RT Journal Article
SR Electronic
T1 Building an Open Representation for Biological Protocols
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.07.05.498808
DO 10.1101/2022.07.05.498808
A1 Bartley, Bryan
A1 Beal, Jacob
A1 Rogers, Miles
A1 Bryce, Daniel
A1 Goldman, Robert P.
A1 Keller, Benjamin
A1 Lee, Peter
A1 Biggers, Vanessa
A1 Nowak, Joshua
A1 Weston, Mark
YR 2022
UL http://biorxiv.org/content/early/2022/07/08/2022.07.05.498808.abstract
AB 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 abstract enough to enable reuse and adaptation. The Protocol Activity Markup Language (PAML) is a free and open protocol representation aiming to address this gap, building on a foundation of UML, Autoprotocol, and SBOL RDF. PAML provides a representation both for protocols and for records of their execution and the resulting data, as well as a framework for exporting from PAML for execution by either humans or laboratory automation. PAML is currently implemented in the form of an RDF knowledge representation, specification document, and Python library, can be exported for execution as either a manual “paper protocol” or Autoprotocol, and is being further developed as an open community effort.Competing Interest StatementThe authors have declared no competing interest.