BETYdb Data Entry Workflow

David LeBauer, Moein Azimi, David Bettinardi, Rachel Bonet, Emily Cheng, Michael Dietze, Patrick Mulrooney, Scott Rohde, Andy Tu

AbstractThis is the userguide for entering data into the BETYdb database. The goal of this guide is to provide a consistent method of data entry that is transparent, reproducible, and well documented. The steps here generally accomplish one of two goals. The first goal is to provide data that is associated with the experimental methods, species, site, and other factors associated with the original study. The second goal is to provide a record of all the transformations, assumptions, and data extraction steps used to migrate data from the primary literature to the standardized framework of the database.

Table Of Contents

  • Getting Started \ref{sec:getting_started}
  • Preparing Publications \ref{sec:preparing_publications}
  • Adding Data
    • Citations \ref{sec:citation}
    • Site \ref{sec:site}
    • Treatments \ref{sec:treatments}
    • Managements \ref{sec:managements}
    • Traits \ref{sec:traits}
    • Yields \ref{sec:yields}
  • Bulk uploads \ref{sec:bulk_upload}
  • QA/QC \ref{sec:qaqc}

Getting Started \label{sec:getting_started}

You will need to create the following accounts:

  • BETYdb (To use the database; request "creator" access during signup to enter data; request "manager" to perform QA/QC
  • Mendeley is used to track and annotate citaitons
  • Google Docs is used to prepare and transform data prior to entry.
  • Redmine is used to track data that need to be checked and/or corrected.

Preparing Publications for Data Entry \label{sec:preparing_publications}


Mendeley provides a central location for the collection, annotation, and tracking of the journal articles that we use. Features of Mendeley that are useful to us inclu