cio 1.4 definition Terms that are considered not trusted by the Bgee team, related to assertions needing additional support. subset_property database_cross_reference has_exact_synonym has_obo_format_version in_subset shorthand 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. has_confidence_element has confidence element X has confidence level Y iff X is a confidence information statement and Y is it associated confidence information level. has_confidence_level has confidence level X has evidence concordance Y iff X is a confidence information statement and Y is it associated evidence concordance. has_evidence_concordance has evidence concordance X has evidence type concordance Y iff X is a confidence information statement and Y is it associated evidence type concordance. has_evidence_type_concordance has evidence type concordance 1 0 0 1 3 1 1 1 0 0 2 1 2 0 1 3 1 1 0 0 1 3 1 1 A statement providing information about the confidence in an assertion, meaning, an information about the level of certainty that an assertion is correct. CIO:0000000 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. confidence information statement CIO:0000000 A statement providing information about the confidence in an assertion, meaning, an information about the level of certainty that an assertion is correct. Bgee:fbb 0 0 A confidence information statement defined from a single evidence. CIO:0000001 confidence statement from single evidence CIO:0000001 A confidence information statement defined from a single evidence. Bgee:fbb 1 1 A confidence information statement defined from a set of evidence lines. CIO:0000002 confidence statement from multiple evidence lines CIO:0000002 A confidence information statement defined from a set of evidence lines. Bgee:fbb A confidence statement from single evidence related to assertions supported by a highly reliable evidence. gold CIO:0000003 high confidence from single evidence CIO:0000003 A confidence statement from single evidence related to assertions supported by a highly reliable evidence. Bgee:fbb gold neXtProt A confidence statement from single evidence related to assertions supported by moderately trusted evidence. silver CIO:0000004 medium confidence from single evidence CIO:0000004 A confidence statement from single evidence related to assertions supported by moderately trusted evidence. Bgee:fbb silver neXtProt A confidence statement from single evidence related to assertions supported by not-trusted evidence. bronze CIO:0000005 low confidence from single evidence CIO:0000005 bronze neXtProt A confidence statement from single evidence related to assertions supported by not-trusted evidence. Bgee:fbb A confidence statement from multiple evidence lines, all using a same experimental or computational type. CIO:0000006 confidence statement from multiple evidence lines of same type CIO:0000006 A confidence statement from multiple evidence lines, all using a same experimental or computational type. Bgee:fbb A confidence statement from multiple evidence lines, of different experimental or computational types. CIO:0000007 confidence statement from multiple evidence lines of multiple types CIO:0000007 A confidence statement from multiple evidence lines, of different experimental or computational types. Bgee:fbb A confidence statement from multiple evidence lines of multiple types, that are all congruent. CIO:0000008 confidence statement from congruent evidence lines of multiple types CIO:0000008 A confidence statement from multiple evidence lines of multiple types, that are all congruent. Bgee:fbb A confidence statement from multiple evidence lines of multiple types, some of which being contradictory. CIO:0000009 confidence statement from conflicting evidence lines of multiple types CIO:0000009 A confidence statement from multiple evidence lines of multiple types, some of which being contradictory. Bgee:fbb 0 0 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. CIO:0000010 confidence statement from strongly conflicting evidence lines of multiple types CIO:0000010 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. Bgee:fbb 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. CIO:0000011 confidence statement from weakly conflicting evidence lines of multiple types CIO:0000011 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. Bgee:fbb A confidence statement from congruent evidence lines of multiple types, of an overall high confidence level. CIO:0000012 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. confidence statement from congruent evidence lines of multiple types, overall confidence high CIO:0000012 A confidence statement from congruent evidence lines of multiple types, of an overall high confidence level. Bgee:fbb A confidence statement from congruent evidence lines of multiple types, of an overall moderately trusted confidence level. CIO:0000013 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. confidence statement from congruent evidence lines of multiple types, overall confidence medium CIO:0000013 A confidence statement from congruent evidence lines of multiple types, of an overall moderately trusted confidence level. Bgee:fbb A confidence statement from congruent evidence lines of multiple types, of an overall not-trusted confidence level. CIO:0000014 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. confidence statement from congruent evidence lines of multiple types, overall confidence low CIO:0000014 A confidence statement from congruent evidence lines of multiple types, of an overall not-trusted confidence level. Bgee:fbb Confidence statement from multiple evidence lines of same type, some of which being contradictory. CIO:0000015 confidence statement from conflicting evidence lines of same type CIO:0000015 Confidence statement from multiple evidence lines of same type, some of which being contradictory. Bgee:fbb Confidence statement from multiple evidence lines of same type, that are all congruent. CIO:0000016 confidence statement from congruent evidence lines of same type CIO:0000016 Confidence statement from multiple evidence lines of same type, that are all congruent. Bgee:fbb A confidence statement from congruent evidence lines of same type, of an overall high confidence level. CIO:0000017 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. confidence statement from congruent evidence lines of same type, overall confidence high CIO:0000017 A confidence statement from congruent evidence lines of same type, of an overall high confidence level. Bgee:fbb A confidence statement from congruent evidence lines of same type, of an overall not-trusted confidence level. CIO:0000018 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. confidence statement from congruent evidence lines of same type, overall confidence low CIO:0000018 A confidence statement from congruent evidence lines of same type, of an overall not-trusted confidence level. Bgee:fbb A confidence statement from congruent evidence lines of same type, of an overall moderately trusted confidence level. CIO:0000019 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. confidence statement from congruent evidence lines of same type, overall confidence medium CIO:0000019 A confidence statement from congruent evidence lines of same type, of an overall moderately trusted confidence level. Bgee:fbb 0 0 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. CIO:0000020 confidence statement from strongly conflicting evidence lines of same type CIO:0000020 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. Bgee:fbb 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. CIO:0000021 confidence statement from weakly conflicting evidence lines of same type CIO:0000021 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. Bgee:fbb Confidence statement from weakly conflicting evidence lines of same type, of an overall high confidence level. CIO:0000022 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. confidence statement from weakly conflicting evidence lines of same type, overall confidence high CIO:0000022 Confidence statement from weakly conflicting evidence lines of same type, of an overall high confidence level. Bgee:fbb Confidence statement from weakly conflicting evidence lines of same type, of an overall not-trusted confidence level. CIO:0000023 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. confidence statement from weakly conflicting evidence lines of same type, overall confidence low CIO:0000023 Confidence statement from weakly conflicting evidence lines of same type, of an overall not-trusted confidence level. Bgee:fbb Confidence statement from weakly conflicting evidence lines of same type, of an overall moderately trusted confidence level. CIO:0000024 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. confidence statement from weakly conflicting evidence lines of same type, overall confidence medium CIO:0000024 Confidence statement from weakly conflicting evidence lines of same type, of an overall moderately trusted confidence level. Bgee:fbb Confidence statement from weakly conflicting evidence lines of multiple types, of an overall high confidence level. CIO:0000025 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. confidence statement from weakly conflicting evidence lines of multiple types, overall confidence high CIO:0000025 Confidence statement from weakly conflicting evidence lines of multiple types, of an overall high confidence level. Bgee:fbb Confidence statement from weakly conflicting evidence lines of multiple types, of an overall not-trusted confidence level. CIO:0000026 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. confidence statement from weakly conflicting evidence lines of multiple types, overall confidence low CIO:0000026 Confidence statement from weakly conflicting evidence lines of multiple types, of an overall not-trusted confidence level. Bgee:fbb Confidence statement from weakly conflicting evidence lines of multiple types, of an overall moderately trusted confidence level. CIO:0000027 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. confidence statement from weakly conflicting evidence lines of multiple types, overall confidence medium CIO:0000027 Confidence statement from weakly conflicting evidence lines of multiple types, of an overall moderately trusted confidence level. Bgee:fbb A confidence information element representing the different levels of confidence, used to compose confidence information statements. CIO:0000028 confidence level CIO:0000028 A confidence information element representing the different levels of confidence, used to compose confidence information statements. Bgee:fbb A confidence level representing a high trust in an evidence. CIO:0000029 high confidence level CIO:0000029 A confidence level representing a high trust in an evidence. Bgee:fbb A confidence level representing a moderate trust in an evidence. CIO:0000030 medium confidence level CIO:0000030 A confidence level representing a moderate trust in an evidence. Bgee:fbb A confidence level representing an absence of trust in an evidence. CIO:0000031 low confidence level CIO:0000031 A confidence level representing an absence of trust in an evidence. Bgee:fbb A confidence information element representing the type of concordance of evidence lines supporting an assertion, used to compose confidence information statements. CIO:0000032 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. evidence concordance CIO:0000032 A confidence information element representing the type of concordance of evidence lines supporting an assertion, used to compose confidence information statements. Bgee:fbb An evidence concordance of multiple evidence lines that are congruent. CIO:0000033 The assumption here is that assertions supported by a single evidence are less trustworthy than assertions supported by multiple evidence lines. congruent CIO:0000033 An evidence concordance of multiple evidence lines that are congruent. Bgee:fbb An evidence concordance of multiple evidence lines that are conflicting. CIO:0000034 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). conflicting CIO:0000034 An evidence concordance of multiple evidence lines that are conflicting. Bgee:fbb A conflicting concordance for evidence lines that are strongly conflicting. CIO:0000035 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. strongly conflicting CIO:0000035 A conflicting concordance for evidence lines that are strongly conflicting. Bgee:fbb A conflicting concordance for evidence lines that are weakly conflicting. CIO:0000036 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. weakly conflicting CIO:0000036 A conflicting concordance for evidence lines that are weakly conflicting. Bgee:fbb An evidence type concordance for evidence lines that are from a same type. CIO:0000037 same type CIO:0000037 An evidence type concordance for evidence lines that are from a same type. Bgee:fbb An evidence type concordance for evidence lines that are from different types. CIO:0000038 different type CIO:0000038 An evidence type concordance for evidence lines that are from different types. Bgee:fbb A confidence statement from single evidence related to assertions that have been rejected, for instance, following paper retraction, author misinterpretation, or curator misinterpretation. CIO:0000039 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. rejected CIO:0000039 A confidence statement from single evidence related to assertions that have been rejected, for instance, following paper retraction, author misinterpretation, or curator misinterpretation. Bgee:fbb Confidence information element represent intrinsic properties of confidence information statements, allowing to compose them. CIO:0000040 confidence information element CIO:0000040 Confidence information element represent intrinsic properties of confidence information statements, allowing to compose them. Bgee:fbb A confidence information element representing the concordance of experimental or computational types of evidence lines supporting an assertion, used to compose confidence information statements. CIO:0000041 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. evidence type concordance CIO:0000041 A confidence information element representing the concordance of experimental or computational types of evidence lines supporting an assertion, used to compose confidence information statements. Bgee:fbb An evidence concordance for confidence information about an assertion produced from a single evidence. CIO:0000042 The assumption here is that assertions supported by a single evidence are less trustworthy than assertions supported by multiple evidence lines. single evidence CIO:0000042 An evidence concordance for confidence information about an assertion produced from a single evidence. Bgee:fbb An evidence concordance for confidence information about an assertion produced from multiple evidence lines. CIO:0000043 The assumption here is that assertions supported by a single evidence are less trustworthy than assertions supported by multiple evidence lines. concordance of multiple evidence lines CIO:0000043 An evidence concordance for confidence information about an assertion produced from multiple evidence lines. Bgee:fbb cio 1.4 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. provides_greater_confidence_than provides greater confidence than