output of research study study finding - While the act of generating a finding is simpler, it does involve some cognitive effort that could be guided by some method (i.e., one defining what experimental context should be included in the finding statement, and how this and the observed outcomes are reported). Which means that findings are not the direct output of an assay, which merely generates data. So perhaps in SEPIO we commit to only considering research processes at the level of studies - such that even assays would potentially involve some act of summarizing the results as a finding. - Note that at present 'study data sets' can serve the same 'organizational' purpose as 'study findings' - we should converge on one recommended way to perform this level of organization of evidence data. Findings statements tend to take the form of "We observed that . . . ", or "Assay X revelaned that . . . ", or "X was determined to be Y in a study of . . . ". For example: "Smith et. al observed that a positive response to imatinib treatment was two-fold higher in a cohort of leukemia patients bearing Bcr-Abl fusions compared to those lacking this driver mutaiton." A statement summarizing the outcome of a sequencing analysis: "DNA sequencing data from patient X revealed an A->T mutation at position 2143 in gene Y". A statement summarizing the outcome of a variant population frequency study: "The frequency of variant X was determined to be 0.00015 in a cohort of non-finnish european subjects described in the ExAC dataset." study outcome A statement describing the immediate results of a research study, describing what was directly observed, measured, or derived through mathematical calculation. SEPIO distinguishes two high-level subtypes of statements: 1. Findings are statements that report the immediate, objective results of an experiment, observation, or study - without bias or interpretation. A finding statement results simply from an act of reporting or summarizing these direct observations, calculations, or measurements. 2. Assertions, by contrast, result from acts of interpretation and/or inference, based on information used as evidence. The statement here is a conclusion drawn from critical evaluation of this more foundational information, and its validity depends on the quality of this information and its interpretation as evidence. A study finding is a statement that summarizes the immediate results of a particular experiment or study. It describes only what was directly observed, measured, or calculated, and optionally the experimental context of these observations. It does not describe more general conclusions that may have been inferred from such results. As such, the scope of what a finding describes is limited to the direct participants in the study - i.e. it is about only the instances observed or measured in the study. It makes no broader inference or conclusion about types or classes to which these instances belong. This is not to say that the onserved findings are necessarily accurate or correct - only that they were indeed made in a particular study. For example, the finding that "Sequencing of DNA from patient X revealed an A->T mutation at position 2143 in gene Y" is a matter of fact - this was the outcome of the assay, even if the finding is an artifact of low sequencing coverage. Metadata about the finding (e.g. sequencing methods/reagents used, coverage or read depth) are recoded so users can judge for themselves whether the objectively reported finding accurtely reflects the biology it describes. In SEPIO, a high-level distinction is made between statements that are 'findings' vs 'assertions'. Findings are statements that report/summarize what was directly observed or calculated in a study, and are about only the immediate participants in the experiment or study. As such, findings involve no interpretation or inference from the data to draw broader conclusions. Assertions, by contrast, are statements that derive from some degree of interpretation or inference based on the evaluation of 'evidence', and often make broader claims about the types or categories to which study participants belong. This distinction is important because the provenance and validity of a 'finding' statement does not depend on subjective interpretation of 'evidence' in the same way that of an assertion does. This has modeling implications for how findings and assertions are linked to information that supports them. In practices, instances of 'study findings' are used to group one or more data items from a particular research study that are relevant as evidence for an assertion. The utility of this class is in allowing the shared provenance of these data items to be more efficiently represented - as things like agent, date, and methods can be described once for the data set and inferred to apply to all individual data items that comprise it. statement