimetry evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T23:36:26Z
has_broad_synonym: ITC evidence
has_obo_namespace: eco
id: ECO:0005647

Axiom
annotated source: isothermal titration calorimetry evidence used in manual assertion
annotated property: subClassOf
annotated target: affinity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: isothermal titration calorimetry evidence used in manual assertion
annotated property: definition
annotated target: A type of isothermal titration calorimetry evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

luciferase reporter gene assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: luciferase reporter gene assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence used in manual assertion
subclass of: luciferase reporter gene assay evidence
has GO evidence code: IEP
definition: A type of luciferase reporter gene assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T23:44:52Z
has_obo_namespace: eco
id: ECO:0005648

Axiom
annotated source: luciferase reporter gene assay evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

Axiom
annotated source: luciferase reporter gene assay evidence used in manual assertion
annotated property: definition
annotated target: A type of luciferase reporter gene assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

machine learning prediction of motif instance evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: machine learning prediction of motif instance evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: match to sequence model evidence used in manual assertion
subclass of: machine learning prediction of motif instance evidence
has GO evidence code: ISM
definition: A type of machine learning prediction of motif instance evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-06T23:51:30Z
has_obo_namespace: eco
id: ECO:0005649

Axiom
annotated source: machine learning prediction of motif instance evidence used in manual assertion
annotated property: subClassOf
annotated target: match to sequence model evidence used in manual assertion
is_inferred: true

Axiom
annotated source: machine learning prediction of motif instance evidence used in manual assertion
annotated property: definition
annotated target: A type of machine learning prediction of motif instance evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

machine learning prediction of motif instance evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: machine learning prediction of motif instance evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: match to sequence model evidence used in automatic assertion
subclass of: machine learning prediction of motif instance evidence
has GO evidence code: IEA
definition: A type of machine learning prediction of motif instance evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T23:54:00Z
has_obo_namespace: eco
id: ECO:0005650

Axiom
annotated source: machine learning prediction of motif instance evidence used in automatic assertion
annotated property: subClassOf
annotated target: match to sequence model evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: machine learning prediction of motif instance evidence used in automatic assertion
annotated property: definition
annotated target: A type of machine learning prediction of motif instance evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence
subclass of: ECO_0007819
has GO evidence code: IEA
definition: A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-06T23:57:30Z
has_broad_synonym: MALDI-TOF mass spectrometry evidence
has_broad_synonym: MALDI-TOF-MS evidence
has_obo_namespace: eco
id: ECO:0005651

Axiom
annotated source: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007819
is_inferred: true

Axiom
annotated source: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in automatic assertion
annotated property: definition
annotated target: A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
subclass of: nucleic acid binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T14:42:28Z
has_broad_synonym: MPE-EDTA Fe(II) footprinting evidence
has_broad_synonym: Methidiumpropyl-EDTA Fe(II) footprinting evidence
has_obo_namespace: eco
has_related_synonym: MPE Fe(II) footprinting
id: ECO:0005652

Axiom
annotated source: methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in manual assertion
annotated property: subClassOf
annotated target: nucleic acid binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in manual assertion
annotated property: definition
annotated target: A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

northern assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: northern blot evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: northern blot evidence
subclass of: transcript expression evidence used in manual assertion
has GO evidence code: IEP
definition: A type of northern assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T14:48:03Z
has_broad_synonym: RNA blot evidence
has_broad_synonym: northern assay evidence
has_obo_namespace: eco
has_related_synonym: transcript levels (e.g. Northerns)
id: ECO:0005653

Axiom
annotated source: northern assay evidence used in manual assertion
annotated property: subClassOf
annotated target: transcript expression evidence used in manual assertion
is_inferred: true

Axiom
annotated source: northern assay evidence used in manual assertion
annotated property: definition
annotated target: A type of northern assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

phylogenetic footprinting evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: phylogenetic footprinting evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: phylogenetic footprinting evidence
subclass of: motif discovery evidence used in manual assertion
has GO evidence code: ISA
definition: A type of phylogenetic footprinting evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T14:50:52Z
has_obo_namespace: eco
id: ECO:0005654

Axiom
annotated source: phylogenetic footprinting evidence used in manual assertion
annotated property: subClassOf
annotated target: motif discovery evidence used in manual assertion
is_inferred: true

Axiom
annotated source: phylogenetic footprinting evidence used in manual assertion
annotated property: definition
annotated target: A type of phylogenetic footprinting evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

phylogenetic footprinting evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: phylogenetic footprinting evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: phylogenetic footprinting evidence
subclass of: motif discovery evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of phylogenetic footprinting evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-09T14:51:55Z
has_obo_namespace: eco
id: ECO:0005655

Axiom
annotated source: phylogenetic footprinting evidence used in automatic assertion
annotated property: subClassOf
annotated target: motif discovery evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: phylogenetic footprinting evidence used in automatic assertion
annotated property: definition
annotated target: A type of phylogenetic footprinting evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

methylation interference footprinting evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: methylation interference footprinting evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: methylation interference footprinting evidence
subclass of: nucleic acid binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of methylation interference footprinting evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T14:55:25Z
has_exact_synonym: premethylation interference footprinting evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0005656

Axiom
annotated source: methylation interference footprinting evidence used in manual assertion
annotated property: subClassOf
annotated target: nucleic acid binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: methylation interference footprinting evidence used in manual assertion
annotated property: definition
annotated target: A type of methylation interference footprinting evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

primer extension assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: primer extension assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: transcript expression evidence used in manual assertion
subclass of: primer extension assay evidence
has GO evidence code: IEP
definition: A type of primer extension assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T14:58:38Z
has_obo_namespace: eco
id: ECO:0005657

Axiom
annotated source: primer extension assay evidence used in manual assertion
annotated property: subClassOf
annotated target: transcript expression evidence used in manual assertion
is_inferred: true

Axiom
annotated source: primer extension assay evidence used in manual assertion
annotated property: definition
annotated target: A type of primer extension assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

position-specific scoring matrix motif search evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: position-specific scoring matrix motif search evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: motif similarity evidence used in manual assertion
subclass of: position-specific scoring matrix motif search evidence
has GO evidence code: ISM
definition: A type of position-specific scoring matrix motif search evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T15:01:31Z
has_broad_synonym: PSSM motif search evidence
has_obo_namespace: eco
id: ECO:0005658

Axiom
annotated source: position-specific scoring matrix motif search evidence used in manual assertion
annotated property: subClassOf
annotated target: motif similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: position-specific scoring matrix motif search evidence used in manual assertion
annotated property: definition
annotated target: A type of position-specific scoring matrix motif search evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

position-specific scoring matrix motif search evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: position-specific scoring matrix motif search evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: motif similarity evidence used in automatic assertion
subclass of: position-specific scoring matrix motif search evidence
has GO evidence code: IEA
definition: A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-09T15:02:31Z
has_broad_synonym: PSSM motif search evidence
has_obo_namespace: eco
id: ECO:0005659

Axiom
annotated source: position-specific scoring matrix motif search evidence used in automatic assertion
annotated property: subClassOf
annotated target: motif similarity evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: position-specific scoring matrix motif search evidence used in automatic assertion
annotated property: definition
annotated target: A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

quantitative polymerase chain reaction evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: quantitative polymerase chain reaction evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: quantitative polymerase chain reaction evidence
subclass of: experimental evidence used in manual assertion
has GO evidence code: EXP
definition: A type of quantitative polymerase chain reaction evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T15:09:01Z
has_obo_namespace: eco
id: ECO:0005660

Axiom
annotated source: quantitative polymerase chain reaction evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: quantitative polymerase chain reaction evidence used in manual assertion
annotated property: definition
annotated target: A type of quantitative polymerase chain reaction evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

rapid amplification of cDNA ends polymerase chain reaction evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: rapid amplification of cDNA ends polymerase chain reaction evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: rapid amplification of cDNA ends polymerase chain reaction evidence
has GO evidence code: EXP
definition: A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T15:19:20Z
has_broad_synonym: RACE PCR evidence
has_obo_namespace: eco
id: ECO:0005661

Axiom
annotated source: rapid amplification of cDNA ends polymerase chain reaction evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: rapid amplification of cDNA ends polymerase chain reaction evidence used in manual assertion
annotated property: definition
annotated target: A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

regular expression motif search evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: regular expression motif search evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: motif similarity evidence used in manual assertion
subclass of: regular expression motif search evidence
has GO evidence code: ISM
definition: A type of regular expression motif search evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T16:13:55Z
has_obo_namespace: eco
id: ECO:0005662

Axiom
annotated source: regular expression motif search evidence used in manual assertion
annotated property: subClassOf
annotated target: motif similarity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: regular expression motif search evidence used in manual assertion
annotated property: definition
annotated target: A type of regular expression motif search evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

regular expression motif search evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: regular expression motif search evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: motif similarity evidence used in automatic assertion
subclass of: regular expression motif search evidence
has GO evidence code: IEA
definition: A type of regular expression motif search evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-09T16:15:03Z
has_obo_namespace: eco
id: ECO:0005663

Axiom
annotated source: regular expression motif search evidence used in automatic assertion
annotated property: subClassOf
annotated target: motif similarity evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: regular expression motif search evidence used in automatic assertion
annotated property: definition
annotated target: A type of regular expression motif search evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

RNA sequencing assay evidence used in manual assertion
type: Class
created_by: snadendla
creation_date: 2016-05-09T16:18:35Z
has_obo_namespace: eco
id: ECO:0005664
comment: Use ECO:0006068 (RNA-seq evidence used in manual assertion) in place of this term.
deprecated: true

RNA sequencing assay evidence used in automatic assertion
type: Class
created_by: snadendla
creation_date: 2016-05-09T16:19:38Z
has_obo_namespace: eco
id: ECO:0005665
comment: Use ECO:0006069 (RNA-seq evidence used in automatic assertion) in place of this term.
deprecated: true

S1 nuclease protection assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: S1 nuclease protection assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: nuclease protection assay evidence used in manual assertion
subclass of: S1 nuclease protection assay evidence
has GO evidence code: EXP
definition: A type of S1 nuclease protection assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T16:22:58Z
has_obo_namespace: eco
id: ECO:0005666

Axiom
annotated source: S1 nuclease protection assay evidence used in manual assertion
annotated property: subClassOf
annotated target: nuclease protection assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: S1 nuclease protection assay evidence used in manual assertion
annotated property: definition
annotated target: A type of S1 nuclease protection assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

site-directed mutagenesis phenotypic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: site-directed mutagenesis phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mutant phenotype evidence used in manual assertion
subclass of: site-directed mutagenesis phenotypic evidence
has GO evidence code: IMP
definition: A type of site-directed phenotypic mutagenesis evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T16:29:13Z
has_broad_synonym: site directed mutagenesis evidence
has_exact_synonym: site-directed mutagenesis evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0005667

Axiom
annotated source: site-directed mutagenesis phenotypic evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

Axiom
annotated source: site-directed mutagenesis phenotypic evidence used in manual assertion
annotated property: definition
annotated target: A type of site-directed phenotypic mutagenesis evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

survival rate analysis evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: survival rate analysis evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: knockout evidence used in manual assertion
subclass of: survival rate analysis evidence
has GO evidence code: IMP
definition: A type of survival rate analysis evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T16:31:08Z
has_obo_namespace: eco
id: ECO:0005668

Axiom
annotated source: survival rate analysis evidence used in manual assertion
annotated property: subClassOf
annotated target: knockout evidence used in manual assertion
is_inferred: true

Axiom
annotated source: survival rate analysis evidence used in manual assertion
annotated property: definition
annotated target: A type of survival rate analysis evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

ultraviolet light footprinting evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: ultraviolet light footprinting evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: ultraviolet light footprinting evidence
subclass of: nucleic acid binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of ultraviolet light footprinting evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-09T16:33:44Z
has_obo_namespace: eco
has_related_synonym: UV footprinting
id: ECO:0005669

Axiom
annotated source: ultraviolet light footprinting evidence used in manual assertion
annotated property: subClassOf
annotated target: nucleic acid binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: ultraviolet light footprinting evidence used in manual assertion
annotated property: definition
annotated target: A type of ultraviolet light footprinting evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

x-ray crystallography evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: x-ray crystallography evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: crystallography evidence used in manual assertion
subclass of: x-ray crystallography evidence
has GO evidence code: EXP
definition: A type of x-ray crystallography evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-10T11:53:00Z
has_obo_namespace: eco
id: ECO:0005670

Axiom
annotated source: x-ray crystallography evidence used in manual assertion
annotated property: subClassOf
annotated target: crystallography evidence used in manual assertion
is_inferred: true

Axiom
annotated source: x-ray crystallography evidence used in manual assertion
annotated property: definition
annotated target: A type of x-ray crystallography evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

x-ray crystallography evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: x-ray crystallography evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: x-ray crystallography evidence
subclass of: ECO_0007374
has GO evidence code: IEA
definition: A type of x-ray crystallography evidence that is used in an automatic assertion.
created_by: snadendla
creation_date: 2016-05-10T11:54:03Z
has_obo_namespace: eco
id: ECO:0005671

Axiom
annotated source: x-ray crystallography evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007374
is_inferred: true

Axiom
annotated source: x-ray crystallography evidence used in automatic assertion
annotated property: definition
annotated target: A type of x-ray crystallography evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

xylE reporter gene assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: xylE reporter gene assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence used in manual assertion
subclass of: xylE reporter gene assay evidence
has GO evidence code: IEP
definition: A type of xylE reporter gene assay evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-10T11:57:15Z
has_obo_namespace: eco
id: ECO:0005672

Axiom
annotated source: xylE reporter gene assay evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

Axiom
annotated source: xylE reporter gene assay evidence used in manual assertion
annotated property: definition
annotated target: A type of xylE reporter gene assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

ad-hoc qualitative phenotype observation evidence
type: Class
subclass of: experimental phenotypic evidence
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2016-05-10T12:57:41Z
has_obo_namespace: eco
id: ECO:0005673

Axiom
annotated source: ad-hoc qualitative phenotype observation evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:15150239

ad-hoc qualitative phenotype observation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: ad-hoc qualitative phenotype observation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: ad-hoc qualitative phenotype observation evidence
subclass of: ECO_0007634
has GO evidence code: EXP
definition: A type of ad-hoc qualitative phenotype observation that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-10T14:28:47Z
has_obo_namespace: eco
id: ECO:0005674

Axiom
annotated source: ad-hoc qualitative phenotype observation evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: ad-hoc qualitative phenotype observation evidence used in manual assertion
annotated property: definition
annotated target: A type of ad-hoc qualitative phenotype observation that is used in a manual assertion.
database_cross_reference: ECO:SN

ad-hoc quantitative phenotype observation evidence
type: Class
subclass of: experimental phenotypic evidence
definition: 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.
ontology term requester: CollecTF
created_by: snadendla
creation_date: 2016-05-10T14:30:50Z
has_obo_namespace: eco
id: ECO:0005675

Axiom
annotated source: ad-hoc quantitative phenotype observation evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: PMID:15150239

ad-hoc quantitative phenotype observation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: ad-hoc quantitative phenotype observation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: ad-hoc quantitative phenotype observation evidence
subclass of: ECO_0007634
has GO evidence code: EXP
definition: A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion.
created_by: snadendla
creation_date: 2016-05-10T14:34:50Z
has_obo_namespace: eco
id: ECO:0005676

Axiom
annotated source: ad-hoc quantitative phenotype observation evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: ad-hoc quantitative phenotype observation evidence used in manual assertion
annotated property: definition
annotated target: A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

dilution assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of 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.
has_exact_synonym: critical dilution assay
has_exact_synonym: spot assay
comment: 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.

Axiom
annotated source: dilution assay evidence
annotated property: definition
annotated target: A type of 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.
database_cross_reference: http://www.sciencedirect.com/science/article/pii/016770129400068I

enzymatic activity assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: enzymatic activity assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: enzymatic activity assay evidence
subclass of: direct assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of enzyme assay evidence that is used in a manual assertion.
has_broad_synonym: enzyme assays
has_obo_namespace: eco
id: ECO:0005801

Axiom
annotated source: enzymatic activity assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: enzymatic activity assay evidence used in manual assertion
annotated property: definition
annotated target: A type of enzyme assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

cell transfection experiment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cell transfection experiment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: cell transfection experiment evidence
has GO evidence code: EXP
definition: A type of cell transfection experiment evidence that is used in a manual assertion.
has_obo_namespace: eco
id: ECO:0005802

Axiom
annotated source: cell transfection experiment evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cell transfection experiment evidence used in manual assertion
annotated property: definition
annotated target: A type of cell transfection experiment evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

motility assay evidence
type: Class
subclass of: direct assay evidence
example of usage: A motility assay at 37 degrees C revealed a non-motile phenotype for all strains, as expected (data not shown).
definition: A type of direct assay evidence where the motility of a cell or cells is determined.
has_obo_namespace: eco
id: ECO:0005803

Axiom
annotated source: motility assay evidence
annotated property: example of usage
annotated target: A motility assay at 37 degrees C revealed a non-motile phenotype for all strains, as expected (data not shown).
database_cross_reference: PMID:20830609

Axiom
annotated source: motility assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where the motility of a cell or cells is determined.
database_cross_reference: ECO:SN

immunofluorescence evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunofluorescence evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: immunofluorescence evidence
subclass of: experimental evidence used in manual assertion
has GO evidence code: EXP
definition: A type of immunofluorescence evidence that is used in a manual assertion.
has_broad_synonym: immunofluorescence
has_obo_namespace: eco
id: ECO:0005804

Axiom
annotated source: immunofluorescence evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunofluorescence evidence used in manual assertion
annotated property: definition
annotated target: A type of immunofluorescence evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

yeast 2-hybrid evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: yeast 2-hybrid evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: yeast 2-hybrid evidence
subclass of: bait-prey hybrid interaction evidence used in manual assertion
has GO evidence code: IPI
definition: A type of yeast 2-hybrid evidence that is used in a manual assertion.
has_broad_synonym: yeast two-hybrid assay
has_obo_namespace: eco
id: ECO:0005805

Axiom
annotated source: yeast 2-hybrid evidence used in manual assertion
annotated property: subClassOf
annotated target: bait-prey hybrid interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: yeast 2-hybrid evidence used in manual assertion
annotated property: definition
annotated target: A type of yeast 2-hybrid evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

Cya fusion reporter assay evidence
type: Class
subclass of: ectopic expression evidence
subclass of: reporter gene assay evidence
definition: 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.
created_by: rctauber
creation_date: 2016-06-15T08:42:16Z
has_obo_namespace: eco
id: ECO:0006001

Axiom
annotated source: Cya fusion reporter assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:10217833
database_cross_reference: PMID:14702323

Cya fusion reporter assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Cya fusion reporter assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence used in manual assertion
subclass of: ectopic expression evidence used in manual assertion
subclass of: Cya fusion reporter assay evidence
has GO evidence code: IEP
definition: A type of Cya fusion reporter assay evidence that is used in a manual assertion.
ontology term requester: CollecTF
created_by: rctauber
creation_date: 2010-06-15T08:44:10Z
has_obo_namespace: eco
id: ECO:0006002

Axiom
annotated source: Cya fusion reporter assay evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

Axiom
annotated source: Cya fusion reporter assay evidence used in manual assertion
annotated property: subClassOf
annotated target: ectopic expression evidence used in manual assertion
is_inferred: true

Axiom
annotated source: Cya fusion reporter assay evidence used in manual assertion
annotated property: definition
annotated target: A type of Cya fusion reporter assay evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

electron microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: electron microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: microscopy evidence used in manual assertion
subclass of: electron microscopy evidence
has GO evidence code: IDA
definition: A type of electron microscopy evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-10-12T12:32:29Z
has_obo_namespace: eco
id: ECO:0006003

Axiom
annotated source: electron microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: electron microscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of electron microscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

super-resolution microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: super-resolution microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: microscopy evidence used in manual assertion
subclass of: super-resolution microscopy evidence
has GO evidence code: IDA
definition: A type of super-resolution microscopy evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-10-12T12:32:29Z
has_obo_namespace: eco
id: ECO:0006004

Axiom
annotated source: super-resolution microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: super-resolution microscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of super-resolution microscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

fractionation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: fractionation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: fractionation evidence
subclass of: direct assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of fractionation evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-10-12T12:32:29Z
has_obo_namespace: eco
id: ECO:0006005

Axiom
annotated source: fractionation evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: fractionation evidence used in manual assertion
annotated property: definition
annotated target: A type of fractionation evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

electrophysiology assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: electrophysiology assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: electrophysiology assay evidence
subclass of: direct assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of electrophysiology assay evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-10-12T12:32:29Z
has_obo_namespace: eco
id: ECO:0006006

Axiom
annotated source: electrophysiology assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: electrophysiology assay evidence used in manual assertion
annotated property: definition
annotated target: A type of electrophysiology assay evidence that is used in a manual assertion.
comment: ECO:RCT

chromatin immunoprecipitation-chip evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: chromatin immunoprecipitation-chip evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: chromatin immunoprecipitation-chip evidence
subclass of: immunoprecipitation evidence used in manual assertion
has GO evidence code: IPI
definition: A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-10-21T11:55:53Z
has_broad_synonym: ChIP-chip evidence
has_broad_synonym: ChIP-on-chip evidence
has_obo_namespace: eco
id: ECO:0006007

Axiom
annotated source: chromatin immunoprecipitation-chip evidence used in manual assertion
annotated property: subClassOf
annotated target: immunoprecipitation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: chromatin immunoprecipitation-chip evidence used in manual assertion
annotated property: definition
annotated target: A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

chromatin immunoprecipitation- exonuclease evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: chromatin immunoprecipitation- exonuclease evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: chromatin immunoprecipitation- exonuclease evidence
subclass of: immunoprecipitation evidence used in manual assertion
has GO evidence code: IPI
definition: A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-10-21T11:55:53Z
has_broad_synonym: ChIP-exo
has_obo_namespace: eco
id: ECO:0006008

Axiom
annotated source: chromatin immunoprecipitation- exonuclease evidence used in manual assertion
annotated property: subClassOf
annotated target: immunoprecipitation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: chromatin immunoprecipitation- exonuclease evidence used in manual assertion
annotated property: definition
annotated target: A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

chromatin immunoprecipitation-seq evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: chromatin immunoprecipitation-seq evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: chromatin immunoprecipitation-seq evidence
subclass of: immunoprecipitation evidence used in manual assertion
has GO evidence code: IPI
definition: A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-10-21T11:55:53Z
has_broad_synonym: ChIP-SEQ evidence
has_broad_synonym: ChIP-seq evidence
has_obo_namespace: eco
id: ECO:0006009

Axiom
annotated source: chromatin immunoprecipitation-seq evidence used in manual assertion
annotated property: subClassOf
annotated target: immunoprecipitation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: chromatin immunoprecipitation-seq evidence used in manual assertion
annotated property: definition
annotated target: A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

mRNA interactome capture evidence
type: Class
subclass of: nucleic acid binding evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002436
definition: 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.
created_by: rctauber
creation_date: 2016-10-21T12:28:17Z
has_exact_synonym: ultraviolet light cross-linking RNA binding evidence
has_obo_namespace: eco
id: ECO:0006010

Axiom
annotated source: mRNA interactome capture evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:27729395

mRNA interactome capture evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: mRNA interactome capture evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mRNA interactome capture evidence
subclass of: nucleic acid binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of mRNA interactome capture evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-10-21T12:28:17Z
has_broad_synonym: ultraviolet light cross-linking RNA binding evidence
has_obo_namespace: eco
id: ECO:0006011

Axiom
annotated source: mRNA interactome capture evidence used in manual assertion
annotated property: subClassOf
annotated target: nucleic acid binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: mRNA interactome capture evidence used in manual assertion
annotated property: definition
annotated target: A type of mRNA interactome capture evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

patch-clamp recording evidence
type: Class
subclass of: electrophysiology assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0005216
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002177
definition: 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.
created_by: rctauber
creation_date: 2016-11-28T11:44:05Z
has_obo_namespace: eco
id: ECO:0006012

Axiom
annotated source: patch-clamp recording evidence
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT

patch-clamp recording evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: patch-clamp recording evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: electrophysiology assay evidence used in manual assertion
subclass of: patch-clamp recording evidence
has GO evidence code: IDA
definition: A type of patch-clamp recording evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-11-28T11:44:05Z
has_obo_namespace: eco
id: ECO:0006013

Axiom
annotated source: patch-clamp recording evidence used in manual assertion
annotated property: definition
annotated target: A type of patch-clamp recording evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

whole-cell patch-clamp recording evidence
type: Class
subclass of: patch-clamp recording evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002178
definition: 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.
created_by: rctauber
creation_date: 2016-11-28T11:44:05Z
has_obo_namespace: eco
id: ECO:0006014

Axiom
annotated source: whole-cell patch-clamp recording evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:27341060

whole-cell patch-clamp recording evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: whole-cell patch-clamp recording evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: patch-clamp recording evidence used in manual assertion
subclass of: whole-cell patch-clamp recording evidence
has GO evidence code: IDA
definition: A type of whole-cell patch-clamp recording evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-11-28T11:44:05Z
has_obo_namespace: eco
id: ECO:0006015

Axiom
annotated source: whole-cell patch-clamp recording evidence used in manual assertion
annotated property: definition
annotated target: A type of whole-cell patch-clamp recording evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

author statement from published clinical study
type: Class
subclass of: author statement supported by traceable reference
definition: A type of traceable author statement that is based on a publication about a clinical study.
created_by: rctauber
creation_date: 2016-11-30T09:44:47Z
has_exact_synonym: published clinical study evidence
has_obo_namespace: eco
has_related_synonym: traceable author statement from published clinical study
id: ECO:0006016

author statement from published clinical study used in manual assertion
type: Class
equivalent class: Class
  intersection of: author statement from published clinical study
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: author statement supported by traceable reference used in manual assertion
subclass of: author statement from published clinical study
has GO evidence code: TAS
definition: A type of author statement from published clinical study that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-11-30T09:44:47Z
has_broad_synonym: published clinical study evidence
has_exact_synonym: PCS
has_obo_namespace: eco
id: ECO:0006017
comment: 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.

Axiom
annotated source: author statement from published clinical study used in manual assertion
annotated property: subClassOf
annotated target: author statement supported by traceable reference used in manual assertion
is_inferred: true

Axiom
annotated source: author statement from published clinical study used in manual assertion
annotated property: has_exact_synonym
annotated target: PCS
database_cross_reference: HPO:PCS

inference based on individual clinical experience
type: Class
subclass of: curator inference
definition: A type of curator inference that is based on the individual clinical experience of a clinician
created_by: rctauber
creation_date: 2016-11-30T09:44:47Z
has_exact_synonym: individual clinical experience evidence
has_obo_namespace: eco
id: ECO:0006018

inference based on individual clinical experience used in manual assertion
type: Class
equivalent class: Class
  intersection of: inference based on individual clinical experience
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: curator inference used in manual assertion
subclass of: inference based on individual clinical experience
has GO evidence code: IC
definition: A type of inference based on individual clinical experience that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-11-30T09:44:47Z
has_broad_synonym: individual clinical experience evidence
has_exact_synonym: ICE
has_obo_namespace: eco
id: ECO:0006019
comment: 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.

Axiom
annotated source: inference based on individual clinical experience used in manual assertion
annotated property: subClassOf
annotated target: curator inference used in manual assertion
is_inferred: true

Axiom
annotated source: inference based on individual clinical experience used in manual assertion
annotated property: has_exact_synonym
annotated target: ICE
database_cross_reference: HPO:ICE

biofilm formation assay evidence
type: Class
subclass of: cell proliferation assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0042710
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000978
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0001147
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: OBI_0001285
definition: A type of cell proliferation assay evidence in which biofilm growth is monitored and detected from attachment to development.
created_by: rctauber
creation_date: 2016-12-05T09:33:18Z
has_exact_synonym: biofilm assay evidence
has_obo_namespace: eco
id: ECO:0006020

Axiom
annotated source: biofilm formation assay evidence
annotated property: definition
annotated target: A type of cell proliferation assay evidence in which biofilm growth is monitored and detected from attachment to development.
database_cross_reference: PMID:10547784

biofilm formation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: biofilm formation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: biofilm formation assay evidence
has GO evidence code: IDA
definition: A type of biofilm formation assay evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-12-05T09:33:18Z
has_obo_namespace: eco
id: ECO:0006021

Axiom
annotated source: biofilm formation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: biofilm formation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of biofilm formation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

microtiter plate biofilm assay evidence
type: Class
subclass of: biofilm formation assay evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000978
    intersection of: Restriction
      on property: has participant
      some values from: OBI_0000192
definition: 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.
created_by: rctauber
creation_date: 2016-12-05T09:33:18Z
has_exact_synonym: 96-well biofilm assay evidence
has_obo_namespace: eco
id: ECO:0006022

Axiom
annotated source: microtiter plate biofilm assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:10547784

microtiter plate biofilm assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: microtiter plate biofilm assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: biofilm formation assay evidence used in manual assertion
subclass of: microtiter plate biofilm assay evidence
has GO evidence code: IDA
definition: A type of microtiter plate biofilm assay evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-12-05T09:33:18Z
has_obo_namespace: eco
id: ECO:0006023

Axiom
annotated source: microtiter plate biofilm assay evidence used in manual assertion
annotated property: subClassOf
annotated target: biofilm formation assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: microtiter plate biofilm assay evidence used in manual assertion
annotated property: definition
annotated target: A type of microtiter plate biofilm assay evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

air-liquid interface assay evidence
type: Class
subclass of: biofilm formation assay evidence
definition: 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.
created_by: rctauber
creation_date: 2016-12-05T09:33:18Z
has_exact_synonym: ALI biofilm assay evidence
has_obo_namespace: eco
id: ECO:0006024
comment: Tilting of the plate positions the air-liquid interface on a clear portion to improve visability.

Axiom
annotated source: air-liquid interface assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18770545

air-liquid interface assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: air-liquid interface assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: biofilm formation assay evidence used in manual assertion
subclass of: air-liquid interface assay evidence
has GO evidence code: IDA
definition: A type of air-liquid interface assay evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-12-05T09:33:18Z
has_broad_synonym: ALI biofilm assay evidence
has_obo_namespace: eco
id: ECO:0006025

Axiom
annotated source: air-liquid interface assay evidence used in manual assertion
annotated property: subClassOf
annotated target: biofilm formation assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: air-liquid interface assay evidence used in manual assertion
annotated property: definition
annotated target: A type of air-liquid interface assay evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

colony biofilm assay evidence
type: Class
subclass of: biofilm formation assay evidence
definition: 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.
created_by: rctauber
creation_date: 2016-12-05T09:33:18Z
has_obo_namespace: eco
id: ECO:0006026
comment: The plates commonly contain different carbon sources or antibiotic treatments to observe properties of the cells.

Axiom
annotated source: colony biofilm assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18770545

colony biofilm assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: colony biofilm assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: biofilm formation assay evidence used in manual assertion
subclass of: colony biofilm assay evidence
has GO evidence code: IDA
definition: A type of colony biofilm assay evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-12-05T09:33:18Z
has_obo_namespace: eco
id: ECO:0006027

Axiom
annotated source: colony biofilm assay evidence used in manual assertion
annotated property: subClassOf
annotated target: biofilm formation assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: colony biofilm assay evidence used in manual assertion
annotated property: definition
annotated target: A type of colony biofilm assay evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

Kadouri drip-fed biofilm assay evidence
type: Class
subclass of: biofilm formation assay evidence
definition: 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.
created_by: rctauber
creation_date: 2016-12-05T09:33:18Z
has_obo_namespace: eco
id: ECO:0006028

Axiom
annotated source: Kadouri drip-fed biofilm assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18770545

Kadouri drip-fed biofilm assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Kadouri drip-fed biofilm assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: biofilm formation assay evidence used in manual assertion
subclass of: Kadouri drip-fed biofilm assay evidence
has GO evidence code: IDA
definition: A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-12-05T09:33:18Z
has_obo_namespace: eco
id: ECO:0006029

Axiom
annotated source: Kadouri drip-fed biofilm assay evidence used in manual assertion
annotated property: subClassOf
annotated target: biofilm formation assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: Kadouri drip-fed biofilm assay evidence used in manual assertion
annotated property: definition
annotated target: A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

co-immunoprecipitation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: co-immunoprecipitation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: co-immunoprecipitation evidence
subclass of: immunoprecipitation evidence used in manual assertion
has GO evidence code: IPI
definition: A type of co-immunoprecipitation evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2016-01-13T11:32:26Z
has_broad_synonym: co-immunoprecipitation
has_obo_namespace: eco
id: ECO:0006030

Axiom
annotated source: co-immunoprecipitation evidence used in manual assertion
annotated property: subClassOf
annotated target: immunoprecipitation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: co-immunoprecipitation evidence used in manual assertion
annotated property: definition
annotated target: A type of co-immunoprecipitation evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

immunolocalization evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunolocalization evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: immunolocalization evidence
subclass of: microscopy evidence used in manual assertion
has GO evidence code: IDA
definition: A type of immunolocalization evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-01-23T07:54:37Z
has_broad_synonym: immunolocalization
has_obo_namespace: eco
id: ECO:0006031

Axiom
annotated source: immunolocalization evidence used in manual assertion
annotated property: subClassOf
annotated target: microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunolocalization evidence used in manual assertion
annotated property: definition
annotated target: A type of immunolocalization evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

optogenetic evidence
type: Class
subclass of: experimental phenotypic evidence
definition: A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators.
created_by: rctauber
creation_date: 2017-01-23T11:58:48Z
has_exact_synonym: optogenetic actuator evidence
has_obo_namespace: eco
id: ECO:0006032

Axiom
annotated source: optogenetic evidence
annotated property: definition
annotated target: A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators.
database_cross_reference: GOC:DOS
database_cross_reference: PMID:17035522

optogenetic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: optogenetic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: optogenetic evidence
subclass of: ECO_0007634
has GO evidence code: EXP
definition: A type of optogenetic evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-01-23T11:58:48Z
has_broad_synonym: optogenetic actuator evidence
has_obo_namespace: eco
id: ECO:0006033

Axiom
annotated source: optogenetic evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: optogenetic evidence used in manual assertion
annotated property: definition
annotated target: A type of optogenetic evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

fluorescent sensor evidence
type: Class
subclass of: fluorescence evidence
definition: A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor.
created_by: rctauber
creation_date: 2017-01-23T11:58:48Z
has_obo_namespace: eco
id: ECO:0006034
comment: Examples include sensors for ion concentration and potential difference across a membrane.

Axiom
annotated source: fluorescent sensor evidence
annotated property: definition
annotated target: A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor.
database_cross_reference: GOC:DOS

fluorescent sensor evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: fluorescent sensor evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: fluorescence evidence used in manual assertion
subclass of: fluorescent sensor evidence
has GO evidence code: IDA
definition: A type of fluorescent sensor evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-01-23T11:58:48Z
has_obo_namespace: eco
id: ECO:0006035

Axiom
annotated source: fluorescent sensor evidence used in manual assertion
annotated property: subClassOf
annotated target: fluorescence evidence used in manual assertion
is_inferred: true

Axiom
annotated source: fluorescent sensor evidence used in manual assertion
annotated property: definition
annotated target: A type of fluorescent sensor evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

genetically encoded fluorescent sensor evidence
type: Class
subclass of: fluorescent sensor evidence
definition: A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor.
created_by: rctauber
creation_date: 2017-01-23T11:58:48Z
has_exact_synonym: optogenetic sensor evidence
has_obo_namespace: eco
id: ECO:0006036

Axiom
annotated source: genetically encoded fluorescent sensor evidence
annotated property: definition
annotated target: A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor.
database_cross_reference: GOC:DOS

genetically encoded fluorescent sensor evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: genetically encoded fluorescent sensor evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: fluorescent sensor evidence used in manual assertion
subclass of: genetically encoded fluorescent sensor evidence
has GO evidence code: IDA
definition: A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-01-23T11:58:48Z
has_broad_synonym: optogenetic sensor evidence
has_obo_namespace: eco
id: ECO:0006037

Axiom
annotated source: genetically encoded fluorescent sensor evidence used in manual assertion
annotated property: subClassOf
annotated target: fluorescent sensor evidence used in manual assertion
is_inferred: true

Axiom
annotated source: genetically encoded fluorescent sensor evidence used in manual assertion
annotated property: definition
annotated target: A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

genetically encoded fluorescent electrophysiology assay evidence
type: Class
subclass of: electrophysiology assay evidence
subclass of: fluorescent sensor evidence
definition: A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors.
created_by: rctauber
creation_date: 2017-01-23T11:58:48Z
has_exact_synonym: electrophysiology - optical assay evidence
has_obo_namespace: eco
id: ECO:0006038
comment: Examples include genetically encoded sensors that detect potential difference across plasma membrane.

Axiom
annotated source: genetically encoded fluorescent electrophysiology assay evidence
annotated property: definition
annotated target: A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors.
database_cross_reference: GOC:DOS

genetically encoded fluorescent electrophysiology assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: genetically encoded fluorescent electrophysiology assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: electrophysiology assay evidence used in manual assertion
subclass of: fluorescent sensor evidence used in manual assertion
subclass of: genetically encoded fluorescent electrophysiology assay evidence
has GO evidence code: IDA
definition: A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-01-23T11:58:48Z
has_broad_synonym: electrophysiology - optical assay evidence
has_obo_namespace: eco
id: ECO:0006039

Axiom
annotated source: genetically encoded fluorescent electrophysiology assay evidence used in manual assertion
annotated property: subClassOf
annotated target: electrophysiology assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: genetically encoded fluorescent electrophysiology assay evidence used in manual assertion
annotated property: subClassOf
annotated target: fluorescent sensor evidence used in manual assertion
is_inferred: true

Axiom
annotated source: genetically encoded fluorescent electrophysiology assay evidence used in manual assertion
annotated property: definition
annotated target: A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

genetically encoded fluorescent ion concentration sensor assay evidence
type: Class
subclass of: genetically encoded fluorescent electrophysiology assay evidence
definition: 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.
created_by: rctauber
creation_date: 2017-01-23T11:58:48Z
has_obo_namespace: eco
id: ECO:0006040
comment: Examples include the genetically encoded calcium indicator GCaMP.

Axiom
annotated source: genetically encoded fluorescent ion concentration sensor assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:DOS

genetically encoded fluorescent ion concentration sensor assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: genetically encoded fluorescent ion concentration sensor assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: genetically encoded fluorescent electrophysiology assay evidence used in manual assertion
subclass of: genetically encoded fluorescent ion concentration sensor assay evidence
has GO evidence code: IDA
definition: A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-01-23T11:58:48Z
has_obo_namespace: eco
id: ECO:0006041

Axiom
annotated source: genetically encoded fluorescent ion concentration sensor assay evidence used in manual assertion
annotated property: subClassOf
annotated target: genetically encoded fluorescent electrophysiology assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: genetically encoded fluorescent ion concentration sensor assay evidence used in manual assertion
annotated property: definition
annotated target: A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

cell fractionation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cell fractionation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: cell fractionation evidence
subclass of: fractionation evidence used in manual assertion
has GO evidence code: IDA
definition: A type of cell fractionation evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-02-21T07:26:28Z
has_broad_synonym: cell fractionation
has_obo_namespace: eco
id: ECO:0006042

Axiom
annotated source: cell fractionation evidence used in manual assertion
annotated property: subClassOf
annotated target: fractionation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cell fractionation evidence used in manual assertion
annotated property: definition
annotated target: A type of cell fractionation evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

extracellular recording evidence
type: Class
subclass of: electrophysiology assay evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0001508
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000454
definition: A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons.
created_by: rctauber
creation_date: 2017-02-21T07:26:28Z
has_obo_namespace: eco
id: ECO:0006043

Axiom
annotated source: extracellular recording evidence
annotated property: definition
annotated target: A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons.
database_cross_reference: url:http://www.nature.com/subjects/extracellular-recording

extracellular recording evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: extracellular recording evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: electrophysiology assay evidence used in manual assertion
subclass of: extracellular recording evidence
has GO evidence code: IDA
definition: A type of extracellular recording evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-02-21T07:26:28Z
has_obo_namespace: eco
id: ECO:0006044

Axiom
annotated source: extracellular recording evidence used in manual assertion
annotated property: subClassOf
annotated target: electrophysiology assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: extracellular recording evidence used in manual assertion
annotated property: definition
annotated target: A type of extracellular recording evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

single-unit extracellular recording evidence
type: Class
subclass of: extracellular recording evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002187
definition: A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron.
created_by: rctauber
creation_date: 2017-02-21T07:26:28Z
has_obo_namespace: eco
id: ECO:0006045

Axiom
annotated source: single-unit extracellular recording evidence
annotated property: definition
annotated target: A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron.
database_cross_reference: doi:10.1385/0-89603-185-3:1

single-unit extracellular recording evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: single-unit extracellular recording evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: extracellular recording evidence used in manual assertion
subclass of: single-unit extracellular recording evidence
has GO evidence code: IDA
definition: A type of single-unit extracellular recording evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-02-21T07:26:28Z
has_obo_namespace: eco
id: ECO:0006046

Axiom
annotated source: single-unit extracellular recording evidence used in manual assertion
annotated property: subClassOf
annotated target: extracellular recording evidence used in manual assertion
is_inferred: true

Axiom
annotated source: single-unit extracellular recording evidence used in manual assertion
annotated property: definition
annotated target: A type of single-unit extracellular recording evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

field potential recording evidence
type: Class
subclass of: extracellular recording evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0002189
definition: A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes.
created_by: rctauber
creation_date: 2017-02-21T07:26:28Z
has_narrow_synonym: local field potential recording evidence
has_obo_namespace: eco
id: ECO:0006047

Axiom
annotated source: field potential recording evidence
annotated property: definition
annotated target: A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes.
database_cross_reference: ECO:RCT

field potential recording evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: field potential recording evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: extracellular recording evidence used in manual assertion
subclass of: field potential recording evidence
has GO evidence code: IDA
definition: A type of field potential recording evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-02-21T07:26:28Z
has_obo_namespace: eco
has_related_synonym: local field potential recording evidence
id: ECO:0006048

Axiom
annotated source: field potential recording evidence used in manual assertion
annotated property: subClassOf
annotated target: extracellular recording evidence used in manual assertion
is_inferred: true

Axiom
annotated source: field potential recording evidence used in manual assertion
annotated property: definition
annotated target: A type of field potential recording evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

genetic transformation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: genetic transformation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mutant phenotype evidence used in manual assertion
subclass of: genetic transformation evidence
has GO evidence code: IMP
definition: A type of genetic transformation evidence that is used in a manual assertion
created_by: rctauber
creation_date: 2017-02-21T18:08:58Z
has_obo_namespace: eco
id: ECO:0006049

Axiom
annotated source: genetic transformation evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

Axiom
annotated source: genetic transformation evidence used in manual assertion
annotated property: definition
annotated target: A type of genetic transformation evidence that is used in a manual assertion
database_cross_reference: ECO:RCT

anti-sense experiment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: anti-sense experiment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: anti-sense experiment evidence
subclass of: mutant phenotype evidence used in manual assertion
has GO evidence code: IMP
definition: A type of anti-sense experiment evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-02-21T18:08:58Z
has_broad_synonym: anti-sense experiments
has_obo_namespace: eco
id: ECO:0006050

Axiom
annotated source: anti-sense experiment evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

Axiom
annotated source: anti-sense experiment evidence used in manual assertion
annotated property: definition
annotated target: A type of anti-sense experiment evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

morpholino experiment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: morpholino experiment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: morpholino experiment evidence
subclass of: mutant phenotype evidence used in manual assertion
has GO evidence code: IMP
definition: A type of morpholino experiment evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-02-21T18:08:58Z
has_broad_synonym: anti-sense evidence
has_obo_namespace: eco
id: ECO:0006051

Axiom
annotated source: morpholino experiment evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

Axiom
annotated source: morpholino experiment evidence used in manual assertion
annotated property: definition
annotated target: A type of morpholino experiment evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

RNAi evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: RNAi evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: RNAi evidence
subclass of: mutant phenotype evidence used in manual assertion
has GO evidence code: IMP
definition: A type of RNAi evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-02-21T18:08:58Z
has_broad_synonym: RNAi experiment
has_obo_namespace: eco
id: ECO:0006052

Axiom
annotated source: RNAi evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

Axiom
annotated source: RNAi evidence used in manual assertion
annotated property: definition
annotated target: A type of RNAi evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

pharmacological assay evidence
type: Class
subclass of: experimental phenotypic evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0042221
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: has part
      some values from: OBI_0600007
definition: 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.
created_by: dosumis
creation_date: 2017-03-07T08:51:02Z
has_obo_namespace: eco
id: ECO:0006053

Axiom
annotated source: pharmacological assay evidence
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:DOS

pharmacological assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: pharmacological assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: pharmacological assay evidence
subclass of: ECO_0007634
has GO evidence code: EXP
definition: 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.
created_by: rctauber
creation_date: 2017-03-07T08:51:02Z
has_obo_namespace: eco
id: ECO:0006054

Axiom
annotated source: pharmacological assay evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007634
is_inferred: true

Axiom
annotated source: pharmacological assay evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:DOS

high throughput evidence
type: Class
subclass of: evidence
definition: A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
created_by: mchibucos
creation_date: 2017-03-28T14:48:39Z
has_exact_synonym: HT evidence
has_exact_synonym: high-throughput evidence
has_narrow_synonym: high throughput cell biology evidence
has_narrow_synonym: high throughput screening evidence
has_obo_namespace: eco
id: ECO:0006055
comment: Some relevant articles include: PMID: 23340846, doi:10.1038/nmeth0607-523

Axiom
annotated source: high throughput evidence
annotated property: definition
annotated target: A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
database_cross_reference: ECO:MCC

high throughput evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: high throughput evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: evidence used in manual assertion
subclass of: high throughput evidence
has GO evidence code: HTP
definition: 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.
created_by: rctauber
creation_date: 2017-03-28T14:48:39Z
has_broad_synonym: HT evidence
has_broad_synonym: high-throughput evidence
database_cross_reference: GOECO:HTP
has_exact_synonym: HTP
has_exact_synonym: inferred from high throughput experiment
has_obo_namespace: eco
has_related_synonym: high throughput cell biology evidence
has_related_synonym: high throughput screening evidence
id: ECO:0006056

Axiom
annotated source: high throughput evidence used in manual assertion
annotated property: subClassOf
annotated target: evidence used in manual assertion
is_inferred: true

Axiom
annotated source: high throughput evidence used in manual assertion
annotated property: has GO evidence code
annotated target: HTP
comment: Default

Axiom
annotated source: high throughput evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT

inferred from high throughput experiment
type: Axiom
annotated source: high throughput evidence used in manual assertion
annotated property: database_cross_reference
annotated target: GOECO:HTP

Axiom
annotated source: high throughput evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: HTP
database_cross_reference: GOECO:HTP

Axiom
annotated source: high throughput evidence used in manual assertion
annotated property: has_exact_synonym
annotated target: inferred from high throughput experiment
database_cross_reference: GOECO:HTP

high throughput evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: high throughput evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: evidence used in automatic assertion
subclass of: high throughput evidence
has GO evidence code: IEA
definition: 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.
created_by: rctauber
creation_date: 2017-03-28T14:48:39Z
has_broad_synonym: HT evidence
has_broad_synonym: high-throughput evidence
has_obo_namespace: eco
has_related_synonym: high throughput cell biology evidence
has_related_synonym: high throughput screening evidence
id: ECO:0006057

Axiom
annotated source: high throughput evidence used in automatic assertion
annotated property: subClassOf
annotated target: evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: high throughput evidence used in automatic assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT

high throughput cell biology evidence
type: Class
subclass of: high throughput evidence
definition: A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
created_by: mchibucos
creation_date: 2017-03-28T14:48:39Z
has_obo_namespace: eco
has_related_synonym: omics experiment
id: ECO:0006058
comment: HT methodologies may incorporate techniques from optics, chemistry, biology or image analysis (https://en.wikipedia.org/wiki/High_throughput_biology)

Axiom
annotated source: high throughput cell biology evidence
annotated property: definition
annotated target: A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
database_cross_reference: ECO:MCC

high throughput cell biology evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: high throughput cell biology evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: high throughput evidence used in manual assertion
subclass of: high throughput cell biology evidence
has GO evidence code: HTP
definition: 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.
created_by: rctauber
creation_date: 2017-03-28T14:48:39Z
has_obo_namespace: eco
has_related_synonym: omics experiment
id: ECO:0006059

Axiom
annotated source: high throughput cell biology evidence used in manual assertion
annotated property: subClassOf
annotated target: high throughput evidence used in manual assertion
is_inferred: true

Axiom
annotated source: high throughput cell biology evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT

high throughput cell biology evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: high throughput cell biology evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: high throughput evidence used in automatic assertion
subclass of: high throughput cell biology evidence
has GO evidence code: IEA
definition: 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.
created_by: rctauber
creation_date: 2017-03-28T14:48:39Z
has_obo_namespace: eco
has_related_synonym: omics experiment
id: ECO:0006060

Axiom
annotated source: high throughput cell biology evidence used in automatic assertion
annotated property: subClassOf
annotated target: high throughput evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: high throughput cell biology evidence used in automatic assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT

immunofluorescence wide-field microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunofluorescence wide-field microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: immunofluorescence wide-field microscopy evidence
subclass of: immunofluorescence evidence used in manual assertion
subclass of: wide-field fluorescence microscopy evidence used in manual assertion
has GO evidence code: IDA
definition: 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.
created_by: rctauber
creation_date: 2017-05-15T08:57:07Z
has_broad_synonym: wide-field epifluorescence microscopy evidence
has_obo_namespace: eco
id: ECO:0006061

Axiom
annotated source: immunofluorescence wide-field microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: immunofluorescence evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunofluorescence wide-field microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: wide-field fluorescence microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunofluorescence wide-field microscopy evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057135

wide-field fluorescence microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: wide-field fluorescence microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: wide-field microscopy evidence used in manual assertion
subclass of: wide-field fluorescence microscopy evidence
has GO evidence code: IDA
definition: 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.
created_by: rctauber
creation_date: 2017-05-15T09:01:19Z
has_obo_namespace: eco
id: ECO:0006062

Axiom
annotated source: wide-field fluorescence microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: wide-field microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: wide-field fluorescence microscopy evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:SN
database_cross_reference: url:http://www.bristol.ac.uk/synaptic/research/techniques/widefield.html

over expression analysis evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: over expression analysis evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: over expression analysis evidence
subclass of: genetic transformation evidence used in manual assertion
has GO evidence code: IMP
definition: 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.
created_by: rctauber
creation_date: 2017-05-15T09:03:49Z
has_obo_namespace: eco
has_related_synonym: analysis of overexpression/ectopic expression phenotype
id: ECO:0006063

Axiom
annotated source: over expression analysis evidence used in manual assertion
annotated property: subClassOf
annotated target: genetic transformation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: over expression analysis evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:22419077

cell-free assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cell-free assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: cell-free assay evidence
subclass of: direct assay evidence used in manual assertion
has GO evidence code: IDA
definition: A type of cell-free assay evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-05-15T09:08:17Z
has_broad_synonym: in vitro assay evidence
has_obo_namespace: eco
id: ECO:0006064

Axiom
annotated source: cell-free assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cell-free assay evidence used in manual assertion
annotated property: definition
annotated target: A type of cell-free assay evidence that is used in a manual assertion.
database_cross_reference: PMID:18453125

in vitro cell based assay evidence used in manual assertion
type: Class
created_by: rctauber
creation_date: 2017-05-15T09:11:13Z
has_obo_namespace: eco
id: ECO:0006065
comment: Use children of ECO:0001565 (cell-based assay evidence) in place of this term.
deprecated: true

fluorescence recovery after photobleaching evidence
type: Class
subclass of: fluorescence evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0033036
subclass of: Restriction
  on property: is_specified_output_of
  some values from: fluorescence microscopy
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
definition: 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.
ontology term requester: dosumis
created_by: rctauber
creation_date: 2017-05-16T10:55:40Z
has_exact_synonym: FRAP evidence
has_obo_namespace: eco
id: ECO:0006066
comment: FRAP is a fluorescence microscopy-based technique.

Axiom
annotated source: fluorescence recovery after photobleaching evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:26314367

Axiom
annotated source: fluorescence recovery after photobleaching evidence
annotated property: comment
annotated target: FRAP is a fluorescence microscopy-based technique.
database_cross_reference: PMID:26314367

fluorescence recovery after photobleaching evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: fluorescence recovery after photobleaching evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: fluorescence evidence used in manual assertion
subclass of: fluorescence recovery after photobleaching evidence
has GO evidence code: IDA
definition: 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.
created_by: rctauber
creation_date: 2017-05-16T10:55:40Z
has_broad_synonym: FRAP evidence
has_obo_namespace: eco
id: ECO:0006067

Axiom
annotated source: fluorescence recovery after photobleaching evidence used in manual assertion
annotated property: subClassOf
annotated target: fluorescence evidence used in manual assertion
is_inferred: true

RNA-sequencing evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: RNA-sequencing evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: transcript expression evidence used in manual assertion
subclass of: RNA-sequencing evidence
has GO evidence code: IEP
definition: A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
created_by: rctauber
creation_date: 2017-06-28T10:37:02Z
has_broad_synonym: WTSS evidence
has_broad_synonym: whole transcriptome shotgun sequencing
has_exact_synonym: RNA-seq evidence used in manual assertion
has_exact_synonym: RNAseq evidence used in manual assertion
has_obo_namespace: eco
has_related_synonym: RNA sequencing|differential gene expression evidence from RNA-seq experiment
id: ECO:0006068

Axiom
annotated source: RNA-sequencing evidence used in manual assertion
annotated property: subClassOf
annotated target: transcript expression evidence used in manual assertion
is_inferred: true

Axiom
annotated source: RNA-sequencing evidence used in manual assertion
annotated property: definition
annotated target: A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
database_cross_reference: ECO:MCC

RNA-sequencing evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: RNA-sequencing evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: RNA-sequencing evidence
subclass of: ECO_0007303
has GO evidence code: IEA
definition: A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
created_by: rctauber
creation_date: 2017-06-28T10:37:02Z
has_broad_synonym: WTSS evidence
has_broad_synonym: whole transcriptome shotgun sequencing
has_exact_synonym: RNA-seq evidence used in automatic assertion
has_exact_synonym: RNAseq evidence used in automatic assertion
has_obo_namespace: eco
has_related_synonym: RNA sequencing|differential gene expression evidence from RNA-seq experiment
id: ECO:0006069

Axiom
annotated source: RNA-sequencing evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007303
is_inferred: true

Axiom
annotated source: RNA-sequencing evidence used in automatic assertion
annotated property: definition
annotated target: A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
database_cross_reference: ECO:MCC

immuno-labelling electron microscopy evidence
type: Class
subclass of: electron microscopy evidence
subclass of: Restriction
  on property: is about
  some values from: GO_0033036
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0000070
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: Class
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: OBI_0001631
    intersection of: Restriction
      on property: has part
      some values from: OBI_0001632
definition: A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
ontology term requester: dosumis
created_by: rctauber
creation_date: 2017-07-05T09:59:10Z
has_exact_synonym: immunolabelling electron microscopy evidence
has_obo_namespace: eco
id: ECO:0006070

Axiom
annotated source: immuno-labelling electron microscopy evidence
annotated property: definition
annotated target: A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
database_cross_reference: PMID:25151300

immuno-labelling electron microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immuno-labelling electron microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: electron microscopy evidence used in manual assertion
subclass of: immuno-labelling electron microscopy evidence
has GO evidence code: IDA
definition: 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.
definition source: PMID:25151300
ontology term requester: dosumis
created_by: rctauber
creation_date: 2017-07-05T09:59:10Z
has_broad_synonym: immunolabelling electron microscopy evidence
has_obo_namespace: eco
id: ECO:0006071

Axiom
annotated source: immuno-labelling electron microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: electron microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immuno-labelling electron microscopy evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:25151300

immunofluorescence super resolution microscopy evidence
type: Class
subclass of: super-resolution microscopy evidence
definition: 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.
ontology term requester: dosumis
created_by: rctauber
creation_date: 2017-07-05T09:59:10Z
has_obo_namespace: eco
id: ECO:0006072

Axiom
annotated source: immunofluorescence super resolution microscopy evidence
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:19245833

immunofluorescence super resolution microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunofluorescence super resolution microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: super-resolution microscopy evidence used in manual assertion
subclass of: immunofluorescence super resolution microscopy evidence
has GO evidence code: IDA
definition: 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.
ontology term requester: dosumis
created_by: rctauber
creation_date: 2017-07-05T09:59:10Z
has_obo_namespace: eco
id: ECO:0006073

Axiom
annotated source: immunofluorescence super resolution microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: super-resolution microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunofluorescence super resolution microscopy evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:19245833

co-purification evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: co-purification evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: co-purification evidence
subclass of: physical interaction evidence used in manual assertion
has GO evidence code: IPI
definition: 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:19Z
has_broad_synonym: co-purification
has_obo_namespace: eco
id: ECO:0006074

Axiom
annotated source: co-purification evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: co-purification evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: TAIR:TED

affinity evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: affinity evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: affinity evidence
subclass of: physical interaction evidence used in manual assertion
has GO evidence code: IPI
definition: A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities.
created_by: rctauber
creation_date: 2017-09-14T09:19:20Z
has_obo_namespace: eco
has_related_synonym: ligand binding evidence
id: ECO:0006075

Axiom
annotated source: affinity evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: affinity evidence used in manual assertion
annotated property: definition
annotated target: A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities.
database_cross_reference: ECO:MCC

protein binding evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein binding evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: protein binding evidence
subclass of: affinity evidence used in manual assertion
has GO evidence code: IPI
definition: A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex.
created_by: rctauber
creation_date: 2017-09-14T09:19:21Z
has_obo_namespace: eco
id: ECO:0006076

Axiom
annotated source: protein binding evidence used in manual assertion
annotated property: subClassOf
annotated target: affinity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: protein binding evidence used in manual assertion
annotated property: definition
annotated target: A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex.
database_cross_reference: GO:0005515

bait-prey hybrid interaction evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: bait-prey hybrid interaction evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: bait-prey hybrid interaction evidence
subclass of: protein binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of bait-prey hybrid interaction 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:22Z
has_exact_synonym: bait-prey protein pull-down evidence
has_obo_namespace: eco
id: ECO:0006077

Axiom
annotated source: bait-prey hybrid interaction evidence used in manual assertion
annotated property: subClassOf
annotated target: protein binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: bait-prey hybrid interaction evidence used in manual assertion
annotated property: definition
annotated target: A type of bait-prey hybrid interaction 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.
database_cross_reference: ECO:MCC

immunological assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: immunological assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: immunological assay evidence
subclass of: affinity evidence used in manual assertion
has GO evidence code: IPI
definition: 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:23Z
has_obo_namespace: eco
id: ECO:0006078

Axiom
annotated source: immunological assay evidence used in manual assertion
annotated property: subClassOf
annotated target: affinity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: immunological assay evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ERO:0001362

yeast one-hybrid evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: yeast one-hybrid evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: yeast one-hybrid evidence
subclass of: bait-prey hybrid interaction evidence used in manual assertion
has GO evidence code: IPI
definition: 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:24Z
has_broad_synonym: yeast one-hybrid assay
has_obo_namespace: eco
id: ECO:0006079

Axiom
annotated source: yeast one-hybrid evidence used in manual assertion
annotated property: subClassOf
annotated target: bait-prey hybrid interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: yeast one-hybrid evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

split-ubiquitin functional complementation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: split-ubiquitin functional complementation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: split-ubiquitin functional complementation evidence
subclass of: protein fragment functional complementation evidence used in manual assertion
has GO evidence code: IPI
definition: A type of split-ubiquitin functional complementation 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:25Z
has_broad_synonym: split-ubiquitin assay
has_obo_namespace: eco
id: ECO:0006080

Axiom
annotated source: split-ubiquitin functional complementation evidence used in manual assertion
annotated property: subClassOf
annotated target: protein fragment functional complementation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: split-ubiquitin functional complementation evidence used in manual assertion
annotated property: definition
annotated target: A type of split-ubiquitin functional complementation 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.
database_cross_reference: PMID:15064465

far-Western blotting evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: far-Western blotting evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: far-Western blotting evidence
subclass of: physical interaction evidence used in manual assertion
has GO evidence code: IPI
definition: 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:26Z
has_broad_synonym: far-Western analysis
has_obo_namespace: eco
id: ECO:0006081

Axiom
annotated source: far-Western blotting evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: far-Western blotting evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:18079728

affinity chromatography evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: affinity chromatography evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: affinity chromatography evidence
subclass of: affinity evidence used in manual assertion
has GO evidence code: IPI
definition: 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:27Z
has_broad_synonym: affinity chromatography
has_obo_namespace: eco
id: ECO:0006082

Axiom
annotated source: affinity chromatography evidence used in manual assertion
annotated property: subClassOf
annotated target: affinity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: affinity chromatography evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

nucleic acid binding evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: nucleic acid binding evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: nucleic acid binding evidence
subclass of: affinity evidence used in manual assertion
has GO evidence code: IPI
definition: A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid.
created_by: rctauber
creation_date: 2017-09-14T09:19:28Z
has_obo_namespace: eco
id: ECO:0006083

Axiom
annotated source: nucleic acid binding evidence used in manual assertion
annotated property: subClassOf
annotated target: affinity evidence used in manual assertion
is_inferred: true

Axiom
annotated source: nucleic acid binding evidence used in manual assertion
annotated property: definition
annotated target: A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid.
database_cross_reference: GO:0003676

ribohomopolymer binding assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: ribohomopolymer binding assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: ribohomopolymer binding assay evidence
subclass of: nucleic acid binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer.
created_by: rctauber
creation_date: 2017-09-14T09:19:29Z
has_broad_synonym: ribohomopolymer binding assay
has_obo_namespace: eco
id: ECO:0006084

Axiom
annotated source: ribohomopolymer binding assay evidence used in manual assertion
annotated property: subClassOf
annotated target: nucleic acid binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: ribohomopolymer binding assay evidence used in manual assertion
annotated property: definition
annotated target: A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer.
database_cross_reference: PMC:102612

protein:ion binding evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein:ion binding evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: protein:ion binding evidence
subclass of: protein binding evidence used in manual assertion
has GO evidence code: IPI
definition: 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:30Z
has_obo_namespace: eco
id: ECO:0006085

Axiom
annotated source: protein:ion binding evidence used in manual assertion
annotated property: subClassOf
annotated target: protein binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: protein:ion binding evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:2377604

Southwestern blot evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Southwestern blot evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: Southwestern blot evidence
subclass of: nucleic acid binding evidence used in manual assertion
has GO evidence code: IPI
definition: 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:31Z
has_broad_synonym: Southwestern analysis
has_obo_namespace: eco
id: ECO:0006086

Axiom
annotated source: Southwestern blot evidence used in manual assertion
annotated property: subClassOf
annotated target: nucleic acid binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: Southwestern blot evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT

Northwestern blot evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Northwestern blot evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: Northwestern blot evidence
subclass of: nucleic acid binding evidence used in manual assertion
has GO evidence code: IPI
definition: 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:32Z
has_broad_synonym: Northwestern analysis
has_obo_namespace: eco
id: ECO:0006087

Axiom
annotated source: Northwestern blot evidence used in manual assertion
annotated property: subClassOf
annotated target: nucleic acid binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: Northwestern blot evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:RCT

systematic evolution of ligands by exponential amplification evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: systematic evolution of ligands by exponential amplification evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: systematic evolution of ligands by exponential amplification evidence
subclass of: physical interaction evidence used in manual assertion
has GO evidence code: IPI
definition: 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:33Z
has_broad_synonym: SELEX evidence
has_broad_synonym: in vitro selection evidence
has_obo_namespace: eco
has_related_synonym: in vitro evolution evidence
id: ECO:0006088

Axiom
annotated source: systematic evolution of ligands by exponential amplification evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: systematic evolution of ligands by exponential amplification evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: ECO:MCC

bacterial one-hybrid evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: bacterial one-hybrid evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: bacterial one-hybrid evidence
subclass of: bait-prey hybrid interaction evidence used in manual assertion
has GO evidence code: IPI
definition: 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).
created_by: rctauber
creation_date: 2017-09-14T09:19:34Z
has_broad_synonym: B1H evidence
has_obo_namespace: eco
id: ECO:0006089

Axiom
annotated source: bacterial one-hybrid evidence used in manual assertion
annotated property: subClassOf
annotated target: bait-prey hybrid interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: bacterial one-hybrid evidence used in manual assertion
annotated property: definition
annotated target: 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).
database_cross_reference: ECO:MCC

protein-oligonucleotide microarray binding evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein-oligonucleotide microarray binding evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: protein-oligonucleotide microarray binding evidence
subclass of: protein binding evidence used in manual assertion
subclass of: nucleic acid binding evidence used in manual assertion
has GO evidence code: IPI
definition: A type of protein-oligonucleotide microarray binding 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:35Z
has_broad_synonym: PBM evidence
has_obo_namespace: eco
id: ECO:0006090

Axiom
annotated source: protein-oligonucleotide microarray binding evidence used in manual assertion
annotated property: subClassOf
annotated target: protein binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: protein-oligonucleotide microarray binding evidence used in manual assertion
annotated property: subClassOf
annotated target: nucleic acid binding evidence used in manual assertion
is_inferred: true

Axiom
annotated source: protein-oligonucleotide microarray binding evidence used in manual assertion
annotated property: definition
annotated target: A type of protein-oligonucleotide microarray binding 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.
database_cross_reference: PMID:22146299

functional complementation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: functional complementation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: functional complementation evidence
subclass of: genetic interaction evidence used in manual assertion
has GO evidence code: IGI
definition: 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:36Z
has_broad_synonym: functional complementation
has_obo_namespace: eco
id: ECO:0006091

Axiom
annotated source: functional complementation evidence used in manual assertion
annotated property: subClassOf
annotated target: genetic interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: functional complementation evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:27403640

transgenic rescue experiment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: transgenic rescue experiment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: transgenic rescue experiment evidence
subclass of: functional complementation evidence used in manual assertion
has GO evidence code: IGI
definition: 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:37Z
has_obo_namespace: eco
id: ECO:0006092

Axiom
annotated source: transgenic rescue experiment evidence used in manual assertion
annotated property: subClassOf
annotated target: functional complementation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: transgenic rescue experiment evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://www.nature.com/gt/journal/v11/n15/full/3302282a.html

transient rescue experiment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: transient rescue experiment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: transient rescue experiment evidence
subclass of: functional complementation evidence used in manual assertion
has GO evidence code: IGI
definition: A type of transient rescue experiment evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-09-14T09:19:38Z
has_obo_namespace: eco
id: ECO:0006093

Axiom
annotated source: transient rescue experiment evidence used in manual assertion
annotated property: subClassOf
annotated target: functional complementation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: transient rescue experiment evidence used in manual assertion
annotated property: definition
annotated target: A type of transient rescue experiment evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

suppressor/enhancer interaction phenotypic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: suppressor/enhancer interaction phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: suppressor/enhancer interaction phenotypic evidence
subclass of: genetic interaction evidence used in manual assertion
has GO evidence code: IGI
definition: A type of suppressor/enhancer interaction phenotypic evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-09-14T09:19:39Z
has_broad_synonym: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)
has_exact_synonym: suppressor/enhancer interaction evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0006094

Axiom
annotated source: suppressor/enhancer interaction phenotypic evidence used in manual assertion
annotated property: subClassOf
annotated target: genetic interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: suppressor/enhancer interaction phenotypic evidence used in manual assertion
annotated property: definition
annotated target: A type of suppressor/enhancer interaction phenotypic evidence that is used in a manual assertion.
database_cross_reference: url:http://www.wormbook.org/chapters/www:geneticsuppression/geneticsuppression.html

double mutant phenotypic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: double mutant phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: double mutant phenotypic evidence
subclass of: mutant phenotype evidence used in manual assertion
has GO evidence code: IGI
definition: A type of double mutant phenotypic evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-09-14T09:19:40Z
has_broad_synonym: double mutant analysis
has_exact_synonym: double mutant phenotype evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0006095

Axiom
annotated source: double mutant phenotypic evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

Axiom
annotated source: double mutant phenotypic evidence used in manual assertion
annotated property: definition
annotated target: A type of double mutant phenotypic evidence that is used in a manual assertion.
database_cross_reference: ECO:RCT

epistatic interaction phenotypic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: epistatic interaction phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: epistatic interaction phenotypic evidence
subclass of: genetic interaction evidence used in manual assertion
has GO evidence code: IGI
definition: A type of epistatic interaction phenotypic evidence that is used in a manual assertion.
created_by: rctauber
creation_date: 2017-09-14T09:19:41Z
has_broad_synonym: epistatic interactions
has_exact_synonym: epistatic interaction evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0006096

Axiom
annotated source: epistatic interaction phenotypic evidence used in manual assertion
annotated property: subClassOf
annotated target: genetic interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: epistatic interaction phenotypic evidence used in manual assertion
annotated property: definition
annotated target: A type of epistatic interaction phenotypic evidence that is used in a manual assertion.
database_cross_reference: PMID:18852697

functional complementation in heterologous system evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: functional complementation in heterologous system evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: functional complementation in heterologous system evidence
subclass of: functional complementation evidence used in manual assertion
has GO evidence code: IGI
definition: 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.
created_by: rctauber
creation_date: 2017-09-14T09:19:42Z
has_broad_synonym: functional complementation in heterologous system
has_obo_namespace: eco
id: ECO:0006097

Axiom
annotated source: functional complementation in heterologous system evidence used in manual assertion
annotated property: subClassOf
annotated target: functional complementation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: functional complementation in heterologous system evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: TAIR:TED

temperature-sensitive mutant phenotypic evidence
type: Class
subclass of: mutant phenotype evidence
definition: A type of mutant phenotype evidence resulting from altered gene function at higher temperatures.
ontology term requester: pgaudet
created_by: rctauber
creation_date: 2017-09-18T07:58:28Z
has_exact_synonym: Ts mutation evidence
has_exact_synonym: temperature-sensitive mutant phenotype evidence
has_obo_namespace: eco
id: ECO:0006098

Axiom
annotated source: temperature-sensitive mutant phenotypic evidence
annotated property: definition
annotated target: A type of mutant phenotype evidence resulting from altered gene function at higher temperatures.
database_cross_reference: GOC:PG
database_cross_reference: PMID:19596904

temperature-sensitive mutant phenotypic evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: temperature-sensitive mutant phenotypic evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mutant phenotype evidence used in manual assertion
subclass of: temperature-sensitive mutant phenotypic evidence
has GO evidence code: IMP
definition: A type of temperature-sensitive mutant phenotypic evidence that is used in a manual assertion.
ontology term requester: pgaudet
created_by: rctauber
creation_date: 2017-09-18T07:58:28Z
has_broad_synonym: Ts mutation evidence
has_exact_synonym: temperature-sensitive mutant phenotype evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0006099

Axiom
annotated source: temperature-sensitive mutant phenotypic evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

Axiom
annotated source: temperature-sensitive mutant phenotypic evidence used in manual assertion
annotated property: definition
annotated target: A type of temperature-sensitive mutant phenotypic evidence that is used in a manual assertion.
database_cross_reference: GOC:PG
database_cross_reference: PMID:19596904

recessive mutant phenotype evidence
type: Class
subclass of: mutant phenotype evidence
definition: 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.
ontology term requester: pgaudet
created_by: rctauber
creation_date: 2017-09-18T07:58:28Z
has_obo_namespace: eco
id: ECO:0006100

Axiom
annotated source: recessive mutant phenotype evidence
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:PG
database_cross_reference: NBK:21578

recessive mutant phenotype evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: recessive mutant phenotype evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mutant phenotype evidence used in manual assertion
subclass of: recessive mutant phenotype evidence
has GO evidence code: IMP
definition: 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.
ontology term requester: pgaudet
created_by: rctauber
creation_date: 2017-09-18T07:58:28Z
has_obo_namespace: eco
id: ECO:0006101

Axiom
annotated source: recessive mutant phenotype evidence used in manual assertion
annotated property: subClassOf
annotated target: mutant phenotype evidence used in manual assertion
is_inferred: true

Axiom
annotated source: recessive mutant phenotype evidence used in manual assertion
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:PG
database_cross_reference: NBK:21578

quantum mechanics/molecular mechanics simulation evidence
type: Class
subclass of: ECO_0007672
definition: A type of computational evidence where the active site of the molecular system is described with highly accurate quantum theory, while the contribution of the rest of the system is described with molecular mechanical force field.
created_by: snadendla
has_exact_synonym: QM/MM evidence
has_obo_namespace: eco
id: ECO:0006135

Axiom
annotated source: quantum mechanics/molecular mechanics simulation evidence
annotated property: definition
annotated target: A type of computational evidence where the active site of the molecular system is described with highly accurate quantum theory, while the contribution of the rest of the system is described with molecular mechanical force field.
database_cross_reference: ECO:SN
database_cross_reference: PMID:26930454

quantum mechanics/molecular mechanics simulation evidence used in automatic assertion
type: Class
subclass of: quantum mechanics/molecular mechanics simulation evidence
definition: A type of quantum mechanics/molecular mechanics simulation evidence that is used in an automatic assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006136

Axiom
annotated source: quantum mechanics/molecular mechanics simulation evidence used in automatic assertion
annotated property: definition
annotated target: A type of quantum mechanics/molecular mechanics simulation evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

quantum mechanics/molecular mechanics simulation evidence used in manual assertion
type: Class
subclass of: quantum mechanics/molecular mechanics simulation evidence
definition: A type of quantum mechanics/molecular mechanics simulation evidence that is used in manual assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006137

Axiom
annotated source: quantum mechanics/molecular mechanics simulation evidence used in manual assertion
annotated property: definition
annotated target: A type of quantum mechanics/molecular mechanics simulation evidence that is used in manual assertion.
database_cross_reference: ECO:SN

molecular mechanics simulation evidence
type: Class
subclass of: ECO_0007672
definition: A type of computational evidence where the energy of a molecular system is predicted as a function of its conformation.
created_by: snadendla
has_exact_synonym: MM evidence
has_obo_namespace: eco
id: ECO:0006138

Axiom
annotated source: molecular mechanics simulation evidence
annotated property: definition
annotated target: A type of computational evidence where the energy of a molecular system is predicted as a function of its conformation.
database_cross_reference: ECO:SN
database_cross_reference: url:http://vergil.chemistry.gatech.edu/courses/chem6485/pdf/molmech.pdf

molecular mechanics simulation evidence used in automatic assertion
type: Class
subclass of: molecular mechanics simulation evidence
definition: A type of molecular mechanics simulation evidence that is used in an automatic assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006139

Axiom
annotated source: molecular mechanics simulation evidence used in automatic assertion
annotated property: definition
annotated target: A type of molecular mechanics simulation evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

molecular mechanics simulation evidence used in manual assertion
type: Class
subclass of: molecular mechanics simulation evidence
definition: A type of molecular mechanics simulation evidence that is used in manual assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006140

Axiom
annotated source: molecular mechanics simulation evidence used in manual assertion
annotated property: definition
annotated target: A type of molecular mechanics simulation evidence that is used in manual assertion.
database_cross_reference: ECO:SN

quantum mechanics simulation evidence
type: Class
subclass of: ECO_0007672
definition: A type of computational evidence where the behavior of matter and light on the atomic and subatomic scale is described.
created_by: snadendla
has_exact_synonym: QM evidence
has_exact_synonym: quantum physics evidence
has_exact_synonym: quantum theory evidence
has_obo_namespace: eco
id: ECO:0006141

Axiom
annotated source: quantum mechanics simulation evidence
annotated property: definition
annotated target: A type of computational evidence where the behavior of matter and light on the atomic and subatomic scale is described.
database_cross_reference: ECO:SN
database_cross_reference: url:https://www.britannica.com/science/quantum-mechanics-physics

quantum mechanics simulation evidence used in automatic assertion
type: Class
subclass of: quantum mechanics simulation evidence
definition: A type of quantum mechanics simulation evidence that is used in an automatic assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006142

Axiom
annotated source: quantum mechanics simulation evidence used in automatic assertion
annotated property: definition
annotated target: A type of quantum mechanics simulation evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

quantum mechanics simulation evidence used in manual assertion
type: Class
subclass of: quantum mechanics simulation evidence
definition: A type of quantum mechanics simulation evidence that is used in manual assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006143

Axiom
annotated source: quantum mechanics simulation evidence used in manual assertion
annotated property: definition
annotated target: A type of quantum mechanics simulation evidence that is used in manual assertion.
database_cross_reference: ECO:SN

density functional theory simulation evidence
type: Class
subclass of: quantum mechanics simulation evidence
definition: A type of quantum mechanics simulation evidence that results from the calculation of ground-state electronic structure of atoms, molecules and solid state materials.
created_by: snadendla
has_exact_synonym: DFT evidence
has_obo_namespace: eco
id: ECO:0006144

Axiom
annotated source: density functional theory simulation evidence
annotated property: definition
annotated target: A type of quantum mechanics simulation evidence that results from the calculation of ground-state electronic structure of atoms, molecules and solid state materials.
database_cross_reference: ECO:SN
database_cross_reference: url:https://www.sciencedirect.com/topics/physics-and-astronomy/density-functional-theory

density functional theory simulation evidence used in manual assertion
type: Class
subclass of: density functional theory simulation evidence
definition: A type of density functional theory simulation evidence that is used in manual assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006145

Axiom
annotated source: density functional theory simulation evidence used in manual assertion
annotated property: definition
annotated target: A type of density functional theory simulation evidence that is used in manual assertion.
database_cross_reference: ECO:SN

density functional theory simulation evidence used in automatic assertion
type: Class
subclass of: density functional theory simulation evidence
definition: A type of density functional theory simulation evidence that is used in an automatic assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006146

Axiom
annotated source: density functional theory simulation evidence used in automatic assertion
annotated property: definition
annotated target: A type of density functional theory simulation evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

documented statement evidence
type: Class
subclass of: evidence
definition: A type of evidence in which information is recorded in some documentation system, for example, but not limited to a publication, survey, or medical record.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006151

Axiom
annotated source: documented statement evidence
annotated property: definition
annotated target: A type of evidence in which information is recorded in some documentation system, for example, but not limited to a publication, survey, or medical record.
database_cross_reference: ECO:SN

medical practitioner statement evidence
type: Class
subclass of: documented statement evidence
definition: A type of documented statement evidence in which information is stated by a health care professional, for example, but not limited to a doctor, nurse, or psychologist.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006152

Axiom
annotated source: medical practitioner statement evidence
annotated property: definition
annotated target: A type of documented statement evidence in which information is stated by a health care professional, for example, but not limited to a doctor, nurse, or psychologist.
database_cross_reference: ECO:SN

self-reported individual's statement evidence
type: Class
subclass of: documented statement evidence
definition: A type of documented statement evidence in which information is provided by an individual through means including, but not limited to, paper form, electronic form, or verbal communication, and is captured in a documented record.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006153

Axiom
annotated source: self-reported individual's statement evidence
annotated property: definition
annotated target: A type of documented statement evidence in which information is provided by an individual through means including, but not limited to, paper form, electronic form, or verbal communication, and is captured in a documented record.
database_cross_reference: ECO:SN

self-reported patient statement evidence
type: Class
subclass of: self-reported individual's statement evidence
definition: A type of self-reported individual's statement evidence in which information is provided by a patient in a clinical setting.
ontology term requester: Pablo Botas for Foundation 29, Dx29 project
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006154

Axiom
annotated source: self-reported patient statement evidence
annotated property: definition
annotated target: A type of self-reported individual's statement evidence in which information is provided by a patient in a clinical setting.
database_cross_reference: ECO:SN

documented statement evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: documented statement evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: evidence used in manual assertion
subclass of: documented statement evidence
definition: A type of documented statement evidence that is used in a manual assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006155

Axiom
annotated source: documented statement evidence used in manual assertion
annotated property: subClassOf
annotated target: evidence used in manual assertion
is_inferred: true

Axiom
annotated source: documented statement evidence used in manual assertion
annotated property: definition
annotated target: A type of documented statement evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

documented statement evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: documented statement evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: evidence used in automatic assertion
subclass of: documented statement evidence
has GO evidence code: IEA
definition: A type of documented statement evidence that is used in an automatic assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006156

Axiom
annotated source: documented statement evidence used in automatic assertion
annotated property: subClassOf
annotated target: evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: documented statement evidence used in automatic assertion
annotated property: definition
annotated target: A type of documented statement evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

self-reported individual's statement evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: self-reported individual's statement evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: self-reported individual's statement evidence
subclass of: documented statement evidence used in manual assertion
definition: A type of self-reported individual's statement evidence that is used in a manual assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006157

Axiom
annotated source: self-reported individual's statement evidence used in manual assertion
annotated property: subClassOf
annotated target: documented statement evidence used in manual assertion
is_inferred: true

Axiom
annotated source: self-reported individual's statement evidence used in manual assertion
annotated property: definition
annotated target: A type of self-reported individual's statement evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

self-reported individual's statement evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: self-reported individual's statement evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: self-reported individual's statement evidence
subclass of: documented statement evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of self-reported individual's statement evidence that is used in an automatic assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006158

Axiom
annotated source: self-reported individual's statement evidence used in automatic assertion
annotated property: subClassOf
annotated target: documented statement evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: self-reported individual's statement evidence used in automatic assertion
annotated property: definition
annotated target: A type of self-reported individual's statement evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

self-reported patient statement evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: self-reported patient statement evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: self-reported patient statement evidence
subclass of: self-reported individual's statement evidence used in manual assertion
definition: A type of self-reported patient statement evidence that is used in a manual assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006159

Axiom
annotated source: self-reported patient statement evidence used in manual assertion
annotated property: subClassOf
annotated target: self-reported individual's statement evidence used in manual assertion
is_inferred: true

Axiom
annotated source: self-reported patient statement evidence used in manual assertion
annotated property: definition
annotated target: A type of self-reported patient statement evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

self-reported patient statement evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: self-reported patient statement evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: self-reported patient statement evidence
subclass of: self-reported individual's statement evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of self-reported patient statement evidence that is used in an automatic assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006160

Axiom
annotated source: self-reported patient statement evidence used in automatic assertion
annotated property: subClassOf
annotated target: self-reported individual's statement evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: self-reported patient statement evidence used in automatic assertion
annotated property: definition
annotated target: A type of self-reported patient statement evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

medical practitioner statement evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: medical practitioner statement evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: medical practitioner statement evidence
subclass of: documented statement evidence used in manual assertion
definition: A type of medical practitioner statement evidence that is used in a manual assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006161

Axiom
annotated source: medical practitioner statement evidence used in manual assertion
annotated property: subClassOf
annotated target: documented statement evidence used in manual assertion
is_inferred: true

Axiom
annotated source: medical practitioner statement evidence used in manual assertion
annotated property: definition
annotated target: A type of medical practitioner statement evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

medical practitioner statement evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: medical practitioner statement evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: medical practitioner statement evidence
subclass of: documented statement evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of medical practitioner statement evidence that is used in an automatic assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006162

Axiom
annotated source: medical practitioner statement evidence used in automatic assertion
annotated property: subClassOf
annotated target: documented statement evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: medical practitioner statement evidence used in automatic assertion
annotated property: definition
annotated target: A type of medical practitioner statement evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

nuclear magnetic resonance spectroscopy evidence
type: Class
subclass of: nuclear magnetic resonance evidence
subclass of: Restriction
  on property: is_specified_output_of
  some values from: OBI_0000623
definition: A type of nuclear magnetic resonance evidence used for quantification of metabolites or for the determination of chemical structure or composition.
ontology term requester: SIB:PG
created_by: snadendla
has_exact_synonym: NMR Spectroscopy
has_obo_namespace: eco
id: ECO:0006163

Axiom
annotated source: nuclear magnetic resonance spectroscopy evidence
annotated property: definition
annotated target: A type of nuclear magnetic resonance evidence used for quantification of metabolites or for the determination of chemical structure or composition.
database_cross_reference: ECO:SN
database_cross_reference: PMID: 16428685
database_cross_reference: PMID: 23036848

nuclear magnetic resonance spectroscopy evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: nuclear magnetic resonance spectroscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: nuclear magnetic resonance spectroscopy evidence
subclass of: ECO_0007441
has GO evidence code: IEA
definition: A type of nuclear magnetic resonance spectroscopy evidence that is used in an automatic assertion.
ontology term requester: SIB:PG
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006164

Axiom
annotated source: nuclear magnetic resonance spectroscopy evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007441
is_inferred: true

Axiom
annotated source: nuclear magnetic resonance spectroscopy evidence used in automatic assertion
annotated property: definition
annotated target: A type of nuclear magnetic resonance spectroscopy evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

nuclear magnetic resonance spectroscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: nuclear magnetic resonance spectroscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: nuclear magnetic resonance evidence used in manual assertion
subclass of: nuclear magnetic resonance spectroscopy evidence
has GO evidence code: EXP
definition: A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion.
ontology term requester: SIB:PG
created_by: snadendla
has_broad_synonym: NMR spectroscopy evidence
has_obo_namespace: eco
id: ECO:0006165

Axiom
annotated source: nuclear magnetic resonance spectroscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: nuclear magnetic resonance evidence used in manual assertion
is_inferred: true

Axiom
annotated source: nuclear magnetic resonance spectroscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

nuclear magnetic resonance imaging evidence
type: Class
subclass of: nuclear magnetic resonance evidence
definition: A type of nuclear magnetic resonance evidence used to image anatomy and physiological processes.
ontology term requester: bjonnh
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006166

Axiom
annotated source: nuclear magnetic resonance imaging evidence
annotated property: definition
annotated target: A type of nuclear magnetic resonance evidence used to image anatomy and physiological processes.
database_cross_reference: url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging

nuclear magnetic resonance imaging evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: nuclear magnetic resonance imaging evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: nuclear magnetic resonance imaging evidence
subclass of: ECO_0007441
has GO evidence code: IEA
definition: A type of nuclear magnetic resonance imaging evidence that is used in an automatic assertion.
ontology term requester: bjonnh
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006167

Axiom
annotated source: nuclear magnetic resonance imaging evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007441
is_inferred: true

Axiom
annotated source: nuclear magnetic resonance imaging evidence used in automatic assertion
annotated property: definition
annotated target: A type of nuclear magnetic resonance imaging evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

nuclear magnetic resonance imaging evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: nuclear magnetic resonance imaging evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: nuclear magnetic resonance evidence used in manual assertion
subclass of: nuclear magnetic resonance imaging evidence
has GO evidence code: EXP
definition: A type of nuclear magnetic resonance imaging evidence that is used in a manual assertion.
ontology term requester: bjonnh
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006168

Axiom
annotated source: nuclear magnetic resonance imaging evidence used in manual assertion
annotated property: subClassOf
annotated target: nuclear magnetic resonance evidence used in manual assertion
is_inferred: true

Axiom
annotated source: nuclear magnetic resonance imaging evidence used in manual assertion
annotated property: definition
annotated target: A type of nuclear magnetic resonance imaging evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

quantitative western immunoblotting evidence
type: Class
subclass of: qualitative western immunoblotting evidence
definition: A type of qualitative western immunoblotting evidence where detection of the signal is carried out through digital imaging and the signal is normalized with methods such as standard curves built from reference housekeeping proteins or total transferred protein measurements.
ontology term requester: GO:Val
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006169

Axiom
annotated source: quantitative western immunoblotting evidence
annotated property: definition
annotated target: A type of qualitative western immunoblotting evidence where detection of the signal is carried out through digital imaging and the signal is normalized with methods such as standard curves built from reference housekeeping proteins or total transferred protein measurements.
database_cross_reference: ECO:SN
database_cross_reference: PMID:25852189

quantitative western immunoblotting evidence used in manual evidence
type: Class
equivalent class: Class
  intersection of: quantitative western immunoblotting evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: qualitative western immunoblotting evidence used in manual assertion
subclass of: quantitative western immunoblotting evidence
has GO evidence code: IEP
definition: A type of quantitative western immunoblotting evidence that is used in a manual assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006170

Axiom
annotated source: quantitative western immunoblotting evidence used in manual evidence
annotated property: subClassOf
annotated target: qualitative western immunoblotting evidence used in manual assertion
is_inferred: true

Axiom
annotated source: quantitative western immunoblotting evidence used in manual evidence
annotated property: definition
annotated target: A type of quantitative western immunoblotting evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

quantitative western immunoblotting evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: quantitative western immunoblotting evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: quantitative western immunoblotting evidence
subclass of: ECO_0007306
has GO evidence code: IEA
definition: A type of quantitatative western immunoblotting evidence that is used in an automatic assertion.
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006171

Axiom
annotated source: quantitative western immunoblotting evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007306
is_inferred: true

Axiom
annotated source: quantitative western immunoblotting evidence used in automatic assertion
annotated property: definition
annotated target: A type of quantitatative western immunoblotting evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

mixed support of intron positions by RNA-sequencing alignment evidence
type: Class
subclass of: support of intron positions by RNA-sequencing alignment evidence
definition: A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignments from a mixture of samples support all of the intron positions (exon pairs) predicted for a transcript.
ontology term requester: NCBI-RefSeq
created_by: snadendla
has_exact_synonym: mixed support of intron positions by RNA-seq alignment evidence
has_obo_namespace: eco
id: ECO:0006172
comment: Mixed support entails that all exon pairs represented in the transcript are supported, but require a combination of evidence from multiple samples. For example, for a transcript containing five exons, if liver RNA-seq reads support the first two introns and brain RNA-seq supports the last three introns, then neither sample meets the criteria for full support (ECO:0000343) but the combination of samples qualifies as Mixed support. Mixed support may result from differential expression, or low expression levels that benefit from combining data.

Axiom
annotated source: mixed support of intron positions by RNA-sequencing alignment evidence
annotated property: definition
annotated target: A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignments from a mixture of samples support all of the intron positions (exon pairs) predicted for a transcript.
database_cross_reference: ECO:SN

mixed support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: mixed support of intron positions by RNA-sequencing alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
subclass of: mixed support of intron positions by RNA-sequencing alignment evidence
has GO evidence code: IEA
definition: A type of mixed support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
ontology term requester: NCBI-RefSeq
created_by: snadendla
has_exact_synonym: mixed support of intron positions by RNA-seq alignment evidence used in automatic assertion
has_obo_namespace: eco
id: ECO:0006173

Axiom
annotated source: mixed support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
annotated property: subClassOf
annotated target: support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: mixed support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
annotated property: definition
annotated target: A type of mixed support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

mixed support of intron positions by RNA-sequencing alignment evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: mixed support of intron positions by RNA-sequencing alignment evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: support of intron positions by RNA-sequencing alignment evidence used in manual assertion
subclass of: mixed support of intron positions by RNA-sequencing alignment evidence
has GO evidence code: IEP
definition: A type of mixed support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion
ontology term requester: NCBI-RefSeq
created_by: snadendla
has_exact_synonym: mixed support of intron positions by RNA-seq alignment evidence used in manual assertion
has_obo_namespace: eco
id: ECO:0006174

Axiom
annotated source: mixed support of intron positions by RNA-sequencing alignment evidence used in manual assertion
annotated property: subClassOf
annotated target: support of intron positions by RNA-sequencing alignment evidence used in manual assertion
is_inferred: true

Axiom
annotated source: mixed support of intron positions by RNA-sequencing alignment evidence used in manual assertion
annotated property: definition
annotated target: A type of mixed support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion
database_cross_reference: ECO:SN

nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence
type: Class
subclass of: nuclear magnetic resonance spectroscopy evidence
definition: A type of nuclear magnetic resonance spectroscopy evidence resulting from measuring the change in a certain type of NMR spectrum as a result of the spontenaous exchange of hydrogen and deuterium nuclei between the sample and the solvent.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: NMR HDX
has_obo_namespace: eco
id: ECO:0006175

Axiom
annotated source: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence
annotated property: definition
annotated target: A type of nuclear magnetic resonance spectroscopy evidence resulting from measuring the change in a certain type of NMR spectrum as a result of the spontenaous exchange of hydrogen and deuterium nuclei between the sample and the solvent.
database_cross_reference: PMID:20960033
database_cross_reference: PMID:28538145
database_cross_reference: url:https://en.wikipedia.org/wiki/Hydrogen%E2%80%93deuterium_exchange#NMR_spectroscopy

proton-based nuclear magnetic resonance evidence
type: Class
subclass of: nuclear magnetic resonance spectroscopy evidence
definition: A type of nuclear magnetic resonance spectroscopy evidence in which the electromagnetic singal being measured comes from the perturbation of hydrogen nuclei resulting in a one dimensional spectrum.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_broad_synonym: 1D NMR
has_exact_synonym: proton NMR
has_obo_namespace: eco
id: ECO:0006176

Axiom
annotated source: proton-based nuclear magnetic resonance evidence
annotated property: definition
annotated target: A type of nuclear magnetic resonance spectroscopy evidence in which the electromagnetic singal being measured comes from the perturbation of hydrogen nuclei resulting in a one dimensional spectrum.
database_cross_reference: url:https://en.wikipedia.org/wiki/Proton_nuclear_magnetic_resonance

circular dichroism evidence
type: Class
subclass of: structure determination evidence
subclass of: spectrometry evidence
definition: A type of spectrometry evidence derived from irradiating a sample with light (either visible, infrared or ultraviolet wavelengths) and observing the difference of absorption of left-handed and right-handed light by the sample by comparing the extent of circular polarization in the incident and the emitted light.
ontology term requester: DisProt:BalintMeszaros
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: CD
has_obo_namespace: eco
id: ECO:0006177

Axiom
annotated source: circular dichroism evidence
annotated property: definition
annotated target: A type of spectrometry evidence derived from irradiating a sample with light (either visible, infrared or ultraviolet wavelengths) and observing the difference of absorption of left-handed and right-handed light by the sample by comparing the extent of circular polarization in the incident and the emitted light.
database_cross_reference: PMID:17464384
database_cross_reference: url:https://en.wikipedia.org/wiki/Circular_dichroism

synchrotron radiation circular dichroism evidence
type: Class
subclass of: circular dichroism evidence
definition: A type of circular dichroism evidence where the source of radiation is radially accelerated particles, most often moving on a circular path in a synchrotron, typically providing lower wavelengths and therefore higher signal-to-noise ratio compared to regular circular dichroism measurements.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: SRCD
has_obo_namespace: eco
id: ECO:0006178

Axiom
annotated source: synchrotron radiation circular dichroism evidence
annotated property: definition
annotated target: A type of circular dichroism evidence where the source of radiation is radially accelerated particles, most often moving on a circular path in a synchrotron, typically providing lower wavelengths and therefore higher signal-to-noise ratio compared to regular circular dichroism measurements.
database_cross_reference: PMID:20658968

far-UV circular dichroism evidence
type: Class
subclass of: circular dichroism evidence
definition: A type of circular dichroism evidence whose spectrum is in the range of 190-230 nm, providing information mainly about amide bonds and through which the relative proportion of secondary structure elements of a protein can be estimated.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: far-UV CD
has_obo_namespace: eco
id: ECO:0006179

Axiom
annotated source: far-UV circular dichroism evidence
annotated property: definition
annotated target: A type of circular dichroism evidence whose spectrum is in the range of 190-230 nm, providing information mainly about amide bonds and through which the relative proportion of secondary structure elements of a protein can be estimated.
database_cross_reference: PMID:17464384

near-UV circular dichroism evidence
type: Class
subclass of: circular dichroism evidence
definition: A type of circular dichroism evidence whose spectrum is in the range of 250-350 nm , providing information mainly about aromatic residues, i.e. phenylalanine, tyrosine and tryptophan, through which it provides information on the tertiary structure of a protein.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: near-UV CD
has_obo_namespace: eco
id: ECO:0006180

Axiom
annotated source: near-UV circular dichroism evidence
annotated property: definition
annotated target: A type of circular dichroism evidence whose spectrum is in the range of 250-350 nm , providing information mainly about aromatic residues, i.e. phenylalanine, tyrosine and tryptophan, through which it provides information on the tertiary structure of a protein.
database_cross_reference: PMID:17464384

cryogenic electron microscopy evidence
type: Class
subclass of: electron microscopy evidence
definition: A type of electron microscopy evidence where the sample being studied has been cooled to cryogenic temperatures (typically below -153 degrees Celsius) prior to the experiment.
ontology term requester: DisProt:BalintMeszaros
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: cryo-EM
has_obo_namespace: eco
id: ECO:0006181

Axiom
annotated source: cryogenic electron microscopy evidence
annotated property: definition
annotated target: A type of electron microscopy evidence where the sample being studied has been cooled to cryogenic temperatures (typically below -153 degrees Celsius) prior to the experiment.
database_cross_reference: PMID:31078399
database_cross_reference: url:https://en.wikipedia.org/wiki/Cryogenic_electron_microscopy

small-angle X-ray scattering evidence
type: Class
subclass of: ECO_0007061
definition: A type of light scattering evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight and structural transitions by irradiating the sample with an X-ray beam and the scattered intensity is probed at small angles (typically in the range of 0.1-10 degrees) by a detector.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: SAXS
has_obo_namespace: eco
id: ECO:0006182

Axiom
annotated source: small-angle X-ray scattering evidence
annotated property: definition
annotated target: A type of light scattering evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight and structural transitions by irradiating the sample with an X-ray beam and the scattered intensity is probed at small angles (typically in the range of 0.1-10 degrees) by a detector.
database_cross_reference: PMID:26320411
database_cross_reference: url:https://en.wikipedia.org/wiki/Small-angle_X-ray_scattering

particle scattering evidence
type: Class
subclass of: structure determination evidence
definition: A type of structure determination evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight, diffusion and interaction strength by irradiating the sample with a particle beam and the scattered intensity is probed at a certain angle by a detector.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006183

Axiom
annotated source: particle scattering evidence
annotated property: definition
annotated target: A type of structure determination evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight, diffusion and interaction strength by irradiating the sample with a particle beam and the scattered intensity is probed at a certain angle by a detector.
database_cross_reference: DisProt:BalintMeszaros

small-angle neutron scattering evidence
type: Class
subclass of: particle scattering evidence
definition: A type of particle scattering evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight and structural transitions by irradiating the sample with a beam of thermal neutrons and the scattered intensity is probed at small angles (typically in the range of 0.1-10 degrees) by a detector.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: SANS
has_obo_namespace: eco
id: ECO:0006184

Axiom
annotated source: small-angle neutron scattering evidence
annotated property: definition
annotated target: A type of particle scattering evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight and structural transitions by irradiating the sample with a beam of thermal neutrons and the scattered intensity is probed at small angles (typically in the range of 0.1-10 degrees) by a detector.
database_cross_reference: PMID:17714935
database_cross_reference: url:https://en.wikipedia.org/wiki/Small-angle_neutron_scattering

author inference
type: Class
subclass of: author statement
subclass of: inferential evidence
definition: A type of inferential evidence where an assertion is derived by the authors of a scientific publication from another assertion and/or primary data via logical inference or other rational means.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006185

Axiom
annotated source: author inference
annotated property: definition
annotated target: A type of inferential evidence where an assertion is derived by the authors of a scientific publication from another assertion and/or primary data via logical inference or other rational means.
database_cross_reference: DisProt:BalintMeszaros

combinatorial experimental and author inference evidence contained in single publication
type: Class
subclass of: ECO_0007011
definition: A type of combinatorial experimental and author inference evidence where the experimental results and author inference are contained in a single publication.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006186

Axiom
annotated source: combinatorial experimental and author inference evidence contained in single publication
annotated property: definition
annotated target: A type of combinatorial experimental and author inference evidence where the experimental results and author inference are contained in a single publication.
database_cross_reference: ECO:MG

X-ray crystallography-based structural model with missing residue coordinates
type: Class
subclass of: x-ray crystallography evidence
definition: A type of X-ray cystallography evidence in which a structural model is built lacking coordinates for some residues indicating high flexibility or structural disorder in that area of the molecule.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006187

Axiom
annotated source: X-ray crystallography-based structural model with missing residue coordinates
annotated property: definition
annotated target: A type of X-ray cystallography evidence in which a structural model is built lacking coordinates for some residues indicating high flexibility or structural disorder in that area of the molecule.
database_cross_reference: DisProt:BalintMeszaros

X-ray crystallography-based structural model with high relative B-factor values
type: Class
subclass of: x-ray crystallography evidence
definition: A type of X-ray cystallography evidence in which a structural model is built that contains high relative B-factor values indicating flexibility in that area of the molecule.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006188

Axiom
annotated source: X-ray crystallography-based structural model with high relative B-factor values
annotated property: definition
annotated target: A type of X-ray cystallography evidence in which a structural model is built that contains high relative B-factor values indicating flexibility in that area of the molecule.
database_cross_reference: DisProt:BalintMeszaros

cryogenic electron microscopy-based structural model with missing residue coordinates
type: Class
subclass of: cryogenic electron microscopy evidence
definition: A type of cryogenic electron microscopy evidence in which a structural model is built lacking coordinates for some residues indicating high flexibility or structural disorder in that area of the molecule.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006189

Axiom
annotated source: cryogenic electron microscopy-based structural model with missing residue coordinates
annotated property: definition
annotated target: A type of cryogenic electron microscopy evidence in which a structural model is built lacking coordinates for some residues indicating high flexibility or structural disorder in that area of the molecule.
database_cross_reference: DisProt:BalintMeszaros

cryogenic electron microscopy-based structural model with high relative B-factor values
type: Class
subclass of: cryogenic electron microscopy evidence
definition: A type of cryogenic electron microscopy evidence in which a structural model is built that contains high relative B-factor values indicating flexibility in that area of the molecule.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006190

Axiom
annotated source: cryogenic electron microscopy-based structural model with high relative B-factor values
annotated property: definition
annotated target: A type of cryogenic electron microscopy evidence in which a structural model is built that contains high relative B-factor values indicating flexibility in that area of the molecule.
database_cross_reference: DisProt:BalintMeszaros

Fourier-transform infrared spectroscopy evidence
type: Class
subclass of: spectrophotometry evidence
definition: A type of spectrophotometry evidence resulting from the evaluation of a molecule in a fluid or solid state by its ability to alter the transmission of infrared light, where the raw data collected is transformed into the specturm by Fourier transform.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: FT-IR
has_exact_synonym: FTIR
has_obo_namespace: eco
id: ECO:0006191

Axiom
annotated source: Fourier-transform infrared spectroscopy evidence
annotated property: definition
annotated target: A type of spectrophotometry evidence resulting from the evaluation of a molecule in a fluid or solid state by its ability to alter the transmission of infrared light, where the raw data collected is transformed into the specturm by Fourier transform.
database_cross_reference: url:https://en.wikipedia.org/wiki/Fourier-transform_infrared_spectroscopy

heat capacity-based evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence derived from measuring the amount of heat absorbed or released by a sample to monitor chemical reactions, phase transitions or other processes affecting the physical state or chemical composition.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_broad_synonym: calorimetry evidence
has_obo_namespace: eco
id: ECO:0006192

Axiom
annotated source: heat capacity-based evidence
annotated property: definition
annotated target: A type of direct assay evidence derived from measuring the amount of heat absorbed or released by a sample to monitor chemical reactions, phase transitions or other processes affecting the physical state or chemical composition.
database_cross_reference: url:https://en.wikipedia.org/wiki/Calorimetry

differential scanning calorimetry evidence
type: Class
subclass of: heat capacity-based evidence
definition: A type of heat capacity-based evidence where the heat required to increase the temperature of the sample is continuously monitored and compared to the heat required to increase the temperature of a reference (having a largely identical composition compared to the sample, such as the empty buffer compared to a protein solution) over a range of temperatures.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: DSC
has_obo_namespace: eco
id: ECO:0006193

Axiom
annotated source: differential scanning calorimetry evidence
annotated property: definition
annotated target: A type of heat capacity-based evidence where the heat required to increase the temperature of the sample is continuously monitored and compared to the heat required to increase the temperature of a reference (having a largely identical composition compared to the sample, such as the empty buffer compared to a protein solution) over a range of temperatures.
database_cross_reference: url:https://en.wikipedia.org/wiki/Differential_scanning_calorimetry

selective antibody-based structural conformation evidence
type: Class
subclass of: structure determination evidence
subclass of: immunodetection assay evidence
example of usage: Here, we describe the generation, characterisation, and utility of a monoclonal antibody that selectively binds with high affinity to the asymmetric TNF trimer–small molecule complex. The antibody helps to define the molecular dynamics of the apo TNF trimer, reveals the mode of action and specificity of the small molecule inhibitors, acts as a chaperone in solving the human TNF–TNFR1 complex crystal structure, and facilitates the measurement of small molecule target occupancy in complex biological samples.
definition: A type of immunodetection assay evidence that involves the use of antibodies that are selective to conformations of the epitope to which they bind in order to provide information on conformations present in a target molecule.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006194

Axiom
annotated source: selective antibody-based structural conformation evidence
annotated property: example of usage
annotated target: Here, we describe the generation, characterisation, and utility of a monoclonal antibody that selectively binds with high affinity to the asymmetric TNF trimer–small molecule complex. The antibody helps to define the molecular dynamics of the apo TNF trimer, reveals the mode of action and specificity of the small molecule inhibitors, acts as a chaperone in solving the human TNF–TNFR1 complex crystal structure, and facilitates the measurement of small molecule target occupancy in complex biological samples.
database_cross_reference: PMID:33495445

Axiom
annotated source: selective antibody-based structural conformation evidence
annotated property: definition
annotated target: A type of immunodetection assay evidence that involves the use of antibodies that are selective to conformations of the epitope to which they bind in order to provide information on conformations present in a target molecule.
database_cross_reference: DisProt:BalintMeszaros

protein hydrogen-deuterium exchange mass spectrometry evidence
type: Class
subclass of: mass spectrometry evidence
definition: A type of mass spectrometry evidence derived from measuring changes in mass associated with the isotopic exchange between amide hydrogens of the protein backbone and its surrounding solvent, providing information on the structural state, the dynamics and the intrinsic chemical properties of the underlying amino acid sequence.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: HDX-MS
has_obo_namespace: eco
id: ECO:0006195

Axiom
annotated source: protein hydrogen-deuterium exchange mass spectrometry evidence
annotated property: definition
annotated target: A type of mass spectrometry evidence derived from measuring changes in mass associated with the isotopic exchange between amide hydrogens of the protein backbone and its surrounding solvent, providing information on the structural state, the dynamics and the intrinsic chemical properties of the underlying amino acid sequence.
database_cross_reference: PMID:31249422
database_cross_reference: url:https://en.wikipedia.org/wiki/Hydrogen%E2%80%93deuterium_exchange#Mass_spectrometry

nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: nuclear magnetic resonance spectroscopy evidence used in manual assertion
subclass of: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence
has GO evidence code: EXP
definition: A type of nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: NMR HDX
has_obo_namespace: eco
id: ECO:0006196

Axiom
annotated source: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
annotated property: subClassOf
annotated target: nuclear magnetic resonance spectroscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
annotated property: definition
annotated target: A type of nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: nuclear magnetic resonance spectroscopy evidence used in automatic assertion
subclass of: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence
has GO evidence code: IEA
definition: A type of nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: NMR HDX
has_obo_namespace: eco
id: ECO:0006197

Axiom
annotated source: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in automatic assertion
annotated property: subClassOf
annotated target: nuclear magnetic resonance spectroscopy evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in automatic assertion
annotated property: definition
annotated target: A type of nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

proton-based nuclear magnetic resonance evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: proton-based nuclear magnetic resonance evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: nuclear magnetic resonance spectroscopy evidence used in manual assertion
subclass of: proton-based nuclear magnetic resonance evidence
has GO evidence code: EXP
definition: A type of proton-based nuclear magnetic resonance evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_broad_synonym: 1D NMR
has_exact_synonym: proton NMR
has_obo_namespace: eco
id: ECO:0006198

Axiom
annotated source: proton-based nuclear magnetic resonance evidence used in manual assertion
annotated property: subClassOf
annotated target: nuclear magnetic resonance spectroscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: proton-based nuclear magnetic resonance evidence used in manual assertion
annotated property: definition
annotated target: A type of proton-based nuclear magnetic resonance evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

proton-based nuclear magnetic resonance evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: proton-based nuclear magnetic resonance evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: nuclear magnetic resonance spectroscopy evidence used in automatic assertion
subclass of: proton-based nuclear magnetic resonance evidence
has GO evidence code: IEA
definition: A type of proton-based nuclear magnetic resonance evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_broad_synonym: 1D NMR
has_exact_synonym: proton NMR
has_obo_namespace: eco
id: ECO:0006199

Axiom
annotated source: proton-based nuclear magnetic resonance evidence used in automatic assertion
annotated property: subClassOf
annotated target: nuclear magnetic resonance spectroscopy evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: proton-based nuclear magnetic resonance evidence used in automatic assertion
annotated property: definition
annotated target: A type of proton-based nuclear magnetic resonance evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

circular dichroism evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: circular dichroism evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: circular dichroism evidence
has GO evidence code: EXP
definition: A type of circular dichroism evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: CD
has_obo_namespace: eco
id: ECO:0006200

Axiom
annotated source: circular dichroism evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: circular dichroism evidence used in manual assertion
annotated property: definition
annotated target: A type of circular dichroism evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

circular dichroism evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: circular dichroism evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: circular dichroism evidence
subclass of: ECO_0007815
subclass of: ECO_0007821
has GO evidence code: IEA
definition: A type of circular dichroism evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: CD
has_obo_namespace: eco
id: ECO:0006201

Axiom
annotated source: circular dichroism evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007815
is_inferred: true

Axiom
annotated source: circular dichroism evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007821
is_inferred: true

Axiom
annotated source: circular dichroism evidence used in automatic assertion
annotated property: definition
annotated target: A type of circular dichroism evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

synchrotron radiation circular dichroism evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: synchrotron radiation circular dichroism evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: synchrotron radiation circular dichroism evidence
subclass of: circular dichroism evidence used in manual assertion
has GO evidence code: EXP
definition: A type of synchrotron radiation circular dichroism evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: SRCD
has_obo_namespace: eco
id: ECO:0006202

Axiom
annotated source: synchrotron radiation circular dichroism evidence used in manual assertion
annotated property: subClassOf
annotated target: circular dichroism evidence used in manual assertion
is_inferred: true

Axiom
annotated source: synchrotron radiation circular dichroism evidence used in manual assertion
annotated property: definition
annotated target: A type of synchrotron radiation circular dichroism evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

synchrotron radiation circular dichroism evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: synchrotron radiation circular dichroism evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: synchrotron radiation circular dichroism evidence
subclass of: circular dichroism evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of synchrotron radiation circular dichroism evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: SRCD
has_obo_namespace: eco
id: ECO:0006203

Axiom
annotated source: synchrotron radiation circular dichroism evidence used in automatic assertion
annotated property: subClassOf
annotated target: circular dichroism evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: synchrotron radiation circular dichroism evidence used in automatic assertion
annotated property: definition
annotated target: A type of synchrotron radiation circular dichroism evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

far-UV circular dichroism evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: far-UV circular dichroism evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: far-UV circular dichroism evidence
subclass of: circular dichroism evidence used in manual assertion
has GO evidence code: EXP
definition: A type of far-UV circular dichroism evidence that is used in a manual assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: far-UV CD
has_obo_namespace: eco
id: ECO:0006204

Axiom
annotated source: far-UV circular dichroism evidence used in manual assertion
annotated property: subClassOf
annotated target: circular dichroism evidence used in manual assertion
is_inferred: true

Axiom
annotated source: far-UV circular dichroism evidence used in manual assertion
annotated property: definition
annotated target: A type of far-UV circular dichroism evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

far-UV circular dichroism evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: far-UV circular dichroism evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: far-UV circular dichroism evidence
subclass of: circular dichroism evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of far-UV circular dichroism evidence that is used in an automatic assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: far-UV CD
has_obo_namespace: eco
id: ECO:0006205

Axiom
annotated source: far-UV circular dichroism evidence used in automatic assertion
annotated property: subClassOf
annotated target: circular dichroism evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: far-UV circular dichroism evidence used in automatic assertion
annotated property: definition
annotated target: A type of far-UV circular dichroism evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

near-UV circular dichroism evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: near-UV circular dichroism evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: near-UV circular dichroism evidence
subclass of: circular dichroism evidence used in manual assertion
has GO evidence code: EXP
definition: A type of near-UV circular dichroism evidence that is used in a manual assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: near-UV CD
has_obo_namespace: eco
id: ECO:0006206

Axiom
annotated source: near-UV circular dichroism evidence used in manual assertion
annotated property: subClassOf
annotated target: circular dichroism evidence used in manual assertion
is_inferred: true

Axiom
annotated source: near-UV circular dichroism evidence used in manual assertion
annotated property: definition
annotated target: A type of near-UV circular dichroism evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

near-UV circular dichroism evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: near-UV circular dichroism evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: near-UV circular dichroism evidence
subclass of: circular dichroism evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of near-UV circular dichroism evidence that is used in an automatic assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: near-UV CD
has_obo_namespace: eco
id: ECO:0006207

Axiom
annotated source: near-UV circular dichroism evidence used in automatic assertion
annotated property: subClassOf
annotated target: circular dichroism evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: near-UV circular dichroism evidence used in automatic assertion
annotated property: definition
annotated target: A type of near-UV circular dichroism evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

cryogenic electron microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: cryogenic electron microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: electron microscopy evidence used in manual assertion
subclass of: cryogenic electron microscopy evidence
has GO evidence code: IDA
definition: A type of cryogenic electron microscopy evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: cryo-EM
has_obo_namespace: eco
id: ECO:0006208

Axiom
annotated source: cryogenic electron microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: electron microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cryogenic electron microscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of cryogenic electron microscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

cryogenic electron microscopy evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: cryogenic electron microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: cryogenic electron microscopy evidence
subclass of: ECO_0007493
has GO evidence code: IEA
definition: A type of cryogenic electron microscopy evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: cryo-EM
has_obo_namespace: eco
id: ECO:0006209

Axiom
annotated source: cryogenic electron microscopy evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007493
is_inferred: true

Axiom
annotated source: cryogenic electron microscopy evidence used in automatic assertion
annotated property: definition
annotated target: A type of cryogenic electron microscopy evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

small-angle X-ray scattering evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: small-angle X-ray scattering evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: small-angle X-ray scattering evidence
subclass of: ECO_0007062
has GO evidence code: EXP
definition: A type of small-angle X-ray scattering evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: SAXS
has_obo_namespace: eco
id: ECO:0006210

Axiom
annotated source: small-angle X-ray scattering evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007062
is_inferred: true

Axiom
annotated source: small-angle X-ray scattering evidence used in manual assertion
annotated property: definition
annotated target: A type of small-angle X-ray scattering evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

small-angle X-ray scattering evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: small-angle X-ray scattering evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: small-angle X-ray scattering evidence
subclass of: ECO_0007617
has GO evidence code: IEA
definition: A type of small-angle X-ray scattering evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: SAXS
has_obo_namespace: eco
id: ECO:0006211

Axiom
annotated source: small-angle X-ray scattering evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007617
is_inferred: true

Axiom
annotated source: small-angle X-ray scattering evidence used in automatic assertion
annotated property: definition
annotated target: A type of small-angle X-ray scattering evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

particle scattering evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: particle scattering evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: particle scattering evidence
has GO evidence code: EXP
definition: A type of particle scattering evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006212

Axiom
annotated source: particle scattering evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: particle scattering evidence used in manual assertion
annotated property: definition
annotated target: A type of particle scattering evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

particle scattering evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: particle scattering evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: particle scattering evidence
subclass of: ECO_0007815
has GO evidence code: IEA
definition: A type of particle scattering evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006213

Axiom
annotated source: particle scattering evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007815
is_inferred: true

Axiom
annotated source: particle scattering evidence used in automatic assertion
annotated property: definition
annotated target: A type of particle scattering evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

small-angle neutron scattering evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: small-angle neutron scattering evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: small-angle neutron scattering evidence
subclass of: particle scattering evidence used in manual assertion
has GO evidence code: EXP
definition: A type of small-angle neutron scattering evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: SANS
has_obo_namespace: eco
id: ECO:0006214

Axiom
annotated source: small-angle neutron scattering evidence used in manual assertion
annotated property: subClassOf
annotated target: particle scattering evidence used in manual assertion
is_inferred: true

Axiom
annotated source: small-angle neutron scattering evidence used in manual assertion
annotated property: definition
annotated target: A type of small-angle neutron scattering evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

small-angle neutron scattering evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: small-angle neutron scattering evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: small-angle neutron scattering evidence
subclass of: particle scattering evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of small-angle neutron scattering evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: SANS
has_obo_namespace: eco
id: ECO:0006215

Axiom
annotated source: small-angle neutron scattering evidence used in automatic assertion
annotated property: subClassOf
annotated target: particle scattering evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: small-angle neutron scattering evidence used in automatic assertion
annotated property: definition
annotated target: A type of small-angle neutron scattering evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

author inference used in manual assertion
type: Class
equivalent class: Class
  intersection of: author inference
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: author statement used in manual assertion
subclass of: author inference
subclass of: ECO_0007751
definition: A type of author inference that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006216

Axiom
annotated source: author inference used in manual assertion
annotated property: subClassOf
annotated target: author statement used in manual assertion
is_inferred: true

Axiom
annotated source: author inference used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007751
is_inferred: true

Axiom
annotated source: author inference used in manual assertion
annotated property: definition
annotated target: A type of author inference that is used in a manual assertion.
database_cross_reference: ECO:SN

author inference used in automatic assertion
type: Class
equivalent class: Class
  intersection of: author inference
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: author inference
subclass of: ECO_0007319
subclass of: ECO_0007832
has GO evidence code: IEA
definition: A type of author inference that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006217

Axiom
annotated source: author inference used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007319
is_inferred: true

Axiom
annotated source: author inference used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007832
is_inferred: true

Axiom
annotated source: author inference used in automatic assertion
annotated property: definition
annotated target: A type of author inference that is used in an automatic assertion.
database_cross_reference: ECO:SN

combinatorial experimental and author inference evidence contained in single publication used in manual assertion
type: Class
equivalent class: Class
  intersection of: combinatorial experimental and author inference evidence contained in single publication
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: combinatorial experimental and author inference evidence contained in single publication
subclass of: ECO_0007013
definition: A type of combinatorial experimental and author inference evidence contained in single publication that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006218

Axiom
annotated source: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007013
is_inferred: true

Axiom
annotated source: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
annotated property: definition
annotated target: A type of combinatorial experimental and author inference evidence contained in single publication that is used in a manual assertion.
database_cross_reference: ECO:SN

combinatorial experimental and author inference evidence contained in single publication used in automatic assertion
type: Class
equivalent class: Class
  intersection of: combinatorial experimental and author inference evidence contained in single publication
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: combinatorial experimental and author inference evidence contained in single publication
subclass of: ECO_0007592
has GO evidence code: IEA
definition: A type of combinatorial experimental and author inference evidence contained in single publication that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006219

Axiom
annotated source: combinatorial experimental and author inference evidence contained in single publication used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007592
is_inferred: true

Axiom
annotated source: combinatorial experimental and author inference evidence contained in single publication used in automatic assertion
annotated property: definition
annotated target: A type of combinatorial experimental and author inference evidence contained in single publication that is used in an automatic assertion.
database_cross_reference: ECO:SN

X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
type: Class
equivalent class: Class
  intersection of: X-ray crystallography-based structural model with missing residue coordinates
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: x-ray crystallography evidence used in manual assertion
subclass of: X-ray crystallography-based structural model with missing residue coordinates
has GO evidence code: EXP
definition: A type of X-ray crystallography-based structural model with missing residue coordinates that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006220

Axiom
annotated source: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
annotated property: subClassOf
annotated target: x-ray crystallography evidence used in manual assertion
is_inferred: true

Axiom
annotated source: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
annotated property: definition
annotated target: A type of X-ray crystallography-based structural model with missing residue coordinates that is used in a manual assertion.
database_cross_reference: ECO:SN

X-ray crystallography-based structural model with missing residue coordinates used in automatic assertion
type: Class
equivalent class: Class
  intersection of: X-ray crystallography-based structural model with missing residue coordinates
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: x-ray crystallography evidence used in automatic assertion
subclass of: X-ray crystallography-based structural model with missing residue coordinates
has GO evidence code: IEA
definition: A type of X-ray crystallography-based structural model with missing residue coordinates that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006221

Axiom
annotated source: X-ray crystallography-based structural model with missing residue coordinates used in automatic assertion
annotated property: subClassOf
annotated target: x-ray crystallography evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: X-ray crystallography-based structural model with missing residue coordinates used in automatic assertion
annotated property: definition
annotated target: A type of X-ray crystallography-based structural model with missing residue coordinates that is used in an automatic assertion.
database_cross_reference: ECO:SN

X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
type: Class
equivalent class: Class
  intersection of: X-ray crystallography-based structural model with high relative B-factor values
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: x-ray crystallography evidence used in manual assertion
subclass of: X-ray crystallography-based structural model with high relative B-factor values
has GO evidence code: EXP
definition: A type of X-ray crystallography-based structural model with high relative B-factor values that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006222

Axiom
annotated source: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
annotated property: subClassOf
annotated target: x-ray crystallography evidence used in manual assertion
is_inferred: true

Axiom
annotated source: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
annotated property: definition
annotated target: A type of X-ray crystallography-based structural model with high relative B-factor values that is used in a manual assertion.
database_cross_reference: ECO:SN

X-ray crystallography-based structural model with high relative B-factor values used in automatic assertion
type: Class
equivalent class: Class
  intersection of: X-ray crystallography-based structural model with high relative B-factor values
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: x-ray crystallography evidence used in automatic assertion
subclass of: X-ray crystallography-based structural model with high relative B-factor values
has GO evidence code: IEA
definition: A type of X-ray crystallography-based structural model with high relative B-factor values that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006223

Axiom
annotated source: X-ray crystallography-based structural model with high relative B-factor values used in automatic assertion
annotated property: subClassOf
annotated target: x-ray crystallography evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: X-ray crystallography-based structural model with high relative B-factor values used in automatic assertion
annotated property: definition
annotated target: A type of X-ray crystallography-based structural model with high relative B-factor values that is used in an automatic assertion.
database_cross_reference: ECO:SN

cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
type: Class
equivalent class: Class
  intersection of: cryogenic electron microscopy-based structural model with missing residue coordinates
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: cryogenic electron microscopy-based structural model with missing residue coordinates
subclass of: cryogenic electron microscopy evidence used in manual assertion
has GO evidence code: IDA
definition: A type of cryogenic electron microscopy-based structural model with missing residue coordinates that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006224

Axiom
annotated source: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
annotated property: subClassOf
annotated target: cryogenic electron microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
annotated property: definition
annotated target: A type of cryogenic electron microscopy-based structural model with missing residue coordinates that is used in a manual assertion.
database_cross_reference: ECO:SN

cryogenic electron microscopy-based structural model with missing residue coordinates used in automatic assertion
type: Class
equivalent class: Class
  intersection of: cryogenic electron microscopy-based structural model with missing residue coordinates
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: cryogenic electron microscopy-based structural model with missing residue coordinates
subclass of: cryogenic electron microscopy evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of cryogenic electron microscopy-based structural model with missing residue coordinates that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006225

Axiom
annotated source: cryogenic electron microscopy-based structural model with missing residue coordinates used in automatic assertion
annotated property: subClassOf
annotated target: cryogenic electron microscopy evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: cryogenic electron microscopy-based structural model with missing residue coordinates used in automatic assertion
annotated property: definition
annotated target: A type of cryogenic electron microscopy-based structural model with missing residue coordinates that is used in an automatic assertion.
database_cross_reference: ECO:SN

cryogenic electron microscopy-based structural model with high relative B-factor values used in manual assertion
type: Class
equivalent class: Class
  intersection of: cryogenic electron microscopy-based structural model with high relative B-factor values
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: cryogenic electron microscopy-based structural model with high relative B-factor values
subclass of: cryogenic electron microscopy evidence used in manual assertion
has GO evidence code: IDA
definition: A type of cryogenic electron microscopy-based structural model with high relative B-factor values that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006226

Axiom
annotated source: cryogenic electron microscopy-based structural model with high relative B-factor values used in manual assertion
annotated property: subClassOf
annotated target: cryogenic electron microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: cryogenic electron microscopy-based structural model with high relative B-factor values used in manual assertion
annotated property: definition
annotated target: A type of cryogenic electron microscopy-based structural model with high relative B-factor values that is used in a manual assertion.
database_cross_reference: ECO:SN

cryogenic electron microscopy-based structural model with high relative B-factor values used in automatic assertion
type: Class
equivalent class: Class
  intersection of: cryogenic electron microscopy-based structural model with high relative B-factor values
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: cryogenic electron microscopy-based structural model with high relative B-factor values
subclass of: cryogenic electron microscopy evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of cryogenic electron microscopy-based structural model with high relative B-factor values that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006227

Axiom
annotated source: cryogenic electron microscopy-based structural model with high relative B-factor values used in automatic assertion
annotated property: subClassOf
annotated target: cryogenic electron microscopy evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: cryogenic electron microscopy-based structural model with high relative B-factor values used in automatic assertion
annotated property: definition
annotated target: A type of cryogenic electron microscopy-based structural model with high relative B-factor values that is used in an automatic assertion.
database_cross_reference: ECO:SN

Fourier-transform infrared spectroscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Fourier-transform infrared spectroscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: spectrophotometry evidence used in manual assertion
subclass of: Fourier-transform infrared spectroscopy evidence
has GO evidence code: EXP
definition: A type of Fourier-transform infrared spectroscopy evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: FT-IR
has_exact_synonym: FTIR
has_obo_namespace: eco
id: ECO:0006228

Axiom
annotated source: Fourier-transform infrared spectroscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: spectrophotometry evidence used in manual assertion
is_inferred: true

Axiom
annotated source: Fourier-transform infrared spectroscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of Fourier-transform infrared spectroscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

Fourier-transform infrared spectroscopy evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: Fourier-transform infrared spectroscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: Fourier-transform infrared spectroscopy evidence
subclass of: ECO_0007458
has GO evidence code: IEA
definition: A type of Fourier-transform infrared spectroscopy evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: FT-IR
has_exact_synonym: FTIR
has_obo_namespace: eco
id: ECO:0006229

Axiom
annotated source: Fourier-transform infrared spectroscopy evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007458
is_inferred: true

Axiom
annotated source: Fourier-transform infrared spectroscopy evidence used in automatic assertion
annotated property: definition
annotated target: A type of Fourier-transform infrared spectroscopy evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

heat capacity-based evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: heat capacity-based evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: heat capacity-based evidence
has GO evidence code: IDA
definition: A type of heat capacity-based evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_broad_synonym: calorimetry evidence
has_obo_namespace: eco
id: ECO:0006230

Axiom
annotated source: heat capacity-based evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: heat capacity-based evidence used in manual assertion
annotated property: definition
annotated target: A type of heat capacity-based evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

heat capacity-based evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: heat capacity-based evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: heat capacity-based evidence
subclass of: ECO_0007307
has GO evidence code: IEA
definition: A type of heat capacity-based evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_broad_synonym: calorimetry evidence
has_obo_namespace: eco
id: ECO:0006231

Axiom
annotated source: heat capacity-based evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007307
is_inferred: true

Axiom
annotated source: heat capacity-based evidence used in automatic assertion
annotated property: definition
annotated target: A type of heat capacity-based evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

differential scanning calorimetry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: differential scanning calorimetry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: differential scanning calorimetry evidence
subclass of: heat capacity-based evidence used in manual assertion
has GO evidence code: IDA
definition: A type of differential scanning calorimetry evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: DSC
has_obo_namespace: eco
id: ECO:0006232

Axiom
annotated source: differential scanning calorimetry evidence used in manual assertion
annotated property: subClassOf
annotated target: heat capacity-based evidence used in manual assertion
is_inferred: true

Axiom
annotated source: differential scanning calorimetry evidence used in manual assertion
annotated property: definition
annotated target: A type of differential scanning calorimetry evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

differential scanning calorimetry evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: differential scanning calorimetry evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: differential scanning calorimetry evidence
subclass of: heat capacity-based evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of differential scanning calorimetry evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: DSC
has_obo_namespace: eco
id: ECO:0006233

Axiom
annotated source: differential scanning calorimetry evidence used in automatic assertion
annotated property: subClassOf
annotated target: heat capacity-based evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: differential scanning calorimetry evidence used in automatic assertion
annotated property: definition
annotated target: A type of differential scanning calorimetry evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

selective antibody-based structural conformation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: selective antibody-based structural conformation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: selective antibody-based structural conformation evidence
has GO evidence code: IDA
definition: A type of selective antibody-based structural conformation evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006234

Axiom
annotated source: selective antibody-based structural conformation evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: selective antibody-based structural conformation evidence used in manual assertion
annotated property: definition
annotated target: A type of selective antibody-based structural conformation evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

selective antibody-based structural conformation evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: selective antibody-based structural conformation evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: selective antibody-based structural conformation evidence
subclass of: ECO_0007796
subclass of: ECO_0007815
has GO evidence code: IEA
definition: A type of selective antibody-based structural conformation evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006235

Axiom
annotated source: selective antibody-based structural conformation evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007796
is_inferred: true

Axiom
annotated source: selective antibody-based structural conformation evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007815
is_inferred: true

Axiom
annotated source: selective antibody-based structural conformation evidence used in automatic assertion
annotated property: definition
annotated target: A type of selective antibody-based structural conformation evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein hydrogen-deuterium exchange mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mass spectrometry evidence used in manual assertion
subclass of: protein hydrogen-deuterium exchange mass spectrometry evidence
has GO evidence code: EXP
definition: A type of protein hydrogen-deuterium exchange mass spectrometry evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: HDX-MS
has_obo_namespace: eco
id: ECO:0006236

Axiom
annotated source: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
annotated property: subClassOf
annotated target: mass spectrometry evidence used in manual assertion
is_inferred: true

Axiom
annotated source: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
annotated property: definition
annotated target: A type of protein hydrogen-deuterium exchange mass spectrometry evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

protein hydrogen-deuterium exchange mass spectrometry evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: protein hydrogen-deuterium exchange mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: protein hydrogen-deuterium exchange mass spectrometry evidence
subclass of: ECO_0007433
has GO evidence code: IEA
definition: A type of protein hydrogen-deuterium exchange mass spectrometry evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: HDX-MS
has_obo_namespace: eco
id: ECO:0006237

Axiom
annotated source: protein hydrogen-deuterium exchange mass spectrometry evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007433
is_inferred: true

Axiom
annotated source: protein hydrogen-deuterium exchange mass spectrometry evidence used in automatic assertion
annotated property: definition
annotated target: A type of protein hydrogen-deuterium exchange mass spectrometry evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

galactokinase reporter gene assay evidence
type: Class
subclass of: reporter gene assay evidence
definition: A type of reporter gene assay evidence based on the fusion of the galK gene to a specific promoter for the expression of the enzyme galactokinase.
ontology term requester: OMP:DebbySiegele
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006238

Axiom
annotated source: galactokinase reporter gene assay evidence
annotated property: definition
annotated target: A type of reporter gene assay evidence based on the fusion of the galK gene to a specific promoter for the expression of the enzyme galactokinase.

polyadenylated transcript 3'-end-sequencing evidence
type: Class
subclass of: RNA-sequencing evidence
definition: A type of RNA-sequencing evidence based on sequencing of the 3' ends of cDNA molecules that are selected by presence of a polyadenylated tail.
ontology term requester: NCBI-RefSeq:MurphyTerence
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006239

Axiom
annotated source: polyadenylated transcript 3'-end-sequencing evidence
annotated property: definition
annotated target: A type of RNA-sequencing evidence based on sequencing of the 3' ends of cDNA molecules that are selected by presence of a polyadenylated tail.
database_cross_reference: PMID:31617559

colony boundary assay evidence
type: Class
subclass of: ECO_0007077
definition: A type of colony morphology phenotypic evidence based on the presence or absence of a visually apparent boundary formed between colonies of multiple isolates or strains of the same microbial species growing on a solid surface such as that of an agar culture medium.
ontology term requester: OMP:DebbySiegele
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006240

Axiom
annotated source: colony boundary assay evidence
annotated property: definition
annotated target: A type of colony morphology phenotypic evidence based on the presence or absence of a visually apparent boundary formed between colonies of multiple isolates or strains of the same microbial species growing on a solid surface such as that of an agar culture medium.
database_cross_reference: PMID:18621670

galactokinase reporter gene assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: galactokinase reporter gene assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: expression pattern evidence used in manual assertion
subclass of: galactokinase reporter gene assay evidence
has GO evidence code: IEP
definition: A type of galactokinase reporter gene assay evidence that is used in a manual assertion.
ontology term requester: OMP:DebbySiegele
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006241

Axiom
annotated source: galactokinase reporter gene assay evidence used in manual assertion
annotated property: subClassOf
annotated target: expression pattern evidence used in manual assertion
is_inferred: true

Axiom
annotated source: galactokinase reporter gene assay evidence used in manual assertion
annotated property: definition
annotated target: A type of galactokinase reporter gene assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

galactokinase reporter gene assay evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: galactokinase reporter gene assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: galactokinase reporter gene assay evidence
subclass of: ECO_0007765
has GO evidence code: IEA
definition: A type of galactokinase reporter gene assay evidence that is used in an automatic assertion.
ontology term requester: OMP:DebbySiegele
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006242

Axiom
annotated source: galactokinase reporter gene assay evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007765
is_inferred: true

Axiom
annotated source: galactokinase reporter gene assay evidence used in automatic assertion
annotated property: definition
annotated target: A type of galactokinase reporter gene assay evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

polyadenylated transcript 3'-end-sequencing evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: polyadenylated transcript 3'-end-sequencing evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: RNA-sequencing evidence used in manual assertion
subclass of: polyadenylated transcript 3'-end-sequencing evidence
has GO evidence code: IEP
definition: A type of polyadenylated transcript 3'-end-sequencing evidence that is used in a manual assertion.
ontology term requester: NCBI-RefSeq:MurphyTerence
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006243

Axiom
annotated source: polyadenylated transcript 3'-end-sequencing evidence used in manual assertion
annotated property: subClassOf
annotated target: RNA-sequencing evidence used in manual assertion
is_inferred: true

Axiom
annotated source: polyadenylated transcript 3'-end-sequencing evidence used in manual assertion
annotated property: definition
annotated target: A type of polyadenylated transcript 3'-end-sequencing evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

polyadenylated transcript 3'-end-sequencing evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: polyadenylated transcript 3'-end-sequencing evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: RNA-sequencing evidence used in automatic assertion
subclass of: polyadenylated transcript 3'-end-sequencing evidence
has GO evidence code: IEA
definition: A type of polyadenylated transcript 3'-end-sequencing evidence that is used in an automatic assertion.
ontology term requester: NCBI-RefSeq:MurphyTerence
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006244

Axiom
annotated source: polyadenylated transcript 3'-end-sequencing evidence used in automatic assertion
annotated property: subClassOf
annotated target: RNA-sequencing evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: polyadenylated transcript 3'-end-sequencing evidence used in automatic assertion
annotated property: definition
annotated target: A type of polyadenylated transcript 3'-end-sequencing evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

colony boundary assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: colony boundary assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: colony boundary assay evidence
subclass of: ECO_0007078
has GO evidence code: EXP
definition: A type of colony boundary assay evidence that is used in a manual assertion.
ontology term requester: OMP:DebbySiegele
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006245

Axiom
annotated source: colony boundary assay evidence used in manual assertion
annotated property: subClassOf
annotated target: ECO_0007078
is_inferred: true

Axiom
annotated source: colony boundary assay evidence used in manual assertion
annotated property: definition
annotated target: A type of colony boundary assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

colony boundary assay evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: colony boundary assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: colony boundary assay evidence
subclass of: ECO_0007625
has GO evidence code: IEA
definition: A type of colony boundary assay evidence that is used in an automatic assertion.
ontology term requester: OMP:DebbySiegele
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006246

Axiom
annotated source: colony boundary assay evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007625
is_inferred: true

Axiom
annotated source: colony boundary assay evidence used in automatic assertion
annotated property: definition
annotated target: A type of colony boundary assay evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

analytical ultracentrifugation evidence
type: Class
subclass of: molecule detection assay evidence
definition: A type of molecule detection assay evidence where the hydrodynamic behaviour of macromolecules is used to study their size, shape and interactions, by spinning the sample solution at high centrifugal field (up to above 100000 rpm and 1000000 g), and monitoring the evolution of sample concentration profile versus the axis of rotation.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: AUC
has_obo_namespace: eco
id: ECO:0006247

Axiom
annotated source: analytical ultracentrifugation evidence
annotated property: definition
annotated target: A type of molecule detection assay evidence where the hydrodynamic behaviour of macromolecules is used to study their size, shape and interactions, by spinning the sample solution at high centrifugal field (up to above 100000 rpm and 1000000 g), and monitoring the evolution of sample concentration profile versus the axis of rotation.
database_cross_reference: PMID:12192063

fluorescence polarization evidence
type: Class
subclass of: physical interaction evidence
definition: A type of physical interaction evidence based on the measurement of the change in the degree of polarization of a fluorophore upon binding to a molecular partner.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: FP
has_obo_namespace: eco
id: ECO:0006248

Axiom
annotated source: fluorescence polarization evidence
annotated property: definition
annotated target: A type of physical interaction evidence based on the measurement of the change in the degree of polarization of a fluorophore upon binding to a molecular partner.
database_cross_reference: PMID:21372817

obsolete bait-prey protein pull-down evidence
type: Class
definition: OBSOLETE A type of protein binding evidence resulting from an affinity purification in-vitro technique used to detect physical interactions between two or more proteins, where a molecule of interest - a "bait" - is immobilized and incubated with a protein source containing putative "prey" proteins.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006249
comment: This term has been obsoleted as this is same as the term bait-prey hybrid interaction evidence.
deprecated: true

Axiom
annotated source: obsolete bait-prey protein pull-down evidence
annotated property: definition
annotated target: OBSOLETE A type of protein binding evidence resulting from an affinity purification in-vitro technique used to detect physical interactions between two or more proteins, where a molecule of interest - a "bait" - is immobilized and incubated with a protein source containing putative "prey" proteins.
database_cross_reference: PMID:28667618

rotary shadowing electron microscopy evidence
type: Class
subclass of: electron microscopy evidence
definition: A type of electron microscopy evidence where a heavy metal is evaporated onto surface adsorbed molecules and macromolecular assemblies allowing high-contrast visualization of both individual macromolecules and the surface structure of macromolecular assemblies.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: RS-TEM
has_obo_namespace: eco
id: ECO:0006250

Axiom
annotated source: rotary shadowing electron microscopy evidence
annotated property: definition
annotated target: A type of electron microscopy evidence where a heavy metal is evaporated onto surface adsorbed molecules and macromolecular assemblies allowing high-contrast visualization of both individual macromolecules and the surface structure of macromolecular assemblies.
database_cross_reference: PMID:19247619

electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence
type: Class
subclass of: mass spectrometry evidence
definition: A type of mass spectrometry evidence resulting from the ionization of polar functional groups producing multiple charged ions followed by the detection of ion cyclotron frequencies within a magnetic field, making it suitable for the study of large molecules (>2 kDa).
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: ESI FT-ICR MS
has_obo_namespace: eco
id: ECO:0006251

Axiom
annotated source: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence
annotated property: definition
annotated target: A type of mass spectrometry evidence resulting from the ionization of polar functional groups producing multiple charged ions followed by the detection of ion cyclotron frequencies within a magnetic field, making it suitable for the study of large molecules (>2 kDa).
database_cross_reference: PMID:10575730

magnetic resonance evidence
type: Class
subclass of: experimental evidence
definition: A type of experimental evidence in which particles in strong constant magnetic field are perturbed by a weak oscillating magnetic field and the resulting eletromagnetic signal is captured.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006252

Axiom
annotated source: magnetic resonance evidence
annotated property: definition
annotated target: A type of experimental evidence in which particles in strong constant magnetic field are perturbed by a weak oscillating magnetic field and the resulting eletromagnetic signal is captured.
database_cross_reference: ECO:MG

electron paramagnetic resonance evidence
type: Class
subclass of: magnetic resonance evidence
definition: A type of magnetic resonance evidence in which unpaired electrons in a strong constant magnetic field are perturbed by a weak oscillating magnetic field and the resulting electromagnetic signal is captured.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: EPR
has_exact_synonym: ESR
has_obo_namespace: eco
id: ECO:0006253

Axiom
annotated source: electron paramagnetic resonance evidence
annotated property: definition
annotated target: A type of magnetic resonance evidence in which unpaired electrons in a strong constant magnetic field are perturbed by a weak oscillating magnetic field and the resulting electromagnetic signal is captured.
database_cross_reference: PMID:21826602
database_cross_reference: url:https://en.wikipedia.org/wiki/Electron_paramagnetic_resonance

site-directed spin-labelling electron paramagnetic resonance evidence
type: Class
subclass of: electron paramagnetic resonance evidence
definition: A type of electron paramagnetic resonance evidence where the signal is obtained by labeling the protein in specific sites with a functional group (most often a nitroxide) containing an unpaired electron using site-directed mutagenesis.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: SDSL
has_obo_namespace: eco
id: ECO:0006254

Axiom
annotated source: site-directed spin-labelling electron paramagnetic resonance evidence
annotated property: definition
annotated target: A type of electron paramagnetic resonance evidence where the signal is obtained by labeling the protein in specific sites with a functional group (most often a nitroxide) containing an unpaired electron using site-directed mutagenesis.
database_cross_reference: PMID:21826602
database_cross_reference: url:https://en.wikipedia.org/wiki/Site-directed_spin_labeling

deglycosylation assay evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where the removal of glycan groups from a substrate (RNA, DNA, or protein) is detected.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006255

Axiom
annotated source: deglycosylation assay evidence
annotated property: definition
annotated target: A type of direct assay evidence where the removal of glycan groups from a substrate (RNA, DNA, or protein) is detected.
database_cross_reference: url:https://en.wikipedia.org/wiki/Glycosylation

protein fragment functional complementation evidence
type: Class
subclass of: physical interaction evidence
definition: A type of physical interaction evidence that is based on the detection of a protein-protein interaction between a bait and prey protein by reconstitution of a reporter protein serving as a detectable entity (usually an enzyme or a fluorescent protein), the two halves of which are each attached separately to the bait and prey.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006256

Axiom
annotated source: protein fragment functional complementation evidence
annotated property: definition
annotated target: A type of physical interaction evidence that is based on the detection of a protein-protein interaction between a bait and prey protein by reconstitution of a reporter protein serving as a detectable entity (usually an enzyme or a fluorescent protein), the two halves of which are each attached separately to the bait and prey.
database_cross_reference: PMID:31274323

beta galactosidase functional complementation evidence
type: Class
subclass of: protein fragment functional complementation evidence
definition: A type of protein fragment functional complementaion evidence where the interaction between bait and prey assemble a functional beta galactosidase enzyme.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006257

Axiom
annotated source: beta galactosidase functional complementation evidence
annotated property: definition
annotated target: A type of protein fragment functional complementaion evidence where the interaction between bait and prey assemble a functional beta galactosidase enzyme.
database_cross_reference: PMID:9237989

GAL4-VP16 functional complementation evidence
type: Class
subclass of: protein fragment functional complementation evidence
definition: A type of protein fragment functional complementaion evidence where the interaction between bait and prey assemble a transcriptional activation complex consisting of the GAL4 DNA-binding domain and the transactivation domain from the herpes simplex virus protein VP16.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006258

Axiom
annotated source: GAL4-VP16 functional complementation evidence
annotated property: definition
annotated target: A type of protein fragment functional complementaion evidence where the interaction between bait and prey assemble a transcriptional activation complex consisting of the GAL4 DNA-binding domain and the transactivation domain from the herpes simplex virus protein VP16.
database_cross_reference: PSI-MI:0728

Raman spectroscopy evidence
type: Class
subclass of: spectrophotometry evidence
subclass of: structure determination evidence
definition: A type of spectrophotometry evidence used to determine a structural fingerprint of the molecule in solution by probing its vibrational modes via the inelastic scattering of photons (called Raman scattering).
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: ROA
has_exact_synonym: Raman optical activity
has_obo_namespace: eco
id: ECO:0006259

Axiom
annotated source: Raman spectroscopy evidence
annotated property: definition
annotated target: A type of spectrophotometry evidence used to determine a structural fingerprint of the molecule in solution by probing its vibrational modes via the inelastic scattering of photons (called Raman scattering).
database_cross_reference: url:https://en.wikipedia.org/wiki/Raman_spectroscopy

protein thermal shift assay evidence
type: Class
subclass of: heat capacity-based evidence
definition: A type of heat capacity-based evidence in which the denaturation temperature of a protein sample is measured under varying conditions, such as pH, redox potential, concentration of other molecules or changes in the proteoform, to determine the effect of these factors on protein thermal stability.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006260

Axiom
annotated source: protein thermal shift assay evidence
annotated property: definition
annotated target: A type of heat capacity-based evidence in which the denaturation temperature of a protein sample is measured under varying conditions, such as pH, redox potential, concentration of other molecules or changes in the proteoform, to determine the effect of these factors on protein thermal stability.
database_cross_reference: url:https://en.wikipedia.org/wiki/Thermal_shift_assay

microscale thermophoresis evidence
type: Class
subclass of: physical interaction evidence
subclass of: fluorescence evidence
definition: A type of physical interaction evidence resulting from measuring the change of the fluorescent activity of a molecule as a function of binding to a non-fluorescent partner and its movement in a microspcopic thermal gradient affecting the intensity of fluorescence.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: MST
has_obo_namespace: eco
id: ECO:0006261

Axiom
annotated source: microscale thermophoresis evidence
annotated property: definition
annotated target: A type of physical interaction evidence resulting from measuring the change of the fluorescent activity of a molecule as a function of binding to a non-fluorescent partner and its movement in a microspcopic thermal gradient affecting the intensity of fluorescence.
database_cross_reference: PMID:23270813
database_cross_reference: url:https://en.wikipedia.org/wiki/Microscale_thermophoresis

native protein gel electrophoresis evidence
type: Class
subclass of: gel electrophoresis evidence
definition: A type of gel electrophoresis evidence resulting from the use of non-denaturing conditions so that the proteins being measured are in their native structural states.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: native gel
has_narrow_synonym: BN-PAGE
has_narrow_synonym: CN-PAGE
has_narrow_synonym: QPNC-PAGE
has_narrow_synonym: native PAGE
has_obo_namespace: eco
id: ECO:0006262

Axiom
annotated source: native protein gel electrophoresis evidence
annotated property: definition
annotated target: A type of gel electrophoresis evidence resulting from the use of non-denaturing conditions so that the proteins being measured are in their native structural states.
database_cross_reference: url:https://en.wikipedia.org/wiki/Gel_electrophoresis_of_proteins

turbidity measurement evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where the optical properties of a solution is measured in the visible light spectrum, assessing the haziness or cloudiness as a result of the properties of the solutes or the changes in their material states.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006263

Axiom
annotated source: turbidity measurement evidence
annotated property: definition
annotated target: A type of direct assay evidence where the optical properties of a solution is measured in the visible light spectrum, assessing the haziness or cloudiness as a result of the properties of the solutes or the changes in their material states.
database_cross_reference: url:https://en.wikipedia.org/wiki/Turbidity

competitive binding evidence
type: Class
subclass of: affinity evidence
definition: A type of affinity evidence derived from an experimental setup where the binding properties of a ligand are assessed by measuring the competition with another ligand with already known binding properties.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: competition assay
has_obo_namespace: eco
id: ECO:0006264

Axiom
annotated source: competitive binding evidence
annotated property: definition
annotated target: A type of affinity evidence derived from an experimental setup where the binding properties of a ligand are assessed by measuring the competition with another ligand with already known binding properties.
database_cross_reference: PMID:21115850

protein unfolding evidence
type: Class
subclass of: structure determination evidence
definition: A type of structure determination evidence obtained by monitoring structural changes of a protein as a response to changes of an environmental parameter, such as pH or temperature, or the concentration of a denaturant, such as urea.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: protein denaturation assay
has_obo_namespace: eco
id: ECO:0006265

Axiom
annotated source: protein unfolding evidence
annotated property: definition
annotated target: A type of structure determination evidence obtained by monitoring structural changes of a protein as a response to changes of an environmental parameter, such as pH or temperature, or the concentration of a denaturant, such as urea.
database_cross_reference: url:https://en.wikipedia.org/wiki/Equilibrium_unfolding

urea-induced protein unfolding evidence
type: Class
subclass of: protein unfolding evidence
definition: A type of protein unfolding evidence where the unfolding of the protein is triggered by increasing concentrations of urea.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_broad_synonym: chemical denaturation
has_broad_synonym: chemical unfolding
has_obo_namespace: eco
id: ECO:0006266

Axiom
annotated source: urea-induced protein unfolding evidence
annotated property: definition
annotated target: A type of protein unfolding evidence where the unfolding of the protein is triggered by increasing concentrations of urea.
database_cross_reference: PMID:19708649

pH-induced protein unfolding evidence
type: Class
subclass of: protein unfolding evidence
definition: A type of protein unfolding evidence where the unfolding of the protein is triggered by changes in pH.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006267

Axiom
annotated source: pH-induced protein unfolding evidence
annotated property: definition
annotated target: A type of protein unfolding evidence where the unfolding of the protein is triggered by changes in pH.
database_cross_reference: PMID:23185611

temperature-induced protein unfolding evidence
type: Class
subclass of: protein unfolding evidence
definition: A type of protein unfolding evidence where the unfolding of the protein is triggered by changes in temperature.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: thermal dentauration
has_exact_synonym: thermal unfolding
has_obo_namespace: eco
id: ECO:0006268

Axiom
annotated source: temperature-induced protein unfolding evidence
annotated property: definition
annotated target: A type of protein unfolding evidence where the unfolding of the protein is triggered by changes in temperature.
database_cross_reference: PMID:23185611

cell aggregation evidence
type: Class
subclass of: cell-based assay evidence
definition: A type of cell-based assay evidence resulting from the analysis of cells irreversibly binding to each other.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006269

Axiom
annotated source: cell aggregation evidence
annotated property: definition
annotated target: A type of cell-based assay evidence resulting from the analysis of cells irreversibly binding to each other.
database_cross_reference: PMID:24092433

RNA-protein binding evidence
type: Class
subclass of: protein binding evidence
subclass of: nucleic acid binding evidence
definition: A type of affinity evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to RNA.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006270

Axiom
annotated source: RNA-protein binding evidence
annotated property: definition
annotated target: A type of affinity evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to RNA.
database_cross_reference: PMID:30804549

fluorescence microscopy evidence
type: Class
subclass of: microscopy evidence
subclass of: fluorescence evidence
definition: A type of microscopy evidence that is obtained by using the fluorescence of the studied sample instead of or in addition to the scattering, reflection, attenuation or absorption of light.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006271

Axiom
annotated source: fluorescence microscopy evidence
annotated property: definition
annotated target: A type of microscopy evidence that is obtained by using the fluorescence of the studied sample instead of or in addition to the scattering, reflection, attenuation or absorption of light.
database_cross_reference: url:https://en.wikipedia.org/wiki/Fluorescence_microscope

viscosity measurement evidence
type: Class
subclass of: direct assay evidence
definition: A type of direct assay evidence where the viscosity of a solution is measured to quantify the material properties of the solution, or the changes of these properties in response to changing composition or environmental factors.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: viscometry
has_obo_namespace: eco
id: ECO:0006272

Axiom
annotated source: viscosity measurement evidence
annotated property: definition
annotated target: A type of direct assay evidence where the viscosity of a solution is measured to quantify the material properties of the solution, or the changes of these properties in response to changing composition or environmental factors.
database_cross_reference: url:https://en.wikipedia.org/wiki/Viscometer

dynamic fluorescence quenching evidence
type: Class
subclass of: physical interaction evidence
subclass of: fluorescence evidence
definition: A type of physical interaction evidence derived from the decrease (quenching) of fluorescence as a result of the interaction between a fluorescence donor and acceptor in their excited state.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_broad_synonym: quenching
has_narrow_synonym: Dexter
has_narrow_synonym: FRET
has_narrow_synonym: exciplex
has_obo_namespace: eco
id: ECO:0006273

Axiom
annotated source: dynamic fluorescence quenching evidence
annotated property: definition
annotated target: A type of physical interaction evidence derived from the decrease (quenching) of fluorescence as a result of the interaction between a fluorescence donor and acceptor in their excited state.
database_cross_reference: url:https://en.wikipedia.org/wiki/Quenching_(fluorescence)

static fluorescence quenching evidence
type: Class
subclass of: physical interaction evidence
subclass of: fluorescence evidence
definition: A type of physical interaction evidence derived from the decrease (quenching) of fluorescence as a result of the intramolecular interaction between a fluorescence donor and acceptor creating a non-fluorescent ground state.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_broad_synonym: quenching
has_obo_namespace: eco
id: ECO:0006274

Axiom
annotated source: static fluorescence quenching evidence
annotated property: definition
annotated target: A type of physical interaction evidence derived from the decrease (quenching) of fluorescence as a result of the intramolecular interaction between a fluorescence donor and acceptor creating a non-fluorescent ground state.
database_cross_reference: url:https://en.wikipedia.org/wiki/Quenching_(fluorescence)

analytical ultracentrifugation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: analytical ultracentrifugation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: analytical ultracentrifugation evidence
has GO evidence code: EXP
definition: A type of analytical ultracentrifugation evidence that is used in a manual assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: AUC
has_obo_namespace: eco
id: ECO:0006275

Axiom
annotated source: analytical ultracentrifugation evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: analytical ultracentrifugation evidence used in manual assertion
annotated property: definition
annotated target: A type of analytical ultracentrifugation evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

analytical ultracentrifugation evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: analytical ultracentrifugation evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: analytical ultracentrifugation evidence
subclass of: ECO_0007816
has GO evidence code: IEA
definition: A type of analytical ultracentrifugation evidence that is used in an automatic assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: AUC
has_obo_namespace: eco
id: ECO:0006276

Axiom
annotated source: analytical ultracentrifugation evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007816
is_inferred: true

Axiom
annotated source: analytical ultracentrifugation evidence used in automatic assertion
annotated property: definition
annotated target: A type of analytical ultracentrifugation evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

fluorescence polarization evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: fluorescence polarization evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: physical interaction evidence used in manual assertion
subclass of: fluorescence polarization evidence
has GO evidence code: IPI
definition: A type of fluorescence polarization evidence that is used in a manual assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: FP
has_obo_namespace: eco
id: ECO:0006277

Axiom
annotated source: fluorescence polarization evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: fluorescence polarization evidence used in manual assertion
annotated property: definition
annotated target: A type of fluorescence polarization evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

fluorescence polarization evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: fluorescence polarization evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: fluorescence polarization evidence
subclass of: ECO_0007332
has GO evidence code: IEA
definition: A type of fluorescence polarization evidence that is used in an automatic assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: FP
has_obo_namespace: eco
id: ECO:0006278

Axiom
annotated source: fluorescence polarization evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007332
is_inferred: true

Axiom
annotated source: fluorescence polarization evidence used in automatic assertion
annotated property: definition
annotated target: A type of fluorescence polarization evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

obsolete bait-prey protein pull-down evidence used in manual assertion
type: Class
definition: OBSOLETE A type of bait-prey protein pull-down evidence that is used in a manual assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006279
deprecated: true

Axiom
annotated source: obsolete bait-prey protein pull-down evidence used in manual assertion
annotated property: definition
annotated target: OBSOLETE A type of bait-prey protein pull-down evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

obsolete bait-prey protein pull-down evidence used in automatic assertion
type: Class
definition: OBSOLETE A type of bait-prey protein pull-down evidence that is used in an automatic assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006280
deprecated: true

Axiom
annotated source: obsolete bait-prey protein pull-down evidence used in automatic assertion
annotated property: definition
annotated target: OBSOLETE A type of bait-prey protein pull-down evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

rotary shadowing electron microscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: rotary shadowing electron microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: electron microscopy evidence used in manual assertion
subclass of: rotary shadowing electron microscopy evidence
has GO evidence code: IDA
definition: A type of rotary shadowing electron microscopy evidence that is used in a manual assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: RS-TEM
has_obo_namespace: eco
id: ECO:0006281

Axiom
annotated source: rotary shadowing electron microscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: electron microscopy evidence used in manual assertion
is_inferred: true

Axiom
annotated source: rotary shadowing electron microscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of rotary shadowing electron microscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

rotary shadowing electron microscopy evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: rotary shadowing electron microscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: rotary shadowing electron microscopy evidence
subclass of: ECO_0007493
has GO evidence code: IEA
definition: A type of rotary shadowing electron microscopy evidence that is used in an automatic assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: RS-TEM
has_obo_namespace: eco
id: ECO:0006282

Axiom
annotated source: rotary shadowing electron microscopy evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007493
is_inferred: true

Axiom
annotated source: rotary shadowing electron microscopy evidence used in automatic assertion
annotated property: definition
annotated target: A type of rotary shadowing electron microscopy evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: mass spectrometry evidence used in manual assertion
subclass of: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence
has GO evidence code: EXP
definition: A type of electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence that is used in a manual assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: ESI FT-ICR MS
has_obo_namespace: eco
id: ECO:0006283

Axiom
annotated source: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in manual assertion
annotated property: subClassOf
annotated target: mass spectrometry evidence used in manual assertion
is_inferred: true

Axiom
annotated source: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in manual assertion
annotated property: definition
annotated target: A type of electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence
subclass of: ECO_0007433
has GO evidence code: IEA
definition: A type of electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence that is used in an automatic assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_exact_synonym: ESI FT-ICR MS
has_obo_namespace: eco
id: ECO:0006284

Axiom
annotated source: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007433
is_inferred: true

Axiom
annotated source: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in automatic assertion
annotated property: definition
annotated target: A type of electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

magnetic resonance evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: magnetic resonance evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: experimental evidence used in manual assertion
subclass of: magnetic resonance evidence
has GO evidence code: EXP
definition: A type of magnetic resonance evidence that is used in a manual assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006285

Axiom
annotated source: magnetic resonance evidence used in manual assertion
annotated property: subClassOf
annotated target: experimental evidence used in manual assertion
is_inferred: true

Axiom
annotated source: magnetic resonance evidence used in manual assertion
annotated property: definition
annotated target: A type of magnetic resonance evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

magnetic resonance evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: magnetic resonance evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: magnetic resonance evidence
subclass of: ECO_0007297
has GO evidence code: IEA
definition: A type of magnetic resonance evidence that is used in an automatic assertion.
ontology term requester: DisProt:FedericaQuaglia
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006286

Axiom
annotated source: magnetic resonance evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007297
is_inferred: true

Axiom
annotated source: magnetic resonance evidence used in automatic assertion
annotated property: definition
annotated target: A type of magnetic resonance evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

electron paramagnetic resonance evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: electron paramagnetic resonance evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: electron paramagnetic resonance evidence
subclass of: magnetic resonance evidence used in manual assertion
has GO evidence code: EXP
definition: A type of electron paramagnetic resonance evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: EPR
has_exact_synonym: ESR
has_obo_namespace: eco
id: ECO:0006287

Axiom
annotated source: electron paramagnetic resonance evidence used in manual assertion
annotated property: subClassOf
annotated target: magnetic resonance evidence used in manual assertion
is_inferred: true

Axiom
annotated source: electron paramagnetic resonance evidence used in manual assertion
annotated property: definition
annotated target: A type of electron paramagnetic resonance evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

electron paramagnetic resonance evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: electron paramagnetic resonance evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: electron paramagnetic resonance evidence
subclass of: magnetic resonance evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of electron paramagnetic resonance evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: EPR
has_exact_synonym: ESR
has_obo_namespace: eco
id: ECO:0006288

Axiom
annotated source: electron paramagnetic resonance evidence used in automatic assertion
annotated property: subClassOf
annotated target: magnetic resonance evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: electron paramagnetic resonance evidence used in automatic assertion
annotated property: definition
annotated target: A type of electron paramagnetic resonance evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

site-directed spin-labelling electron paramagnetic resonance evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: site-directed spin-labelling electron paramagnetic resonance evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: site-directed spin-labelling electron paramagnetic resonance evidence
subclass of: electron paramagnetic resonance evidence used in manual assertion
has GO evidence code: EXP
definition: A type of site-directed spin-labelling electron paramagnetic resonance evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: SDSL
has_obo_namespace: eco
id: ECO:0006289

Axiom
annotated source: site-directed spin-labelling electron paramagnetic resonance evidence used in manual assertion
annotated property: subClassOf
annotated target: electron paramagnetic resonance evidence used in manual assertion
is_inferred: true

Axiom
annotated source: site-directed spin-labelling electron paramagnetic resonance evidence used in manual assertion
annotated property: definition
annotated target: A type of site-directed spin-labelling electron paramagnetic resonance evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

site-directed spin-labelling electron paramagnetic resonance evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: site-directed spin-labelling electron paramagnetic resonance evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: site-directed spin-labelling electron paramagnetic resonance evidence
subclass of: electron paramagnetic resonance evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of site-directed spin-labelling electron paramagnetic resonance evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: SDSL
has_obo_namespace: eco
id: ECO:0006290

Axiom
annotated source: site-directed spin-labelling electron paramagnetic resonance evidence used in automatic assertion
annotated property: subClassOf
annotated target: electron paramagnetic resonance evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: site-directed spin-labelling electron paramagnetic resonance evidence used in automatic assertion
annotated property: definition
annotated target: A type of site-directed spin-labelling electron paramagnetic resonance evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

deglycosylation assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: deglycosylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: deglycosylation assay evidence
has GO evidence code: IDA
definition: A type of deglycosylation assay evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006291

Axiom
annotated source: deglycosylation assay evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: deglycosylation assay evidence used in manual assertion
annotated property: definition
annotated target: A type of deglycosylation assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

deglycosylation assay evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: deglycosylation assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: deglycosylation assay evidence
subclass of: ECO_0007307
has GO evidence code: IEA
definition: A type of deglycosylation assay evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006292

Axiom
annotated source: deglycosylation assay evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007307
is_inferred: true

Axiom
annotated source: deglycosylation assay evidence used in automatic assertion
annotated property: definition
annotated target: A type of deglycosylation assay evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

protein fragment functional complementation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein fragment functional complementation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: physical interaction evidence used in manual assertion
subclass of: protein fragment functional complementation evidence
has GO evidence code: IPI
definition: A type of protein fragment functional complementation evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006293

Axiom
annotated source: protein fragment functional complementation evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: protein fragment functional complementation evidence used in manual assertion
annotated property: definition
annotated target: A type of protein fragment functional complementation evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

protein fragment functional complementation evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: protein fragment functional complementation evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: protein fragment functional complementation evidence
subclass of: ECO_0007332
has GO evidence code: IEA
definition: A type of protein fragment functional complementation evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006294

Axiom
annotated source: protein fragment functional complementation evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007332
is_inferred: true

Axiom
annotated source: protein fragment functional complementation evidence used in automatic assertion
annotated property: definition
annotated target: A type of protein fragment functional complementation evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

beta galactosidase functional complementation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: beta galactosidase functional complementation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: beta galactosidase functional complementation evidence
subclass of: protein fragment functional complementation evidence used in manual assertion
has GO evidence code: IPI
definition: A type of beta galactosidase functional complementation evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006295

Axiom
annotated source: beta galactosidase functional complementation evidence used in manual assertion
annotated property: subClassOf
annotated target: protein fragment functional complementation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: beta galactosidase functional complementation evidence used in manual assertion
annotated property: definition
annotated target: A type of beta galactosidase functional complementation evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

beta galactosidase functional complementation evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: beta galactosidase functional complementation evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: beta galactosidase functional complementation evidence
subclass of: protein fragment functional complementation evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of beta galactosidase functional complementation evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006296

Axiom
annotated source: beta galactosidase functional complementation evidence used in automatic assertion
annotated property: subClassOf
annotated target: protein fragment functional complementation evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: beta galactosidase functional complementation evidence used in automatic assertion
annotated property: definition
annotated target: A type of beta galactosidase functional complementation evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

GAL4-VP16 functional complementation evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: GAL4-VP16 functional complementation evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: GAL4-VP16 functional complementation evidence
subclass of: protein fragment functional complementation evidence used in manual assertion
has GO evidence code: IPI
definition: A type of GAL4-VP16 functional complementation evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006297

Axiom
annotated source: GAL4-VP16 functional complementation evidence used in manual assertion
annotated property: subClassOf
annotated target: protein fragment functional complementation evidence used in manual assertion
is_inferred: true

Axiom
annotated source: GAL4-VP16 functional complementation evidence used in manual assertion
annotated property: definition
annotated target: A type of GAL4-VP16 functional complementation evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

GAL4-VP16 functional complementation evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: GAL4-VP16 functional complementation evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: GAL4-VP16 functional complementation evidence
subclass of: protein fragment functional complementation evidence used in automatic assertion
has GO evidence code: IEA
definition: A type of GAL4-VP16 functional complementation evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006298

Axiom
annotated source: GAL4-VP16 functional complementation evidence used in automatic assertion
annotated property: subClassOf
annotated target: protein fragment functional complementation evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: GAL4-VP16 functional complementation evidence used in automatic assertion
annotated property: definition
annotated target: A type of GAL4-VP16 functional complementation evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

Raman spectroscopy evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: Raman spectroscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: spectrophotometry evidence used in manual assertion
subclass of: Raman spectroscopy evidence
has GO evidence code: EXP
definition: A type of Raman spectroscopy evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: ROA
has_exact_synonym: Raman optical activity
has_obo_namespace: eco
id: ECO:0006299

Axiom
annotated source: Raman spectroscopy evidence used in manual assertion
annotated property: subClassOf
annotated target: spectrophotometry evidence used in manual assertion
is_inferred: true

Axiom
annotated source: Raman spectroscopy evidence used in manual assertion
annotated property: definition
annotated target: A type of Raman spectroscopy evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

Raman spectroscopy evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: Raman spectroscopy evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: Raman spectroscopy evidence
subclass of: ECO_0007458
subclass of: ECO_0007815
has GO evidence code: IEA
definition: A type of Raman spectroscopy evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: ROA
has_exact_synonym: Raman optical activity
has_obo_namespace: eco
id: ECO:0006300

Axiom
annotated source: Raman spectroscopy evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007458
is_inferred: true

Axiom
annotated source: Raman spectroscopy evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007815
is_inferred: true

Axiom
annotated source: Raman spectroscopy evidence used in automatic assertion
annotated property: definition
annotated target: A type of Raman spectroscopy evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

protein thermal shift assay evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: protein thermal shift assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: heat capacity-based evidence used in manual assertion
subclass of: protein thermal shift assay evidence
has GO evidence code: IDA
definition: A type of protein thermal shift assay evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006301

Axiom
annotated source: protein thermal shift assay evidence used in manual assertion
annotated property: subClassOf
annotated target: heat capacity-based evidence used in manual assertion
is_inferred: true

Axiom
annotated source: protein thermal shift assay evidence used in manual assertion
annotated property: definition
annotated target: A type of protein thermal shift assay evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

protein thermal shift assay evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: protein thermal shift assay evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: heat capacity-based evidence used in automatic assertion
subclass of: protein thermal shift assay evidence
has GO evidence code: IEA
definition: A type of protein thermal shift assay evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_obo_namespace: eco
id: ECO:0006302

Axiom
annotated source: protein thermal shift assay evidence used in automatic assertion
annotated property: subClassOf
annotated target: heat capacity-based evidence used in automatic assertion
is_inferred: true

Axiom
annotated source: protein thermal shift assay evidence used in automatic assertion
annotated property: definition
annotated target: A type of protein thermal shift assay evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

microscale thermophoresis evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: microscale thermophoresis evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: physical interaction evidence used in manual assertion
subclass of: fluorescence evidence used in manual assertion
subclass of: microscale thermophoresis evidence
has GO evidence code: IPI
definition: A type of microscale thermophoresis evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: MST
has_obo_namespace: eco
id: ECO:0006303

Axiom
annotated source: microscale thermophoresis evidence used in manual assertion
annotated property: subClassOf
annotated target: physical interaction evidence used in manual assertion
is_inferred: true

Axiom
annotated source: microscale thermophoresis evidence used in manual assertion
annotated property: subClassOf
annotated target: fluorescence evidence used in manual assertion
is_inferred: true

Axiom
annotated source: microscale thermophoresis evidence used in manual assertion
annotated property: definition
annotated target: A type of microscale thermophoresis evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

microscale thermophoresis evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: microscale thermophoresis evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: microscale thermophoresis evidence
subclass of: ECO_0007332
subclass of: ECO_0007450
has GO evidence code: IEA
definition: A type of microscale thermophoresis evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: MST
has_obo_namespace: eco
id: ECO:0006304

Axiom
annotated source: microscale thermophoresis evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007332
is_inferred: true

Axiom
annotated source: microscale thermophoresis evidence used in automatic assertion
annotated property: subClassOf
annotated target: ECO_0007450
is_inferred: true

Axiom
annotated source: microscale thermophoresis evidence used in automatic assertion
annotated property: definition
annotated target: A type of microscale thermophoresis evidence that is used in an automatic assertion.
database_cross_reference: ECO:SN

native protein gel electrophoresis evidence used in manual assertion
type: Class
equivalent class: Class
  intersection of: native protein gel electrophoresis evidence
  intersection of: Restriction
    on property: used_in
    some values from: manual assertion
subclass of: direct assay evidence used in manual assertion
subclass of: native protein gel electrophoresis evidence
has GO evidence code: IDA
definition: A type of native protein gel electrophoresis evidence that is used in a manual assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: native gel
has_narrow_synonym: BN-PAGE
has_narrow_synonym: CN-PAGE
has_narrow_synonym: QPNC-PAGE
has_narrow_synonym: native PAGE
has_obo_namespace: eco
id: ECO:0006305

Axiom
annotated source: native protein gel electrophoresis evidence used in manual assertion
annotated property: subClassOf
annotated target: direct assay evidence used in manual assertion
is_inferred: true

Axiom
annotated source: native protein gel electrophoresis evidence used in manual assertion
annotated property: definition
annotated target: A type of native protein gel electrophoresis evidence that is used in a manual assertion.
database_cross_reference: ECO:SN

native protein gel electrophoresis evidence used in automatic assertion
type: Class
equivalent class: Class
  intersection of: native protein gel electrophoresis evidence
  intersection of: Restriction
    on property: used_in
    some values from: automatic assertion
subclass of: native protein gel electrophoresis evidence
subclass of: ECO_0007769
has GO evidence code: IEA
definition: A type of native protein gel electrophoresis evidence that is used in an automatic assertion.
ontology term requester: DisProt:BalintMeszaros
created_by: snadendla
has_exact_synonym: native gel
has_narrow_synonym: BN-PAGE
has_narrow_synonym: CN-PAGE
has_narrow_synonym: QPNC-PAGE
has_narrow_synonym: native PAGE
has_obo_namespace: eco
id: ECO:0006306