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"Pathology report data extraction from relational database using R, with extraction from reports on melanoma of skin as an example"

The olog approach of Spivak and Kent is applied to the practical development of data transfer frameworks, yielding simple rules for construction and assessment of data transfer standards. The simplicity, extensibility and modularity of such descriptions allows discipline experts unfamiliar with complex ontological constructs or toolsets to synthesize multiple pre-existing standards, potentially including a variety of file formats, into a single overarching ontology. These ontologies nevertheless capture all scientifically-relevant prior knowledge, and when expressed in machine-readable form are sufficiently expressive to mediate translation between legacy and modern data formats. A format-independent programming interface informed by this ontology consists of six functions, of which only two handle data. Demonstration software implementing this interface is used to translate between two common diffraction image formats using such an ontology in place of an intermediate format. (Full article...)

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