Swobup - the Swate OBO Updater to foster the standardization process

Mon Feb 01 2021

Joint efforts of TaskArea 1 (standardization), TaskArea 2 (technical infrastructure) and TaskArea 3 (data stewards, community support) focusing on the optimization of digital workflows in plant sciences, have enabled one of our developers from Freiburg to implement a tool that facilitates the use of the Swate tool. The tool operates in the background on the Swate Database hosted at the DataPLANT site in Tübingen.

Swate is a Swate Workflow Annotation Tool for the Excel spreadsheet application. It aims to provide a low-friction workflow annotation experience that makes the usage of controlled vocabularies (ontologies) as easy and intuitive as possible. It is designed to integrate in the familiar spreadsheet environment that is the center of a great deal of data-focused wetlab work.

Swobup (Swate OBO Updater) is used to synchronize terms in a previously defined OBO file uploaded to a Github repository by an authorized user. Swobup parses the OBO file and incorporates the changes into the Swate database. The user then has the updated terms available in the Swate tool without having to manually enter individual terms.

More in depth information on the tool and its features, the necessary steps for setup and configuration are available on the nfdi4plants GitHub page, which allows posting issues, improvement suggestions or pull requests. Feedback is welcome!