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Web Information Systems Engineering – WISE 2007 Workshops

Volume 4832 of the series Lecture Notes in Computer Science pp 17-28

ProtocolDB: Storing Scientific Protocols with a Domain Ontology

  • Michel KinsyAffiliated withScientific Data Management Laboratory, Arizona State University, Tempe AZ 85287-5706
  • , Zoé LacroixAffiliated withScientific Data Management Laboratory, Arizona State University, Tempe AZ 85287-5706
  • , Christophe LegendreAffiliated withScientific Data Management Laboratory, Arizona State University, Tempe AZ 85287-5706
  • , Piotr WlodarczykAffiliated withScientific Data Management Laboratory, Arizona State University, Tempe AZ 85287-5706
  • , Nadia YacoubiAffiliated withScientific Data Management Laboratory, Arizona State University, Tempe AZ 85287-5706

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Abstract

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).