Experimental Data Connector (XDC): Integrating the Capture of Experimental Data and Metadata Using Standard Formats and Digital Repositories

Abstract

Accelerating the development of synthetic biology applications requires reproducible experimental findings. Different standards and repositories exist to exchange experimental data and metadata. However, the associated software tools often do not support a uniform data capture, encoding, and exchange of information. A connection between digital repositories is required to prevent siloing and loss of information. To this end, we developed the Experimental Data Connector (XDC). It captures experimental data and related metadata by encoding it in standard formats and storing the converted data in digital repositories. Experimental data is then uploaded to Flapjack and the metadata to SynBioHub in a consistent manner linking these repositories. This produces complete connected experimental data sets that are exchangeable. The information is captured using a single template Excel Workbook, which can be integrated into existing experimental workflow automation processes and semiautomated capture of results.

Parsley: a web app for parsing data from plate readers

“…Data parsing functions can be found in a variety of packages [ Supplementary Table S2 ( Fernandez-Ricaud et al 2016 , Hughes 2016 , 2022 , Coutin 2019a , b , c , d , e , Fernandez 2019 , Martin et al 2019 , Coutin et al 2020 , Fedorec et al 2020 , Palakkan 2020 , Palakkan and Davies 2020 , Vegh 2020 , Csibra 2021 , Mante 2021 , Shterev et al 2021 , Wirth 2021 , Csibra and Stan 2022 , Montaño-Gutierrez et al 2022 , Osthege 2022 , Osthege et al 2022 , Blazanin 2023a , b , Fedorec 2023 , Giordano 2023 , González-Cebrián and Vignoni 2023 , González-Cebrián et al 2023 , Midani 2023 , Samineni et al 2023 , Swain 2023 )]. Of the 22 tools identified, parsers in 15 of these function in data extraction, 16 in data tidying and 11 in metadata joining, though capabilities in each area vary.…”

“…can only extract data from column formatted files), or where only 1 reading has been taken during an experiment. Most of these tools are analysis packages that contain the occasional parsing function, but a few tools were written specifically as parsing software: AUDIT, plater, PLATEO and XDC ( Hughes 2016 , 2022 , Coutin 2019a , Coutin et al 2020 , Vegh 2020 , Mante 2021 , Samineni et al 2023 ). For instance, the widely used plater package was developed specifically to automate the joining of data and metadata ( Hughes 2016 , 2022 ).…”