Combining ontologies and workflows to design formal protocols for biological laboratories

Area of Science:

• Life Sciences
• Bioinformatics
• Laboratory Automation

Background:

• Natural language laboratory protocols hinder experiment repeatability, distribution, and automation.
• Formalization of scientific knowledge is crucial for advancing research.
• Two levels of formalization are needed for laboratory protocols: entity/operation and procedure execution.

Purpose of the Study:

• To combine ontologies and workflows for comprehensive laboratory protocol formalization.
• To develop a domain-specific ontology and a software tool for protocol formalization.
• To enable structured protocol design for biological laboratory experiments.

Main Methods:

• Developed a laboratory domain-specific ontology.
• Created the Combining Ontologies with Workflows (COW) software tool.
• Integrated ontological concepts into workflows for protocol representation.
• Saved protocols as linked XPDL (workflow) and OWL (ontology) files.

Main Results:

• The COW tool facilitates the formalization of laboratory workflows using ontologies.
• A method was established for designing structured biological laboratory protocols.
• Protocols are stored in standardized interchange languages (XPDL and OWL).
• A freely available distribution package of COW includes installation, ontology, and examples.

Conclusions:

• The COW tool allows wet-lab scientists to define protocols without coding.
• Protocol specifications become clearer, easier to read, and maintainable.
• This approach enhances the automation and reproducibility of laboratory experiments.