Evidence Item

Matthew Brush edited this page Jul 12, 2017 · 12 revisions

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Definition: An Evidence Item is any Information that is used to evaluate the validity of a Proposition put forth by an Assertion. Evidence Item is shown parenthetically above because it is a 'defined class' in SEPIO, representing any piece of Information that plays an evidence role.

Supertypes: Information Content Entity

Subtypes: Evidence Statement, Evidence Data

Description: An Evidence Item is simply an Information Content Entity (ICE) that realizes an 'Evidence Role', through its use in evaluating the validity of some Proposition. The most common types of information artifacts referenced as evidence include:

  1. Measured Data Items: e.g. a '548.5 mg/dl' measurement of blood glucose in mutant mice.
  2. Derived Statistical Calculations: - e.g. a 1.3951e-24 p-value statistic indicating a significant increase relative to wild-type mice.
  3. Data Figures or Tables: e.g. a figure or table that presents the data or statistics or statistics above
  4. Study Findings: e.g. the outcome of a specific study reporting that "C57/BL6 Lepr knock-out mice showed increase blood glucose concentrations after 2 weeks on high-fat diets relative to WT mice"
  5. Prior Assertions: An assertion stating that "Lpr1 leptin receptor mutations can lead to diabetes".

SEPIO makes a high level distinction between Evidence Items that are more elemental data and those that are higher-order Statements based on such data. The former are considered as Evidence Data, and would include 1, 2, and 3 in the list above. The latter are considered Evidence Statements, and would include items 4 and 5 above. More on the distinction between Findings and Assertions is here [1].

Finally, note that Publications are not considered Evidence Items in the SEPIO model, as they are only proxies for where actual evidence information is described.

Examples: The International Mouse Phenotyping Consortium (IMPC) database [1] holds Assertions about causal relationships between genotypes and phenotypes. For the Assertion here [2] that Lepr gene inactivation causes increased circulating glucose levels, Evidence Items reported by IMPC include:

  • a 548.5 mg/dl blood glucose measurement [3] made in a Leprtm1b/tm1b mutant mouse.
  • a 1.3951e-24 p-value [4] derived from this measurement data, indicating a highly significant difference from wild-type mice.

Note that the measurement and statistical values above are Evidence Items that contribute to the same argument for the documented assertion, and would therefore support a single Evidence Line in a SEPIO model. See [5] for more.)

Scope and Usage

Particular ICEs in SEPIO data need not be asserted as instances of the Evidence Item class, as this fact can be inferred its position as a component of an Evidence Line. Rather, a broad range of generic and domain-specific information classes are provided by SEPIO for the purposes of typing ICE instances that serve as Evidence Items (e.g. 'measurement data', 'p-value', 'figure', 'data table','allele frequency data', 'functional data', 'study finding', 'assertion', etc.). The primary utility of the Evidence Item concept is in helping to explain key features and distinctions made in the SEPIO model, e.g. that the notion of an Evidence Line is distinct from these individual Evidence Items that comprise it. SEPIO also defines 'Evidence Statement' and 'Evidence Data' as two broad subtypes of Evidence Item, in order to give precise definitions to these terms which are commonly used in databases and discourse describing on evidence and provenance information.

Attributes

Other than holding an 'Evidence Role', the Evidence Item class is assigned no specific attributes besides those inherited from its parent ICE class.

Property Value Type Cardinality Description
has_role Evidence Role 1..1 Any ICE that qualifies as an Evidence Item bears an Evidence Role.

Jump to: Information Content Entity | Assertion | Evidence Line | Agent | Activity | Contribution | Statement | Proposition

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