Release 1 July 2013
- This version:
- Latest version:
- Revision 2.0
- Olga Giraldo, Ontology Engineering Group, Universidad Politécnica de Madrid
- 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
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).
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
- [BFO]:Robert Arp and Barry Smith. (2008)
Function, Role, and Disposition in Basic Formal Ontology. Available from Nature Precedings.
- [ChEBI]:Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcántara, Michael Darsow, Mickaël Guedj, and Michael Ashburner. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res.Vol. 36(Database issue), pages D344–D350.
- [EXACT]: Larisa N. Soldatova, Wayne Aubrey, Ross D. King and Amanda Clare. (2008).
The EXACT description of biomedical protocols. Bioinformatics.Vol. 24 ISMB 2008, pages i295–i303.
- [IAO] information-artifact-ontology.
- [MGEDO]:Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr. (2006) The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics. Vol. 1; 22(7), pages 866-73.
- [MeSH] Medical Subject Headings.
- [NCI Thesaurus] NCI Thesaurus.
- [NPO] NPO:NanoParticle Ontology for Cancer Nanotechnology Research.
- [OBI]:Mélanie Courtot, William Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman and Alan Ruttenberg. (2008) The OWL of Biomedical Investigations. OWLED.
- [OBO_REL]:Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector and Cornelius Rosse. (2005) Relations in biomedical ontologies. Genome Biology, Vol. 6:R46.
- [P-Plan] P-Plan Ontology.
- [SO]:Karen Eilbeck, Suzanna E Lewis, Christopher J Mungall, Mark Yandell, Lincoln Stein, Richard Durbin and Michael Ashburner. (2005) The Sequence Ontology: a tool for the unification of genome annotations. Genome Biology, Vol. 6:R44.
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.