cio.owl
type: Ontology
has_obo_format_version: 1.4
default-namespace: cio
version IRI: cio.owl

definition
type: AnnotationProperty

bgee not trusted
type: AnnotationProperty
comment: Terms that are considered not trusted by the Bgee team, related to assertions needing additional support.
sub property of: subset_property

subset_property
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

has confidence element
type: ObjectProperty
shorthand: has_confidence_element
definition: X has confidence element Y iff X is a confidence information statement and Y is an associated confidence information element, used to define the statement.
domain: confidence information statement
range: confidence information element

has confidence level
type: ObjectProperty
shorthand: has_confidence_level
definition: X has confidence level Y iff X is a confidence information statement and Y is it associated confidence information level.
range: confidence level
sub property of: has confidence element
domain: Class
  intersection of: confidence information statement
  intersection of: Restriction
    on property: has evidence concordance
    all values from: Class
      complement of: strongly conflicting

has evidence concordance
type: ObjectProperty
shorthand: has_evidence_concordance
definition: X has evidence concordance Y iff X is a confidence information statement and Y is it associated evidence concordance.
domain: confidence information statement
range: evidence concordance
sub property of: has confidence element

has evidence type concordance
type: ObjectProperty
shorthand: has_evidence_type_concordance
definition: X has evidence type concordance Y iff X is a confidence information statement and Y is it associated evidence type concordance.
range: evidence type concordance
sub property of: has confidence element
domain: Class
  intersection of: confidence information statement
  intersection of: Restriction
    on property: has evidence concordance
    all values from: concordance of multiple evidence lines

provides greater confidence than
type: ObjectProperty
type: TransitiveProperty
shorthand: provides_greater_confidence_than
definition: X provides greater confidence than Y iff both X and Y provide a confidence information level, and the level of confidence provided by X is greater than the level of confidence provided by Y.
domain: confidence level
range: confidence level

confidence information statement
type: Class
equivalent class: Class
  union of: Class
    intersection of: Restriction
      on property: has evidence concordance
      all values from: single evidence
    intersection of: Restriction
      on property: has confidence element
      on class: confidence information element
      min qualified cardinality: 1
    intersection of: Restriction
      on property: has confidence level
      on class: confidence level
      min qualified cardinality: 0
    intersection of: Restriction
      on property: has evidence type concordance
      on class: evidence type concordance
      qualified cardinality: 0
    intersection of: Restriction
      on property: has confidence element
      on class: confidence information element
      max qualified cardinality: 2
    intersection of: Restriction
      on property: has confidence level
      on class: confidence level
      max qualified cardinality: 1
  union of: Class
    intersection of: Restriction
      on property: has evidence concordance
      all values from: concordance of multiple evidence lines
    intersection of: Restriction
      on property: has confidence element
      on class: confidence information element
      min qualified cardinality: 2
    intersection of: Restriction
      on property: has confidence level
      on class: confidence level
      min qualified cardinality: 0
    intersection of: Restriction
      on property: has evidence type concordance
      on class: evidence type concordance
      qualified cardinality: 1
    intersection of: Restriction
      on property: has confidence element
      on class: confidence information element
      max qualified cardinality: 3
    intersection of: Restriction
      on property: has confidence level
      on class: confidence level
      max qualified cardinality: 1
equivalent class: Class
  intersection of: Restriction
    on property: has confidence element
    on class: confidence information element
    min qualified cardinality: 1
  intersection of: Restriction
    on property: has confidence level
    on class: confidence level
    min qualified cardinality: 0
  intersection of: Restriction
    on property: has evidence type concordance
    on class: evidence type concordance
    min qualified cardinality: 0
  intersection of: Restriction
    on property: has evidence concordance
    on class: evidence concordance
    qualified cardinality: 1
  intersection of: Restriction
    on property: has confidence element
    on class: confidence information element
    max qualified cardinality: 3
  intersection of: Restriction
    on property: has confidence level
    on class: confidence level
    max qualified cardinality: 1
  intersection of: Restriction
    on property: has evidence type concordance
    on class: evidence type concordance
    max qualified cardinality: 1
subclass of: Restriction
  on property: has confidence level
  on class: confidence level
  max qualified cardinality: 1
subclass of: Restriction
  on property: has confidence element
  on class: confidence information element
  min qualified cardinality: 1
subclass of: Restriction
  on property: has evidence type concordance
  on class: evidence type concordance
  max qualified cardinality: 1
subclass of: Restriction
  on property: has evidence type concordance
  on class: evidence type concordance
  min qualified cardinality: 0
subclass of: Restriction
  on property: has evidence concordance
  on class: evidence concordance
  qualified cardinality: 1
subclass of: Restriction
  on property: has confidence element
  on class: confidence information element
  max qualified cardinality: 3
subclass of: Restriction
  on property: has confidence level
  on class: confidence level
  min qualified cardinality: 0
disjoint with: confidence information element
definition: A statement providing information about the confidence in an assertion, meaning, an information about the level of certainty that an assertion is correct.
id: CIO:0000000
comment: Quality and confidence are distinct concepts: quality refers to the value of a source or of an annotation, whereas confidence refers to the level of certainty that an assertion is correct.

Axiom
annotated target: A statement providing information about the confidence in an assertion, meaning, an information about the level of certainty that an assertion is correct.
database_cross_reference: Bgee:fbb
annotated source: confidence information statement
annotated property: definition

confidence statement from single evidence
type: Class
equivalent class: Class
  intersection of: confidence information statement
  intersection of: Restriction
    on property: has evidence concordance
    all values from: single evidence
  intersection of: Restriction
    on property: has evidence type concordance
    on class: evidence type concordance
    qualified cardinality: 0
subclass of: confidence information statement
subclass of: Restriction
  on property: has evidence concordance
  all values from: single evidence
subclass of: Restriction
  on property: has evidence type concordance
  on class: evidence type concordance
  qualified cardinality: 0
disjoint with: confidence statement from multiple evidence lines
definition: A confidence information statement defined from a single evidence.
id: CIO:0000001

Axiom
annotated target: A confidence information statement defined from a single evidence.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from single evidence
annotated property: definition

confidence statement from multiple evidence lines
type: Class
equivalent class: Class
  intersection of: confidence information statement
  intersection of: Restriction
    on property: has evidence concordance
    all values from: concordance of multiple evidence lines
  intersection of: Restriction
    on property: has evidence type concordance
    on class: evidence type concordance
    qualified cardinality: 1
subclass of: confidence information statement
subclass of: Restriction
  on property: has evidence type concordance
  on class: evidence type concordance
  qualified cardinality: 1
subclass of: Restriction
  on property: has evidence concordance
  all values from: concordance of multiple evidence lines
definition: A confidence information statement defined from a set of evidence lines.
id: CIO:0000002

Axiom
annotated target: A confidence information statement defined from a set of evidence lines.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from multiple evidence lines
annotated property: definition

high confidence from single evidence
type: Class
equivalent class: Class
  intersection of: confidence statement from single evidence
  intersection of: Restriction
    on property: has confidence level
    all values from: high confidence level
subclass of: confidence statement from single evidence
subclass of: Restriction
  on property: has confidence level
  all values from: high confidence level
disjoint with: medium confidence from single evidence
disjoint with: low confidence from single evidence
disjoint with: rejected
definition: A confidence statement from single evidence related to assertions supported by a highly reliable evidence.
id: CIO:0000003
has related synonym: gold

Axiom
annotated target: A confidence statement from single evidence related to assertions supported by a highly reliable evidence.
database_cross_reference: Bgee:fbb
annotated source: high confidence from single evidence
annotated property: definition

Axiom
annotated target: gold
database_cross_reference: neXtProt
annotated source: high confidence from single evidence
annotated property: hasRelatedSynonym

medium confidence from single evidence
type: Class
equivalent class: Class
  intersection of: confidence statement from single evidence
  intersection of: Restriction
    on property: has confidence level
    all values from: medium confidence level
subclass of: confidence statement from single evidence
subclass of: Restriction
  on property: has confidence level
  all values from: medium confidence level
disjoint with: low confidence from single evidence
disjoint with: rejected
definition: A confidence statement from single evidence related to assertions supported by moderately trusted evidence.
id: CIO:0000004
has related synonym: silver

Axiom
annotated target: A confidence statement from single evidence related to assertions supported by moderately trusted evidence.
database_cross_reference: Bgee:fbb
annotated source: medium confidence from single evidence
annotated property: definition

Axiom
database_cross_reference: neXtProt
annotated target: silver
annotated source: medium confidence from single evidence
annotated property: hasRelatedSynonym

low confidence from single evidence
type: Class
equivalent class: Class
  intersection of: confidence statement from single evidence
  intersection of: Restriction
    on property: has confidence level
    all values from: low confidence level
subclass of: confidence statement from single evidence
subclass of: Restriction
  on property: has confidence level
  all values from: low confidence level
disjoint with: rejected
definition: A confidence statement from single evidence related to assertions supported by not-trusted evidence.
id: CIO:0000005
has related synonym: bronze
in_subset: bgee not trusted

Axiom
annotated target: A confidence statement from single evidence related to assertions supported by not-trusted evidence.
database_cross_reference: Bgee:fbb
annotated source: low confidence from single evidence
annotated property: definition

Axiom
annotated target: bronze
database_cross_reference: neXtProt
annotated source: low confidence from single evidence
annotated property: hasRelatedSynonym

confidence statement from multiple evidence lines of same type
type: Class
equivalent class: Class
  intersection of: confidence statement from multiple evidence lines
  intersection of: Restriction
    on property: has evidence type concordance
    all values from: same type
subclass of: confidence statement from multiple evidence lines
subclass of: Restriction
  on property: has evidence type concordance
  all values from: same type
disjoint with: confidence statement from multiple evidence lines of multiple types
definition: A confidence statement from multiple evidence lines, all using a same experimental or computational type.
id: CIO:0000006

Axiom
annotated target: A confidence statement from multiple evidence lines, all using a same experimental or computational type.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from multiple evidence lines of same type
annotated property: definition

confidence statement from multiple evidence lines of multiple types
type: Class
equivalent class: Class
  intersection of: confidence statement from multiple evidence lines
  intersection of: Restriction
    on property: has evidence type concordance
    all values from: different type
subclass of: confidence statement from multiple evidence lines
subclass of: Restriction
  on property: has evidence type concordance
  all values from: different type
definition: A confidence statement from multiple evidence lines, of different experimental or computational types.
id: CIO:0000007

Axiom
annotated target: A confidence statement from multiple evidence lines, of different experimental or computational types.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from multiple evidence lines of multiple types
annotated property: definition

confidence statement from congruent evidence lines of multiple types
type: Class
equivalent class: Class
  intersection of: confidence statement from multiple evidence lines of multiple types
  intersection of: Restriction
    on property: has evidence concordance
    all values from: congruent
subclass of: confidence statement from multiple evidence lines of multiple types
subclass of: Restriction
  on property: has evidence concordance
  all values from: congruent
disjoint with: confidence statement from conflicting evidence lines of multiple types
definition: A confidence statement from multiple evidence lines of multiple types, that are all congruent.
id: CIO:0000008

Axiom
annotated target: A confidence statement from multiple evidence lines of multiple types, that are all congruent.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from congruent evidence lines of multiple types
annotated property: definition

confidence statement from conflicting evidence lines of multiple types
type: Class
equivalent class: Class
  intersection of: confidence statement from multiple evidence lines of multiple types
  intersection of: Restriction
    on property: has evidence concordance
    all values from: conflicting
subclass of: confidence statement from multiple evidence lines of multiple types
subclass of: Restriction
  on property: has evidence concordance
  all values from: conflicting
definition: A confidence statement from multiple evidence lines of multiple types, some of which being contradictory.
id: CIO:0000009

Axiom
annotated target: A confidence statement from multiple evidence lines of multiple types, some of which being contradictory.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from conflicting evidence lines of multiple types
annotated property: definition

confidence statement from strongly conflicting evidence lines of multiple types
type: Class
equivalent class: Class
  intersection of: confidence statement from conflicting evidence lines of multiple types
  intersection of: Restriction
    on property: has evidence concordance
    all values from: strongly conflicting
  intersection of: Restriction
    on property: has confidence level
    on class: confidence level
    qualified cardinality: 0
subclass of: confidence statement from conflicting evidence lines of multiple types
subclass of: Restriction
  on property: has evidence concordance
  all values from: strongly conflicting
subclass of: Restriction
  on property: has confidence level
  on class: confidence level
  qualified cardinality: 0
disjoint with: confidence statement from weakly conflicting evidence lines of multiple types
definition: A confidence statement from conflicting evidence lines of multiple types, where evidence lines are in strong contradiction, meaning that the supporting evidence lines yield different conclusion, several of them being equally likely to be true.
id: CIO:0000010
in_subset: bgee not trusted

Axiom
annotated target: A confidence statement from conflicting evidence lines of multiple types, where evidence lines are in strong contradiction, meaning that the supporting evidence lines yield different conclusion, several of them being equally likely to be true.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from strongly conflicting evidence lines of multiple types
annotated property: definition

confidence statement from weakly conflicting evidence lines of multiple types
type: Class
equivalent class: Class
  intersection of: confidence statement from conflicting evidence lines of multiple types
  intersection of: Restriction
    on property: has evidence concordance
    all values from: weakly conflicting
subclass of: confidence statement from conflicting evidence lines of multiple types
subclass of: Restriction
  on property: has evidence concordance
  all values from: weakly conflicting
definition: A confidence statement from conflicting evidence lines of multiple types, where evidence lines are in weak contradiction, meaning that the overall supported assertion is believed to be true, but a subset of less-reliable evidence lines are in contradiction.
id: CIO:0000011

Axiom
annotated target: A confidence statement from conflicting evidence lines of multiple types, where evidence lines are in weak contradiction, meaning that the overall supported assertion is believed to be true, but a subset of less-reliable evidence lines are in contradiction.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from weakly conflicting evidence lines of multiple types
annotated property: definition

confidence statement from congruent evidence lines of multiple types, overall confidence high
type: Class
equivalent class: Class
  intersection of: confidence statement from congruent evidence lines of multiple types
  intersection of: Restriction
    on property: has confidence level
    all values from: high confidence level
subclass of: confidence statement from congruent evidence lines of multiple types
subclass of: Restriction
  on property: has confidence level
  all values from: high confidence level
disjoint with: confidence statement from congruent evidence lines of multiple types, overall confidence medium
disjoint with: confidence statement from congruent evidence lines of multiple types, overall confidence low
definition: A confidence statement from congruent evidence lines of multiple types, of an overall high confidence level.
id: CIO:0000012
comment: Different strategies can be used to define the overall confidence level: for instance, it could be defined based on the confidence level of the most trusted evidence, from the set of evidence lines supporting the assertion; or, it could be defined based on the number of evidence lines supporting the assertion (e.g., 10 congruent low-confidence evidence lines could allow to have an overall high confidence in an assertion). It is the responsibility of annotation teams to define and communicate the parameters, pertinent to their field, allowing to produce overall confidence levels.

Axiom
annotated target: A confidence statement from congruent evidence lines of multiple types, of an overall high confidence level.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from congruent evidence lines of multiple types, overall confidence high
annotated property: definition

confidence statement from congruent evidence lines of multiple types, overall confidence medium
type: Class
equivalent class: Class
  intersection of: confidence statement from congruent evidence lines of multiple types
  intersection of: Restriction
    on property: has confidence level
    all values from: medium confidence level
subclass of: confidence statement from congruent evidence lines of multiple types
subclass of: Restriction
  on property: has confidence level
  all values from: medium confidence level
disjoint with: confidence statement from congruent evidence lines of multiple types, overall confidence low
definition: A confidence statement from congruent evidence lines of multiple types, of an overall moderately trusted confidence level.
id: CIO:0000013
comment: Different strategies can be used to define the overall confidence level: for instance, it could be defined based on the confidence level of the most trusted evidence, from the set of evidence lines supporting the assertion; or, it could be defined based on the number of evidence lines supporting the assertion (e.g., 10 congruent low-confidence evidence lines could allow to have an overall high confidence in an assertion). It is the responsibility of annotation teams to define and communicate the parameters, pertinent to their field, allowing to produce overall confidence levels.

Axiom
annotated target: A confidence statement from congruent evidence lines of multiple types, of an overall moderately trusted confidence level.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from congruent evidence lines of multiple types, overall confidence medium
annotated property: definition

confidence statement from congruent evidence lines of multiple types, overall confidence low
type: Class
equivalent class: Class
  intersection of: confidence statement from congruent evidence lines of multiple types
  intersection of: Restriction
    on property: has confidence level
    all values from: low confidence level
subclass of: confidence statement from congruent evidence lines of multiple types
subclass of: Restriction
  on property: has confidence level
  all values from: low confidence level
definition: A confidence statement from congruent evidence lines of multiple types, of an overall not-trusted confidence level.
id: CIO:0000014
comment: Different strategies can be used to define the overall confidence level: for instance, it could be defined based on the confidence level of the most trusted evidence, from the set of evidence lines supporting the assertion; or, it could be defined based on the number of evidence lines supporting the assertion (e.g., 10 congruent low-confidence evidence lines could allow to have an overall high confidence in an assertion). It is the responsibility of annotation teams to define and communicate the parameters, pertinent to their field, allowing to produce overall confidence levels.

Axiom
annotated target: A confidence statement from congruent evidence lines of multiple types, of an overall not-trusted confidence level.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from congruent evidence lines of multiple types, overall confidence low
annotated property: definition

confidence statement from conflicting evidence lines of same type
type: Class
equivalent class: Class
  intersection of: confidence statement from multiple evidence lines of same type
  intersection of: Restriction
    on property: has evidence concordance
    all values from: conflicting
subclass of: confidence statement from multiple evidence lines of same type
subclass of: Restriction
  on property: has evidence concordance
  all values from: conflicting
disjoint with: confidence statement from congruent evidence lines of same type
id: CIO:0000015
definition: Confidence statement from multiple evidence lines of same type, some of which being contradictory.

Axiom
database_cross_reference: Bgee:fbb
annotated target: Confidence statement from multiple evidence lines of same type, some of which being contradictory.
annotated source: confidence statement from conflicting evidence lines of same type
annotated property: definition

confidence statement from congruent evidence lines of same type
type: Class
equivalent class: Class
  intersection of: confidence statement from multiple evidence lines of same type
  intersection of: Restriction
    on property: has evidence concordance
    all values from: congruent
subclass of: confidence statement from multiple evidence lines of same type
subclass of: Restriction
  on property: has evidence concordance
  all values from: congruent
id: CIO:0000016
definition: Confidence statement from multiple evidence lines of same type, that are all congruent.

Axiom
database_cross_reference: Bgee:fbb
annotated target: Confidence statement from multiple evidence lines of same type, that are all congruent.
annotated source: confidence statement from congruent evidence lines of same type
annotated property: definition

confidence statement from congruent evidence lines of same type, overall confidence high
type: Class
equivalent class: Class
  intersection of: confidence statement from congruent evidence lines of same type
  intersection of: Restriction
    on property: has confidence level
    all values from: high confidence level
subclass of: confidence statement from congruent evidence lines of same type
subclass of: Restriction
  on property: has confidence level
  all values from: high confidence level
disjoint with: confidence statement from congruent evidence lines of same type, overall confidence low
disjoint with: confidence statement from congruent evidence lines of same type, overall confidence medium
definition: A confidence statement from congruent evidence lines of same type, of an overall high confidence level.
id: CIO:0000017
comment: Different strategies can be used to define the overall confidence level: for instance, it could be defined based on the confidence level of the most trusted evidence, from the set of evidence lines supporting the assertion; or, it could be defined based on the number of evidence lines supporting the assertion (e.g., 10 congruent low-confidence evidence lines could allow to have an overall high confidence in an assertion). It is the responsibility of annotation teams to define and communicate the parameters, pertinent to their field, allowing to produce overall confidence levels.

Axiom
annotated target: A confidence statement from congruent evidence lines of same type, of an overall high confidence level.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from congruent evidence lines of same type, overall confidence high
annotated property: definition

confidence statement from congruent evidence lines of same type, overall confidence low
type: Class
equivalent class: Class
  intersection of: confidence statement from congruent evidence lines of same type
  intersection of: Restriction
    on property: has confidence level
    all values from: low confidence level
subclass of: confidence statement from congruent evidence lines of same type
subclass of: Restriction
  on property: has confidence level
  all values from: low confidence level
disjoint with: confidence statement from congruent evidence lines of same type, overall confidence medium
definition: A confidence statement from congruent evidence lines of same type, of an overall not-trusted confidence level.
id: CIO:0000018
comment: Different strategies can be used to define the overall confidence level: for instance, it could be defined based on the confidence level of the most trusted evidence, from the set of evidence lines supporting the assertion; or, it could be defined based on the number of evidence lines supporting the assertion (e.g., 10 congruent low-confidence evidence lines could allow to have an overall high confidence in an assertion). It is the responsibility of annotation teams to define and communicate the parameters, pertinent to their field, allowing to produce overall confidence levels.

Axiom
annotated target: A confidence statement from congruent evidence lines of same type, of an overall not-trusted confidence level.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from congruent evidence lines of same type, overall confidence low
annotated property: definition

confidence statement from congruent evidence lines of same type, overall confidence medium
type: Class
equivalent class: Class
  intersection of: confidence statement from congruent evidence lines of same type
  intersection of: Restriction
    on property: has confidence level
    all values from: medium confidence level
subclass of: confidence statement from congruent evidence lines of same type
subclass of: Restriction
  on property: has confidence level
  all values from: medium confidence level
definition: A confidence statement from congruent evidence lines of same type, of an overall moderately trusted confidence level.
id: CIO:0000019
comment: Different strategies can be used to define the overall confidence level: for instance, it could be defined based on the confidence level of the most trusted evidence, from the set of evidence lines supporting the assertion; or, it could be defined based on the number of evidence lines supporting the assertion (e.g., 10 congruent low-confidence evidence lines could allow to have an overall high confidence in an assertion). It is the responsibility of annotation teams to define and communicate the parameters, pertinent to their field, allowing to produce overall confidence levels.

Axiom
annotated target: A confidence statement from congruent evidence lines of same type, of an overall moderately trusted confidence level.
database_cross_reference: Bgee:fbb
annotated source: confidence statement from congruent evidence lines of same type, overall confidence medium
annotated property: definition

confidence statement from strongly conflicting evidence lines of same type
type: Class
equivalent class: Class
  intersection of: confidence statement from conflicting evidence lines of same type
  intersection of: Restriction
    on property: has evidence concordance
    all values from: strongly conflicting
  intersection of: Restriction
    on property: has confidence level
    on class: confidence level
    qualified cardinality: 0
subclass of: confidence statement from conflicting evidence lines of same type
subclass of: Restriction
  on property: has evidence concordance
  all values from: strongly conflicting
subclass of: Restriction
  on property: has confidence level
  on class: confidence level
  qualified cardinality: 0
disjoint with: confidence statement from weakly conflicting evidence lines of same type
id: CIO:0000020
definition: Confidence statement from conflicting evidence lines of same type, where evidence lines are in strong contradiction, meaning that the supporting evidence lines yield different conclusion, several of them being equally likely to be true.
in_subset: bgee not trusted

Axiom
database_cross_reference: Bgee:fbb
annotated target: Confidence statement from conflicting evidence lines of same type, where evidence lines are in strong contradiction, meaning that the supporting evidence lines yield different conclusion, several of them being equally likely to be true.
annotated source: confidence statement from strongly conflicting evidence lines of same type
annotated property: definition

confidence statement from weakly conflicting evidence lines of same type
type: Class
equivalent class: Class
  intersection of: confidence statement from conflicting evidence lines of same type
  intersection of: Restriction
    on property: has evidence concordance
    all values from: weakly conflicting
subclass of: confidence statement from conflicting evidence lines of same type
subclass of: Restriction
  on property: has evidence concordance
  all values from: weakly conflicting
id: CIO:0000021
definition: Confidence statement from conflicting evidence lines of same type, where evidence lines are in weak contradiction, meaning that the overall supported assertion is believed to be true, but a subset of less-reliable evidence lines are in contradiction.

Axiom
database_cross_reference: Bgee:fbb
annotated target: Confidence statement from conflicting evidence lines of same type, where evidence lines are in weak contradiction, meaning that the overall supported assertion is believed to be true, but a subset of less-reliable evidence lines are in contradiction.
annotated source: confidence statement from weakly conflicting evidence lines of same type
annotated property: definition

confidence statement from weakly conflicting evidence lines of same type, overall confidence high
type: Class
equivalent class: Class
  intersection of: confidence statement from weakly conflicting evidence lines of same type
  intersection of: Restriction
    on property: has confidence level
    all values from: high confidence level
subclass of: confidence statement from weakly conflicting evidence lines of same type
subclass of: Restriction
  on property: has confidence level
  all values from: high confidence level
disjoint with: confidence statement from weakly conflicting evidence lines of same type, overall confidence low
disjoint with: confidence statement from weakly conflicting evidence lines of same type, overall confidence medium
id: CIO:0000022
definition: Confidence statement from weakly conflicting evidence lines of same type, of an overall high confidence level.
comment: Different strategies can be used to define the overall confidence level: for instance, it could be defined based on the confidence level of the most trusted evidence, from the set of evidence lines supporting (not contradicting) the assertion; or, it could be defined based on the number of evidence lines supporting the assertion (e.g., 10 congruent low-confidence evidence lines could allow to have an overall high confidence in an assertion, even if contradicted by one other low-confidence evidence). It is the responsibility of annotation teams to define and communicate the parameters, pertinent to their field, allowing to produce overall confidence levels.

Axiom
database_cross_reference: Bgee:fbb
annotated target: Confidence statement from weakly conflicting evidence lines of same type, of an overall high confidence level.
annotated source: confidence statement from weakly conflicting evidence lines of same type, overall confidence high
annotated property: definition

confidence statement from weakly conflicting evidence lines of same type, overall confidence low
type: Class
equivalent class: Class
  intersection of: confidence statement from weakly conflicting evidence lines of same type
  intersection of: Restriction
    on property: has confidence level
    all values from: low confidence level
subclass of: confidence statement from weakly conflicting evidence lines of same type
subclass of: Restriction
  on property: has confidence level
  all values from: low confidence level
disjoint with: confidence statement from weakly conflicting evidence lines of same type, overall confidence medium
id: CIO:0000023
definition: Confidence statement from weakly conflicting evidence lines of same type, of an overall not-trusted confidence level.
comment: Different strategies can be used to define the overall confidence level: for instance, it could be defined based on the confidence level of the most trusted evidence, from the set of evidence lines supporting (not contradicting) the assertion; or, it could be defined based on the number of evidence lines supporting the assertion (e.g., 10 congruent low-confidence evidence lines could allow to have an overall high confidence in an assertion, even if contradicted by one other low-confidence evidence). It is the responsibility of annotation teams to define and communicate the parameters, pertinent to their field, allowing to produce overall confidence levels.
in_subset: bgee not trusted

Axiom
database_cross_reference: Bgee:fbb
annotated target: Confidence statement from weakly conflicting evidence lines of same type, of an overall not-trusted confidence level.
annotated source: confidence statement from weakly conflicting evidence lines of same type, overall confidence low
annotated property: definition

confidence statement from weakly conflicting evidence lines of same type, overall confidence medium
type: Class
equivalent class: Class
  intersection of: confidence statement from weakly conflicting evidence lines of same type
  intersection of: Restriction
    on property: has confidence level
    all values from: medium confidence level
subclass of: confidence statement from weakly conflicting evidence lines of same type
subclass of: Restriction
  on property: has confidence level
  all values from: medium confidence level
id: CIO:0000024
definition: Confidence statement from weakly conflicting evidence lines of same type, of an overall moderately trusted confidence level.
comment: Different strategies can be used to define the overall confidence level: for instance, it could be defined based on the confidence level of the most trusted evidence, from the set of evidence lines supporting (not contradicting) the assertion; or, it could be defined based on the number of evidence lines supporting the assertion (e.g., 10 congruent low-confidence evidence lines could allow to have an overall high confidence in an assertion, even if contradicted by one other low-confidence evidence). It is the responsibility of annotation teams to define and communicate the parameters, pertinent to their field, allowing to produce overall confidence levels.

Axiom
database_cross_reference: Bgee:fbb
annotated target: Confidence statement from weakly conflicting evidence lines of same type, of an overall moderately trusted confidence level.
annotated source: confidence statement from weakly conflicting evidence lines of same type, overall confidence medium
annotated property: definition

confidence statement from weakly conflicting evidence lines of multiple types, overall confidence high
type: Class
equivalent class: Class
  intersection of: confidence statement from weakly conflicting evidence lines of multiple types
  intersection of: Restriction
    on property: has confidence level
    all values from: high confidence level
subclass of: confidence statement from weakly conflicting evidence lines of multiple types
subclass of: Restriction
  on property: has confidence level
  all values from: high confidence level
disjoint with: confidence statement from weakly conflicting evidence lines of multiple types, overall confidence low
disjoint with: confidence statement from weakly conflicting evidence lines of multiple types, overall confidence medium
id: CIO:0000025
definition: Confidence statement from weakly conflicting evidence lines of multiple types, of an overall high confidence level.
comment: Different strategies can be used to define the overall confidence level: for instance, it could be defined based on the confidence level of the most trusted evidence, from the set of evidence lines supporting (not contradicting) the assertion; or, it could be defined based on the number of evidence lines supporting the assertion (e.g., 10 congruent low-confidence evidence lines could allow to have an overall high confidence in an assertion, even if contradicted by one other low-confidence evidence). It is the responsibility of annotation teams to define and communicate the parameters, pertinent to their field, allowing to produce overall confidence levels.

Axiom
database_cross_reference: Bgee:fbb
annotated target: Confidence statement from weakly conflicting evidence lines of multiple types, of an overall high confidence level.
annotated source: confidence statement from weakly conflicting evidence lines of multiple types, overall confidence high
annotated property: definition

confidence statement from weakly conflicting evidence lines of multiple types, overall confidence low
type: Class
equivalent class: Class
  intersection of: confidence statement from weakly conflicting evidence lines of multiple types
  intersection of: Restriction
    on property: has confidence level
    all values from: low confidence level
subclass of: confidence statement from weakly conflicting evidence lines of multiple types
subclass of: Restriction
  on property: has confidence level
  all values from: low confidence level
disjoint with: confidence statement from weakly conflicting evidence lines of multiple types, overall confidence medium
id: CIO:0000026
definition: Confidence statement from weakly conflicting evidence lines of multiple types, of an overall not-trusted confidence level.
comment: Different strategies can be used to define the overall confidence level: for instance, it could be defined based on the confidence level of the most trusted evidence, from the set of evidence lines supporting (not contradicting) the assertion; or, it could be defined based on the number of evidence lines supporting the assertion (e.g., 10 congruent low-confidence evidence lines could allow to have an overall high confidence in an assertion, even if contradicted by one other low-confidence evidence). It is the responsibility of annotation teams to define and communicate the parameters, pertinent to their field, allowing to produce overall confidence levels.
in_subset: bgee not trusted

Axiom
database_cross_reference: Bgee:fbb
annotated target: Confidence statement from weakly conflicting evidence lines of multiple types, of an overall not-trusted confidence level.
annotated source: confidence statement from weakly conflicting evidence lines of multiple types, overall confidence low
annotated property: definition

confidence statement from weakly conflicting evidence lines of multiple types, overall confidence medium
type: Class
equivalent class: Class
  intersection of: confidence statement from weakly conflicting evidence lines of multiple types
  intersection of: Restriction
    on property: has confidence level
    all values from: medium confidence level
subclass of: confidence statement from weakly conflicting evidence lines of multiple types
subclass of: Restriction
  on property: has confidence level
  all values from: medium confidence level
id: CIO:0000027
definition: Confidence statement from weakly conflicting evidence lines of multiple types, of an overall moderately trusted confidence level.
comment: Different strategies can be used to define the overall confidence level: for instance, it could be defined based on the confidence level of the most trusted evidence, from the set of evidence lines supporting (not contradicting) the assertion; or, it could be defined based on the number of evidence lines supporting the assertion (e.g., 10 congruent low-confidence evidence lines could allow to have an overall high confidence in an assertion, even if contradicted by one other low-confidence evidence). It is the responsibility of annotation teams to define and communicate the parameters, pertinent to their field, allowing to produce overall confidence levels.

Axiom
database_cross_reference: Bgee:fbb
annotated target: Confidence statement from weakly conflicting evidence lines of multiple types, of an overall moderately trusted confidence level.
annotated source: confidence statement from weakly conflicting evidence lines of multiple types, overall confidence medium
annotated property: definition

confidence level
type: Class
subclass of: confidence information element
disjoint with: evidence concordance
disjoint with: evidence type concordance
definition: A confidence information element representing the different levels of confidence, used to compose confidence information statements.
id: CIO:0000028

Axiom
annotated target: A confidence information element representing the different levels of confidence, used to compose confidence information statements.
database_cross_reference: Bgee:fbb
annotated source: confidence level
annotated property: definition

high confidence level
type: Class
subclass of: confidence level
subclass of: Restriction
  on property: provides greater confidence than
  some values from: medium confidence level
disjoint with: medium confidence level
disjoint with: low confidence level
definition: A confidence level representing a high trust in an evidence.
id: CIO:0000029

Axiom
annotated target: A confidence level representing a high trust in an evidence.
database_cross_reference: Bgee:fbb
annotated source: high confidence level
annotated property: definition

medium confidence level
type: Class
subclass of: confidence level
subclass of: Restriction
  on property: provides greater confidence than
  some values from: low confidence level
disjoint with: low confidence level
definition: A confidence level representing a moderate trust in an evidence.
id: CIO:0000030

Axiom
annotated target: A confidence level representing a moderate trust in an evidence.
database_cross_reference: Bgee:fbb
annotated source: medium confidence level
annotated property: definition

low confidence level
type: Class
subclass of: confidence level
definition: A confidence level representing an absence of trust in an evidence.
id: CIO:0000031

Axiom
annotated target: A confidence level representing an absence of trust in an evidence.
database_cross_reference: Bgee:fbb
annotated source: low confidence level
annotated property: definition

evidence concordance
type: Class
subclass of: confidence information element
disjoint with: evidence type concordance
definition: A confidence information element representing the type of concordance of evidence lines supporting an assertion, used to compose confidence information statements.
id: CIO:0000032
comment: Subclasses are used to define whether there is a single evidence, or multiple evidence lines, in support of an assertion, and whether they are congruent or conflicting.

Axiom
annotated target: A confidence information element representing the type of concordance of evidence lines supporting an assertion, used to compose confidence information statements.
database_cross_reference: Bgee:fbb
annotated source: evidence concordance
annotated property: definition

congruent
type: Class
subclass of: concordance of multiple evidence lines
disjoint with: conflicting
definition: An evidence concordance of multiple evidence lines that are congruent.
id: CIO:0000033
comment: The assumption here is that assertions supported by a single evidence are less trustworthy than assertions supported by multiple evidence lines.

Axiom
annotated target: An evidence concordance of multiple evidence lines that are congruent.
database_cross_reference: Bgee:fbb
annotated source: congruent
annotated property: definition

conflicting
type: Class
subclass of: concordance of multiple evidence lines
comment: An assertion can have several related evidence lines, some supporting the assertion, and some rejecting the assertion (e.g., using the NOT qualifier in GO annotations).
definition: An evidence concordance of multiple evidence lines that are conflicting.
id: CIO:0000034

Axiom
annotated target: An evidence concordance of multiple evidence lines that are conflicting.
database_cross_reference: Bgee:fbb
annotated source: conflicting
annotated property: definition

strongly conflicting
type: Class
subclass of: conflicting
disjoint with: weakly conflicting
definition: A conflicting concordance for evidence lines that are strongly conflicting.
id: CIO:0000035
comment: We distinguish two levels of conflict: weak conflict between evidence lines, e.g., a low confidence evidence negating an assertion, versus several high confidence evidence lines supporting the assertion; and strong conflict between evidence lines, e.g., two high confidence evidence lines contradicting each other. Note that strongly conflicting evidence lines are not used to produce confidence information statements associated to a confidence level (low, medium, high): in that case, the supported assertion is believed to need further validation, as evidence lines yield different conclusions of similar confidence.

Axiom
annotated target: A conflicting concordance for evidence lines that are strongly conflicting.
database_cross_reference: Bgee:fbb
annotated source: strongly conflicting
annotated property: definition

weakly conflicting
type: Class
subclass of: conflicting
definition: A conflicting concordance for evidence lines that are weakly conflicting.
id: CIO:0000036
comment: We distinguish two levels of conflict: weak conflict between evidence lines, e.g., a low confidence evidence negating an assertion, versus several high confidence evidence lines supporting the assertion; and strong conflict between evidence lines, e.g., two high confidence evidence lines contradicting each other.

Axiom
annotated target: A conflicting concordance for evidence lines that are weakly conflicting.
database_cross_reference: Bgee:fbb
annotated source: weakly conflicting
annotated property: definition

same type
type: Class
subclass of: evidence type concordance
disjoint with: different type
definition: An evidence type concordance for evidence lines that are from a same type.
id: CIO:0000037

Axiom
annotated target: An evidence type concordance for evidence lines that are from a same type.
database_cross_reference: Bgee:fbb
annotated source: same type
annotated property: definition

different type
type: Class
subclass of: evidence type concordance
definition: An evidence type concordance for evidence lines that are from different types.
id: CIO:0000038

Axiom
annotated target: An evidence type concordance for evidence lines that are from different types.
database_cross_reference: Bgee:fbb
annotated source: different type
annotated property: definition

rejected
type: Class
subclass of: confidence statement from single evidence
definition: A confidence statement from single evidence related to assertions that have been rejected, for instance, following paper retraction, author misinterpretation, or curator misinterpretation.
id: CIO:0000039
comment: When results are retracted, associated annotations are often removed. Consequently, end-users might not be aware that the result was annotated. Annotating an assertion with this confidence term allows to keep the information available. Such assertions should not interfer with aggregation of multiple evidence lines to generate a confidence level from the branch CIO:0000002 "confidence from multiple evidence lines". This is different from negative annotations, used to negate the interpretation of an annotation. It is also different from conflicting multiple evidence lines, where each single evidence has not been directly invalidated. Rejection is a stronger assertion about an annotation source than conflict, capturing that this evidence should no longer be used.

Axiom
annotated target: A confidence statement from single evidence related to assertions that have been rejected, for instance, following paper retraction, author misinterpretation, or curator misinterpretation.
database_cross_reference: Bgee:fbb
annotated source: rejected
annotated property: definition

confidence information element
type: Class
id: CIO:0000040
definition: Confidence information element represent intrinsic properties of confidence information statements, allowing to compose them.

Axiom
database_cross_reference: Bgee:fbb
annotated target: Confidence information element represent intrinsic properties of confidence information statements, allowing to compose them.
annotated source: confidence information element
annotated property: definition

evidence type concordance
type: Class
subclass of: confidence information element
definition: A confidence information element representing the concordance of experimental or computational types of evidence lines supporting an assertion, used to compose confidence information statements.
id: CIO:0000041
comment: The assumption here is that assertions supported by evidence lines of different experimental or computational types are more trustworthy than assertions supported by evidence lines of a same experimental or computational type.

Axiom
annotated target: A confidence information element representing the concordance of experimental or computational types of evidence lines supporting an assertion, used to compose confidence information statements.
database_cross_reference: Bgee:fbb
annotated source: evidence type concordance
annotated property: definition

single evidence
type: Class
subclass of: evidence concordance
disjoint with: concordance of multiple evidence lines
definition: An evidence concordance for confidence information about an assertion produced from a single evidence.
id: CIO:0000042
comment: The assumption here is that assertions supported by a single evidence are less trustworthy than assertions supported by multiple evidence lines.

Axiom
annotated target: An evidence concordance for confidence information about an assertion produced from a single evidence.
database_cross_reference: Bgee:fbb
annotated source: single evidence
annotated property: definition

concordance of multiple evidence lines
type: Class
subclass of: evidence concordance
definition: An evidence concordance for confidence information about an assertion produced from multiple evidence lines.
id: CIO:0000043
comment: The assumption here is that assertions supported by a single evidence are less trustworthy than assertions supported by multiple evidence lines.

Axiom
annotated target: An evidence concordance for confidence information about an assertion produced from multiple evidence lines.
database_cross_reference: Bgee:fbb
annotated source: concordance of multiple evidence lines
annotated property: definition