Building an Open Representation for Biological Protocols

Abstract

Laboratory protocols are critical to biological research and development, yet difficult to communicate and reproduce across projects, investigators, and organizations. While many attempts have been made to address this challenge, there is currently no available protocol representation that is unambiguous enough for precise interpretation and automation, yet simultaneously "human friendly"and abstract enough to enable reuse and adaptation. The Laboratory Open Protocol language (LabOP) is a free and open protocol representation aiming to address this gap, building on a foundation of UML, Autoprotocol, Aquarium, SBOL RDF, and the Provenance Ontology. LabOP provides a linked-data representation both for protocols and for records of their execution and the resulting data, as well as a framework for exporting from LabOP for execution by either humans or laboratory automation. LabOP is currently implemented in the form of an RDF knowledge representation, specification document, and Python library, and supports execution as manual "paper protocols,"by Autoprotocol or by Opentrons. From this initial implementation, LabOP is being further developed as an open community effort.