Journal article
Building an Open Representation for Biological Protocols
ACM journal on emerging technologies in computing systems, Vol.19(3), pp.1-21
07/31/2023
DOI: 10.1145/3604568
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.
Details
- Title: Subtitle
- Building an Open Representation for Biological Protocols
- Creators
- Bryan Bartley - RTXJacob Beal - RTXMiles Rogers - RTXDaniel Bryce - Smart Information Flow TechnologiesRobert P. Goldman - Smart Information Flow TechnologiesBenjamin Keller - University of WashingtonPeter Lee - Ginkgo BioWorksVanessa Biggers - Strateos, Inc., USAJoshua Nowak - Strateos, Inc., USAMark Weston - Netrias, Inc., USA
- Resource Type
- Journal article
- Publication Details
- ACM journal on emerging technologies in computing systems, Vol.19(3), pp.1-21
- DOI
- 10.1145/3604568
- ISSN
- 1550-4832
- eISSN
- 1550-4840
- Language
- English
- Date published
- 07/31/2023
- Academic Unit
- Electrical and Computer Engineering
- Record Identifier
- 9984627303502771
Metrics
1 Record Views