Digital Biodiversity Monitoring Practices

The ARISE-day and conference in March 2023 was hosted at Naturalis Biodiversity Centre in Leiden, Netherlands . Besides a research centre, Naturalis is also a biodiversity museum. After discussing participatory biodiversity monitoring and automated species identification with ObsIdentify, Michelle tested the limits of this software and experience the internal validation process.

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Between May 18-21, we organised a BioBlitz at Ecodorp Boekel in order to map local species and experience the use of automated species identification applications. The BioBlitz was hosted by Michelle and approximately 11 participants joined in mapping plant, animals, and fungi species via the ObsIdentify mobile application. (More people joined whose data were not collected, including those <18 years old as well as people who joined but didn't register their data online via the application.). During this extended weekend with pleasant weather conditions, we collectively uploaded 310 observations that included 157 different species.

What immediately stands out when looking at this data is the Ecodorp inhabitants' keen interest in observing and identifying plant species. Contrary to the Waarnemingen.nl user statistics that mostly observe birds, this BioBlitz was much more plant-oriented. This does not only reflect the inhabitants' interest and time spent in growing their own food, but we also found that plants were much easier to document compared to moving insects or nearly invisible fungi.

Interviewing participants while mapping species and using the mobile application revealed many interesting stories and observations. One participant was engaged in training their eyesight and found the activity of finding insects very suitable for training eye movement and shifting perspectives. Another participant was forcefully displaced from Yemen and while observing species locally, we talked about the kinds of plants that occur in Yemen, their names, and the relations of family members with native plants.

One participants was concerned about the scientific value of mapping species. She is an experienced volunteer in biodiversity monitoring and shared the principles of systematic monitoring in order to help divide people across the area. A few parents joined the BioBlitz together with their kids as an educational activity. They engaged in conversations together and expressed their excitement about all the different species they encountered. Other participants were more interested in mapping the small gardens in front of their homes to gain knowledge of biodiversity that can be observed close by.

Several participants experienced difficulties in connecting their mobile phones to the application or experienced other limitations such as reaching mobile data limits on their phones. Another much discussed topic involved the precision of the automated species identification. Participants discovered that the application would only automatically record the observation once it reveals >90% accuracy for each observation. This led participants to discard all the 'less successful' observations and delete these images. Participants discussed strategies for 'correctly' photographing plants and observed how certain groups of plants (such as grasses) were much more difficult to identify.

An often recurring comment during the BioBlitz involved people's excitement about using the mobile application. "It is really addictive", on participant mentioned. She explained how she worked on maintaining the food garden during the day, but she was continuously drawn to picturing and recording new observations as different species drew her attention. This way of playfully moving across space reminded Michelle of exploring open-world video games that are designed to elicit curiosity by strategically placing game-entities.

This is just a small sample of reflections and images from the BioBlitz. It reveals how the activity of mapping biodiversity locally is closely connected to people's personal interests and experiences. Rather than a collection of observations that resembles scientific accuracy, the mapping activity provides a more detailed reflection on how participants are drawn to different species. Furthermore, the results don't reflect species occurrences, but instead mainly demonstrate which species are suitable for automated identification with the application's image recognition software.

In the weeks following the BioBlitz, more Ecodorp inhabitants joined as registered users of ObsIdentify and shared experiences and perspectives. People used the application to ask each other questions on which local plants are edible, and they enjoyed quizzing themselves and others on identifying species. Inhabitants are still adding species observations to the platform and more reflections may be added as the fieldwork unfolds.

During the ARISE-day 2023 workshop, I (Michelle) had the opportunity to attend a data management workshop hosted by the Dutch node of GBIF, where I learned more about data standardisation principles for biodiversity data. Here we worked with the Dutch monumental tree dataset to explore how to create a database that can be uploaded to GBIF. What struck me during this workshop were the various ways in which data of individual trees that have historic, cultural, or societal value are transformed into a database that only includes species names, GPS coordinates, plant years, images, and the name of the photographer. In other words, the standardisation process works to create singular categories that work for all GBIF occurrences, thereby eliminating those types of data that make these occurrences unique.

Furthermore, while the Darwin Core protocol is open-source and described as 'flexible', GBIF's standardisation practices align with a more western type of scientific data management that, for instance, prioritises species names, timestamps, location, and ownership data. When such data standardisations are implemented globally, it risks eliminating the possibilities for other types of data to become included in global frameworks. One of the organisers remarked that while FAIR data principles are important for Dutch GBIF data, CARE principles are not really relevant because "these are for Indigenous people and data sovereignty ". Such understandings demonstrate how people involved in biodiversity data management in the Global North can view different data practices as separate initiatives across the world with distinct ethical protocols, while at the same time GBIF is working towards establishing global standards. These experiences materialise the conflicting needs for both data standardisation and unique ways of understanding biodiversity.

With the increasing use of mobile smartphones, applications that assist biodiversity monitoring are now widespread and have millions of users (predominantly in the Global North). These apps focus specifically on recognising plant, animal, and fungi species from image- or sound recordings. Previously, all this data had to be manually evaluated by taxonomists or citizen scientists to identify species. Now, the majority of the most used applications incorporate automated functionality to identify species based on image- or sound-recognition techniques.

Examples of apps with large user bases include iNaturalist, eBird,Merlin (all three developed in the U.S.), the French Pl@ntNet, the Dutch ObsIdentify, and national nodes of iNaturalist such as the UK portal iRecord. Each of these apps collects thousands of observations per day. Depending on the app's infrastructure, besides species identification data, each observation contains metadata about the time, location, as well as user statistics. Some apps, including iNaturalist, rely predominantly on automated observation and citizen science , while others, such as ObsIdentify, selects specific observations to be evaluated by volunteer 'validators' or 'experts'. Some of these technologies can also be directly connected to hardware such a binoculars or cameras to directly record more detailed and high-resolution images.

Rather than developing new taxonomic datasets, these applications are usually connected to larger national and international digital species databases. eBird, for instance, works with the 'Working Group Avian Checklists' to create a single global taxonomy for avian species. ObsIdentify is an app of Observations.org, which is connected to Naturalis, a Dutch national biodiversity institute. Most of the (validated) data in these applications, including iNaturalist, are finally indexed as open data in GBIF, the Global Biodiversity Information Facility.

GBIF contains hundreds of millions of species occurrence records from sources such as museum collections, eDNA, research databases, and citizen data. The intergovernmental initiative started in 1999, has a secretariat in Copenhagen, involves 42 voting-participant countries, and is government-funded. One of its aims is to create protocols for data standards, specifically with the use of the Darwin Core protocol.