ProtocolDB: Storing Scientific Protocols with a Domain Ontology

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This paper addresses a systemic problem in science: although datasets collected through scientific protocols may be properly stored, the protocol itself is often only recorded on paper or stored electronically as the script developed to implement the protocol. Once the scientist who has implemented the protocol leaves the laboratory, this record may be lost. Collected datasets without a description of the process used to produce them become meaningless; furthermore, the experiment designed to produce the data is not reproducible. In this paper we present the ProtocolDB system that aims at assisting scientists in the process of (1) designing and implementing scientific protocols, (2) storing, querying, and transforming scientific protocols, and (3) reasoning about collected experimental data (data provenance).