Abstract
BackgroundAccounts of evidence are vital to evaluate and reproduce scientific findings and integrate data on an informed basis. Currently, such accounts are often inadequate, unstandardized and inaccessible for computational knowledge engineering even though computational technologies, among them those of the semantic web, are ever more employed to represent, disseminate and integrate biomedical data and knowledge.ResultsWe present SEE (Semantic EvidencE), an RDF/OWL based approach for detailed representation of evidence in terms of the argumentative structure of the supporting background for claims even in complex settings. We derive design principles and identify minimal components for the representation of evidence. We specify the Reasoning and Discourse Ontology (RDO), an OWL representation of the model of scientific claims, their subjects, their provenance and their argumentative relations underlying the SEE approach. We demonstrate the application of SEE and illustrate its design patterns in a case study by providing an expressive account of the evidence for certain claims regarding the isolation of the enzyme glutamine synthetase.ConclusionsSEE is suited to provide coherent and computationally accessible representations of evidence-related information such as the materials, methods, assumptions, reasoning and information sources used to establish a scientific finding by adopting a consistently claim-based perspective on scientific results and their evidence. SEE allows for extensible evidence representations, in which the level of detail can be adjusted and which can be extended as needed. It supports representation of arbitrary many consecutive layers of interpretation and attribution and different evaluations of the same data. SEE and its underlying model could be a valuable component in a variety of use cases that require careful representation or examination of evidence for data presented on the semantic web or in other formats.
Highlights
Accounts of evidence are vital to evaluate and reproduce scientific findings and integrate data on an informed basis
SEE and its underlying model could be a valuable component in a variety of use cases that require careful representation or examination of evidence for data presented on the semantic web or in other formats
SEE relies on an abstract model for the representation of claims, provenance and argumentative structure specified in the Reasoning and Discourse Ontology (RDO), a lightweight OWL vocabulary developed for this purpose
Summary
Accounts of evidence are vital to evaluate and reproduce scientific findings and integrate data on an informed basis. Biomedical knowledge is often highly context-dependent and based on evidence obtained from the skilful combination and evaluation of individual results, involving, among other aspects, a range of model organisms, diverse experimental and computational techniques, different forms of interpretation, and various inference schemes. All those aspects - the materials, methods and information sources used, the observations made, the reasoning employed and the context-specific assumptions made - are important for comprehensive evidence accounts. There is, currently no dedicated model supporting a coherent, extensible and semantic-web compatible representation of all those aspects routinely considered by a researcher inspecting the evidence for a given scientific finding, i.e. a representation of (i) the experimental and computational methods and settings that were used to establish the observational results and process the data, (ii) the reasoning including additional findings and assumptions used to infer the result in question, and (iii) information sources and agents through which the corresponding views were communicated and propagated
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