SMART Protocols

Release 1 July 2013

This version:
 
Latest version:
http://purl.org/net/SMARTprotocol
Revision
Revision 2.0
Author:
Olga Giraldo, Ontology Engineering Group, Universidad Politécnica de Madrid
Contributors:
Daniel Garijo, Ontology Engineering Group, Universidad Politécnica de Madrid
Oscar Corcho, Ontology Engineering Group, Universidad Politécnica de Madrid
Alexander Garcia, Linkingdata I/O LLC, Fort Collins, Colorado

Table of Contents

1. SMART Protocol Motivation back to ToC

In life sciences, experimental protocols provide step-by-step descriptions of procedures. These procedures are the means to verify that the results published in scientific articles are reproducible, instead of being produced at random. A laboratory protocol can be visualized from two perspectives: the protocol as a document and as a workflow. The experimental protocol as a document is published, either inside scientific papers in the materials and methods section or as an independent document. Besides, the protocol is a sequence of tasks and executable operations that includes an input and an output, in this sense a protocol is a type of workflow. However, these experimental protocols may present problems (insufficient granularity in the instructions, ambiguity and/or imprecision) due to the use of natural language. In order to address these problems, we are investigating ways for supporting a more systematic and structured description of protocols to improve the reproducibility of experiments.

2. SMART Protocol Description back to ToC

The SeMAntic RepresenTation for Protocols, SMART Protocols, provides a structured OWL DL vocabulary of experimental protocols. (Figure 1) shows an overview of the two ontologies that model SMART Protocols. The ontology that describes the experimental protocol as a document is depicted at the top. The class iao:InformationContentEntity and its subclasses (iao:Document, iao:DocumentPart, iao:TextualEntity and iao:DataSet) were imported from The Information Artifact Ontology (IAO) to represent the document aspects in the protocol. The ontology that describes the experimental protocol as a workflow is depicted at the bottom. The representation of executable aspects of a protocol is captured with the concepts p-plan:Plan, p-plan:Step and p-plan:Variable from P-Plan Ontology (P-Plan).

Figure 1: SMART Protocols as an extension of the ontologies IAO and P-Plan. The document aspects in a protocol are captured with IAO. The workflow aspects in a protocol are captured with P-Plan. The terms proposed in SMART Protocols use the sp prefix.

3. Ontology Documentation back to ToC

    The encoding of the SMART Protocols-Document Ontology can be found here . The documentation is available here

    The encoding of the SMART Protocols-Workflow Ontology can be found here The documentation is available here

    The latest encoding of the merged SMART Protocols modules can be found here

4. References back to ToC

5. Acknowledgements back to ToC

I would like thank Ontology Engineering Group, Wf4Ever project for supporting this research and Silvio Peroni for developing LODE, tool used to create part of the cross-reference sections of this document.