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Datasets that have been collected and stored in genebanks or breeding facilities have the potential to develop new crop varieties. This could ensure future food security. Yet, acquiring, recording, processing, and handling phenotypical data can be time consuming and labour-intensive for plant researchers. 

Here, Franco Röckel digs deeper into his Software Tool Article, which examines how PhenoApp. The open source Android app allows researchers to record field and greenhouse observations on their digital devices. This reduces the time spent manually processing phenotyping data. 

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Please tell us a little about yourself  

My name is Franco Röckel and I work for the Julius Kühn Institute (JKI), the German Federal Research Centre for Cultivated Plants, at the Institute for Grapevine Breeding Geilweilerhof. 

I work in the Grapevine Genetic Resources group. We maintain several internationally heavily-used databases, including the Vitis International Variety Catalogue (VIVC). Furthermore, my group curates the “Deutsche Genbank Reben” (German grapevine gene bank). As such, our research focuses on the characterization and evaluation of biodiversity to protect grapevine variety diversity. Furthermore, as plant geneticists, we perform classical QTL analysis and GWA studies to define and highlight traits important for grapevine breeding. 

What is PhenoApp, and what inspired you to develop it? 

PhenoApp is an easy-to-use Android app for recording field and greenhouse observations on mobile devices. This relieves the labor-intensive and time-consuming process of manual phenotyping. Moreover, it allows for maximum customization and enables fast and seamless data transfer.

As is so often the case, inspiration came from my own working life. I started as a PhD student in 2014 with many field evaluations on the schedule. During the season and twice a week, I went out in the field in the morning with a clipboard to phenotype. In the afternoon, I digitized the recordings. I always found the process of manual phenotyping to be a time-consuming and error-prone process. I tested different digital methods, including, spreadsheets with a dropdown list for predefined scales. In the end, nothing really felt workable for me. The idea to develop our own solution was born.   

What challenges do plant researchers face in their role? 

The handling, processing, and adequate management of phenotyping data is the most challenging step in a plant researchers’ role. Despite the emergence of platforms to help tackle these challenges, the development of such platforms is slow and expensive.

As these new technologies still have their limitations, the manual acquisition of data continues to be an extremely important factor in the field of plant research. PhenoApp provides a solution by streamlining these processes. 

How does PhenoApp help tackle this problem? 

PhenoApp provides users with a graphical interface to digitally record phenotyping data. This reduces the time spent interpreting and digitizing handwritten results.

To use the app, you only need:

• A standard computer

• Microsoft Excel

• Mobile Android-based device

• Plant list with unique locations

• A defined scientific question that can be translated into a descriptor.

Additionally, the easy-to-use and adaptable structure of input and output files enables an easy data handling experience.  Moreover, we have already demonstrated that it is possible to integrate the app into the workflow of laboratory information management systems (LIMS).

In summary, PhenoApp streamlines the acquisition of digital plant research data and genebank management by reducing the labour-intensive and time-consuming step of manual phenotyping.  

Why did you decide to publish your Software Tool Article on F1000Research? 

After identifying journals that publish software tools or apps, we came across F1000Research. Usually, authors and readers do not know the reviewers, and readers do not know the review itself. In contrast to that, the peer review process for F1000Reasearch is completely open. Authors and readers can see the reviewer names and reports, alongside answers and updated manuscript versions. We found that very interesting and, above all, the right way to go when publishing an app.

Additionally, in the responses to the reviews, we have already answered questions that other users may have as well. We also provided additional insight into the future development process that will be very useful for users. 

Why did you decide to share your data and code, and would you do it again? 

As part of the JKI, the German Federal Research Centre for Cultivated Plants, with no commercial interest, open access was clear from the start. I would do it again, of course. I am a dedicated advocate of open access science and the FAIR data principles in general, especially when publicly funded.  

Moreover, by sharing our code, we hope to encourage researchers to further develop PhenoApp. In cooperation with us, we could publish new features in upcoming app versions. This benefits all users.   

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Read the full Software Tool Article today on F1000Research or explore our Plant Science Gateway to discover a plethora of cutting-edge open research.