A complete digitization of German herbaria is possible, sensible and should be started now

Abstract

Plants, fungi and algae are important components of global biodiversity and are fundamental to all ecosystems. They are the basis for human well-being, providing food, materials and medicines. Specimens of all three groups of organisms are accommodated in herbaria, where they are commonly referred to as botanical specimens. The large number of specimens in herbaria provides an ample, permanent and continuously improving knowledge base on these organisms and an indispensable source for the analysis of the distribution of species in space and time critical for current and future research relating to global biodiversity. In order to make full use of this resource, a research infrastructure has to be built that grants comprehensive and free access to the information in herbaria and botanical collections in general. This can be achieved through digitization of the botanical objects and associated data. The botanical research community can count on a long-standing tradition of collaboration among institutions and individuals. It agreed on data standards and standard services even before the advent of computerization and information networking, an example being the Index Herbariorum as a global registry of herbaria helping towards the unique identification of specimens cited in the literature. In the spirit of this collaborative history, 51 representatives from 30 institutions advocate to start the digitization of botanical collections with the overall wall-to-wall digitization of the flat objects stored in German herbaria. Germany has 70 herbaria holding almost 23 million specimens according to a national survey carried out in 2019. 87% of these specimens are not yet digitized. Experiences from other countries like France, the Netherlands, Finland, the US and Australia show that herbaria can be comprehensively and cost-efficiently digitized in a relatively short time due to established workflows and protocols for the high-throughput digitization of flat objects. Most of the herbaria are part of a university (34), fewer belong to municipal museums (10) or state museums (8), six herbaria belong to institutions also supported by federal funds such as Leibniz institutes, and four belong to non-governmental organizations. A common data infrastructure must therefore integrate different kinds of institutions. Making full use of the data gained by digitization requires the set-up of a digital infrastructure for storage, archiving, content indexing and networking as well as standardized access for the scientific use of digital objects. A standards-based portfolio of technical components has already been developed and successfully tested by the Biodiversity Informatics Community over the last two decades, comprising among others access protocols, collection databases, portals, tools for semantic enrichment and annotation, international networking, storage and archiving in accordance with international standards. This was achieved through the funding by national and international programs and initiatives, which also paved the road for the German contribution to the Global Biodiversity Information Facility (GBIF). Herbaria constitute a large part of the German botanical collections that also comprise living collections in botanical gardens and seed banks, DNA- and tissue samples, specimens preserved in fluids or on microscope slides and more. Once the herbaria are digitized, these resources can be integrated, adding to the value of the overall research infrastructure. The community has agreed on tasks that are shared between the herbaria, as the German GBIF model already successfully demonstrates. We have compiled nine scientific use cases of immediate societal relevance for an integrated infrastructure of botanical collections. They address accelerated biodiversity discovery and research, biomonitoring and conservation planning, biodiversity modelling, the generation of trait information, automated image recognition by artificial intelligence, automated pathogen detection, contextualization by interlinking objects, enabling provenance research, as well as education, outreach and citizen science. We propose to start this initiative now in order to valorize German botanical collections as a vital part of a worldwide biodiversity data pool.

International collaboration between collections‐based institutes for halting biodiversity loss and unlocking the useful properties of plants and fungi

“…The digitization of specimens from the world's largest herbarium and fungarium collections requires rapid completion (Borsch et al., 2020) and digital integration, such as that articulated by the Distributed System of Scientific Collections program (DISSCo, 2020). We must address the capacity of national and regional herbaria and fungaria to completely digitize their own collections and integrate their data into international platforms.…”

A survey of biodiversity informatics: Concepts, practices, and challenges

“…The third and final phase consists of capturing high-resolution images of the specimens which can be used for further information extraction with OCR, quality assessment and control, and online publication for interactive exploration by users. High throughput digitization is possible through the use of technologies such as conveyor belts and digitization stations (Borsch et al, 2020). It is also critical to keep globally unique identifiers for each digitized specimen (Güntsch et al, 2017), facilitating consistent access to information and data gathering by biodiversity portals and aggregators (Berendsohn et al, 2011).…”

“…It is also critical to keep globally unique identifiers for each digitized specimen (Güntsch et al, 2017), facilitating consistent access to information and data gathering by biodiversity portals and aggregators (Berendsohn et al, 2011). Some examples of digitization efforts include iDigBio (Paul, Mast, Riccardi, & Nelson, 2013), the Botanic Garden of Rio de Janeiro (Lanna et al, 2018), and German herbaria (Borsch et al, 2020). Some trends and future directions involve the use of artificial intelligence to automate parts of the digitization workflow, such as the automated identification of herbarium specimens using deep learning methods (Carranza-Rojas, Goeau, Bonnet, Mata-Montero, & Joly, 2017).…”

Challenges and lessons learned from digitizing small Brazilian herbaria

“…JPEG files are made available online because the format was adopted as a web standard and because of file size, whereas TIFF files are used for internal purposes such as original metadata files (Downton 2005). Storage of these files can be problematic due to their size, since a raw file is typically about 80 MB (Silva et al 2017), whereas a converted JPEG, which can be used to identify most diagnostic morphological features, is about 10 MB (Borsch et al 2020). Biological collections initially began to store files on CD-ROMs, and then on internal servers (Thiers et al 2016) but image data hosting services and system integration for the remote use of image data is needed (Tegelberg et al 2014), such as cloud or e-infrastructure (Nieva de la Hidalga et al 2019) Conceiving an herbarium database is a fundamental step to entering the digital world.…”

“…Another issue is when data structure does not have a pattern, which makes integrating databases difficult, although it is fundamental in this new era (Wieczorek et al 2012). Thus, automatic and semi-automatic quality control of data become useful (Borsch et al 2020). Global standards were created to solve this interoperability issue, such as the Darwin Core (Wieczorek et al 2012), which defines common terms in datasets, thus improving data integration and sharing.…”