Automated Experimentation

, 2:3

First online:

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Combining ontologies and workflows to design formal protocols for biological laboratories

  • Alessandro MaccagnanAffiliated withCRIBI Biotechnology Centre, University of PaduaDepartment of Pure and Applied Mathematics, University of Padua Email author 
  • , Mauro RivaAffiliated withBMR Genomics
  • , Erika FeltrinAffiliated withCRIBI Biotechnology Centre, University of Padua
  • , Barbara SimionatiAffiliated withBMR Genomics
  • , Tullio VardanegaAffiliated withDepartment of Pure and Applied Mathematics, University of Padua
  • , Giorgio ValleAffiliated withCRIBI Biotechnology Centre, University of Padua
  • , Nicola CannataAffiliated withDepartment of Mathematics and Computer Science, University of Camerino



Laboratory protocols in life sciences tend to be written in natural language, with negative consequences on repeatability, distribution and automation of scientific experiments. Formalization of knowledge is becoming popular in science. In the case of laboratory protocols two levels of formalization are needed: one for the entities and individuals operations involved in protocols and another one for the procedures, which can be manually or automatically executed. This study aims to combine ontologies and workflows for protocol formalization.


A laboratory domain specific ontology and the COW (Combining Ontologies with Workflows) software tool were developed to formalize workflows built on ontologies. A method was specifically set up to support the design of structured protocols for biological laboratory experiments. The workflows were enhanced with ontological concepts taken from the developed domain specific ontology.

The experimental protocols represented as workflows are saved in two linked files using two standard interchange languages (i.e. XPDL for workflows and OWL for ontologies). A distribution package of COW including installation procedure, ontology and workflow examples, is freely available from http://​www.​bmr-genomics.​it/​farm/​cow.


Using COW, a laboratory protocol may be directly defined by wet-lab scientists without writing code, which will keep the resulting protocol's specifications clear and easy to read and maintain.