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This spring, a new project in the Baltic Sea Region focused on tracking plant pests as they emerge and spread. PestSpace has a budget of €3.2 million and involves collaborators from Estonia, Finland, Latvia, Lithuania and Poland. The investigators lead a team from the University of Tartu. They collect environmental DNA and field data to monitor plant diseases and destructive insects. Initially, the researchers are focusing on two preselected crops for the study. The data is being shared between farmers, officials, and researchers to improve their collective response to threats.
At the centre of PestSpace is an innovative biological data management platform called PlutoF.
“The idea is to create an alert system for plant diseases as they move from south to north,” says Urmas Kõljalg, a professor of mycology at the University of Tartu’s Institute of Ecology and Earth Sciences. All of the data collected, he notes, will filter through PlutoF GO, the platform’s mobile application, where its DNA sequences will be uploaded and assessed by machine learning tools, quality controlled by an associated monitoring team, and ultimately identified.
Its project manager, Kadri Põldmaa, likens the output to a weather report that could warn countries of an incoming storm, Kõljalg notes. “You will be able to see dots of certain diseases start to appear,” he says, “and also to react.”
The birth of PlutoF
Hosted at the University of Tartu, PlutoF provides researchers with an online service to collect, manage, and share disparate data. It bills itself as the “common data space for biodiversity.” The data input sources are diverse, from photos or videos of species to written observational notes to DNA sequence data. Its users are varied, and include researchers, data managers, laboratories, universities, museums, and even citizen scientists.
“We have a lot of citizen scientists using PlutoF,” says Kõljalg. For example, most bird watchers in Estonia use PlutoF to capture and share their observations. Others upload the sequence data from animal, soil, and marine samples collected during their fieldwork. PlutoF is the backend platform for eElurikkus, or eBiodiversity, a portal that contains information on all species found in Estonia. “We have almost 40,000 species recorded,” remarks Kõljalg.
Kõljalg has been involved with PlutoF since its inception. Initially, the platform was created for the UNITE Community, of which the University of Tartu is a coordinator. Its aim is to create and maintain a database and sequence management environment. PlutoF was designed to address gaps in existing databases at that time, Kõljalg explained. In the US National Institutes of Health-hosted GenBank database, for example, most sequences listed then did not have full species names attached to them, or the names were misidentified.
“We decided to build a global database for ourselves,” Kõljalg says. The name refers to Pluto, which at the time Plutof was created had been downgraded from a planet to a dwarf planet. Therefore, Kessy Abarenkov, our PhD student, proposed the name Plutof.
The evolution of PlutoF
A lot has changed since 2005, and the platform has evolved. Over the past fifteen years, researchers involved with PlutoF have worked to upgrade its functionality, supported by an an Estonian project called the Natural History Archives and Common Data Space, the aim of which was to support the manageability and accessibility of Estonia’s biodiversity and geological data within a unified data space, as well as to develop AI-based solutions for data analysis.
According to Kõljalg, making all the data available in a user-friendly format has been a challenge, but one that PlutoF’s developers have strived to meet. Making a mobile version of the platform, PlutoF GO, available has also been a priority, as most users use it. PlutoF GO is now available in the Apple and Google Play stores.
“The learning curve is quite high,” says Kõljalg. “You can do a lot of things on this platform. That’s why it’s being used globally.”
Hooked on PlutoF
Much of PlutoF’s recent development has been influenced by Allan Zirk, team lead and product manager of the platform, who became involved with the project a decade ago after working as a programmer at Playtech, a gambling software development company. “It happened by chance,” says Zirk. “I took a break from programming, and it sort of found me, and I got hooked.”
When Zirk arrived, the PlutoF platform underwent a complete overhaul. “We started from scratch, everything from zero,” he recalls. “We had the concept, some of the scheme was there from the previous version, but for everything else, we started from zero.”
Earlier versions of PlutoF were built by scientists for scientists, he noted, but the new platform was redesigned with the user in mind. This was no easy task. Zirk’s team needed to dig into every module and to understand the concept behind it. “There were so many modules for so many different use cases,” he said. “The complex part was to make them have the same feel.”
The result has been an academic platform that looks and feels like a commercial one. The mobile app was rolled out three years ago, and according to Zirk, innovation is ongoing, as PlutoF’s five-person IT team responds to customer feedback and makes changes accordingly.
“We always listen to our users,” Zirk says, noting that PlutoF has 13,000 registered users. “They write to us where they get stuck, tell us what they are missing. In that sense, our users help us.”
PlutoF is gaining traction
According to Zirk, interest in PlutoF is only increasing as it lacks direct competitors. Other platforms tend to focus on one aspect of biodiversity, such as observations or sequences only. PlutoF links everything together with taxonomy. “There isn’t anything similar out there,” he says.
Kõljalg notes that AI is being used more within the platform, such as to guide species identification. Users can upload sequence data, and the AI contained in the platform will predict the most likely corresponding species.
He says that in addition to PestSpace, he would like to see PlutoF only adopted more by countries in the Baltic Sea Region, so that it could become a common hub for sharing biodiversity data. “I see this becoming part of a Baltoscandinavian initiative,” says Kõljalg. “All research organisations in the region could join and use PlutoF.” He notes that most databases out there are maintained at the national level, and said that PlutoF could become a sort of umbrella platform, as it allows sharing of data easily between its users.
PestSpace is therefore a good project for piloting this kind of use, Kõljalg noted. In addition to notifying farmers with information about potential pests and guidance on how to best respond, the project will allow the validation of PlutoF and create guidelines on how the system could be expanded to cover other crops in the future, as well as other countries in the Baltic Sea Region.
This article is written by Justin Petrone. It was originally published on the webpage of e-Estonia.
If this peek into biodiversity has you buzzing, chirping, and roaring with curiosity, don’t stop at one species! Branch out to our next article and read more about how People’s activities make many plants disappear, even far away.
