SeMAntic RepresenTation for experimental Protocols

Resumen

This research address the problem of semantically representing experimental protocols in life sciences and how to relate such information to data. The need for open interoperable data supporting research transparency, systematic reuse of existing data and, experimental reproducibility has been widely acknowledged. Several efforts are providing infrastructure for sharing and storing data. However, data per se does not imply reproducibility; there is the need to know how the data was produced -here is the data, where are the experimental protocols? Several efforts have studied the problem of "is this reproducible?” Fewer efforts have addressed the problem of semantically valid, machine-processable reporting structures. SMART Protocols (SP) makes use of Semantic Web technology, thus facilitating interoperability and machine processability; SP delivers an extendible infrastructure that allows researchers to search for similar protocols, or investigations with similar techniques, methods, instruments, variables and/or populations, etc. In order to achieve such degree of functionality, throughout this investigation a comprehensive vocabulary was gathered by annotating documents; the corresponding infrastructure, henceforth BioH, was specially developed to support this task. the evaluation of the vocabulary thus gathered made it possible to generate the SP gold standard; this is a gold standard corpus specifically engineered for experimental protocols. The tooling and methods applied when building this gold standard can be applied to other domains. Furthermore, this investigation also delivers a semantic publication platform for experimental protocols; Scientific publications aggregate data by encompassing it within a persuasive narrative. The SP approach addresses the problem of supporting such aggregation over a document that is to be born semantic, interoperable and conceived as an aggregator within a web-of-data publishing workflow.