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Using semantics for representing experimental protocols.

Olga Giraldo1, Alexander García2, Federico López3

  • 1Ontology Engineering Group, Madrid, Universidad Politécnica de Madrid, Madrid, 28660, Spain. ogiraldo@fi.upm.es.

Journal of Biomedical Semantics
|November 15, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces the SMART Protocols ontology and SIRO model to standardize experimental protocols for better reproducibility and data retrieval in life sciences research. This framework enables precise searching of protocols based on key elements.

Keywords:
Graph theoryKnowledge representationLinked dataOntologiesRDF for experimental protocolsSemantic web

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Area of Science:

  • Life Sciences
  • Biomedical Research
  • Experimental Biology

Background:

  • Experimental protocols are crucial for reproducibility in biological and biomedical research but often lack standardized descriptions.
  • Current protocol representations are frequently cursory, hindering effective reuse and data integration.
  • A unified framework for syntactic and semantic representation of experimental protocols is needed.

Purpose of the Study:

  • To present the SMART Protocols ontology for representing experimental protocols as structured workflows.
  • To introduce the Sample Instrument Reagent Objective (SIRO) model for capturing minimal common information across protocols.
  • To enhance search, retrieval, and classification of experimental protocols.

Main Methods:

  • Developed the SMART Protocols ontology to embed domain-specific knowledge within a document structure.
  • Defined the SIRO model, analogous to the PICO model in evidence-based medicine.
  • Evaluated the ontology and model using SPARQL queries against a corpus of protocols.

Main Results:

  • The SMART Protocols ontology and SIRO model provide a standardized framework for experimental protocols.
  • The approach enables answering specific queries, such as identifying protocols using particular sample types (e.g., tumor tissue).
  • Demonstrated the utility of the ontology and model in facilitating protocol search and classification.

Conclusions:

  • Standardizing experimental protocol reporting requires collaborative efforts from researchers, publishers, and funding agencies.
  • The SP Ontology and SIRO model represent a significant contribution to improving protocol reusability and reproducibility.
  • The developed framework supports researchers in managing and utilizing laboratory protocols more effectively.