02503nas a2200217 4500008004100000022001400041245005700055210005300112260001500165300000800180490000600188520176400194653001201958653001501970653001401985653001601999653001702015653001602032100003302048856020402081 2023 eng d a2628-238000aThe correct authorship of Arthropoda—A reappraisal0 acorrect authorship of Arthropoda—A reappraisal c04/05/2023 a1-80 v63 a

Abstract: The scientific name Arthropoda has been repeatedly cited with various incorrect authorship data. This unsatisfactory situation was reviewed in 2013 and the “correct citation” was affirmed to be “Arthropoda von Siebold, 1848” based on the available evidence. Here, the review of historical literature is expanded with additional sources from the Biodiversity Heritage Library. The Greek compound noun “Arthropoda” was used as a scientific name at the rank of class already in 1843, containing the subclasses Crustacea, Arachnoidea, and Insecta. Additionally, the French morphological term “arthropodes” has been used in Zoology since at least 1832. The new citation of the name is proposed as “Arthropoda Gravenhorst, 1843”.

Zusammenfassung: Der wissenschaftliche Name Arthropoda wurde wiederholt mit verschiedenen falschen Urheberangaben zitiert. Die unbefriedigende Situation wurde 2013 überprüft und die „korrekte Zitierung“ auf der Grundlage der verfügbaren Literatur mit „Arthropoda von Siebold, 1848“ bestätigt. Hier wird die Recherche historischer Literatur um zusätzliche Quellen aus der Biodiversity Heritage Library erweitert. Das griechische zusammengesetzte Substantiv „Arthropoda“ wurde bereits 1843 als wissenschaftlicher Name im Rang einer Klasse verwendet, der die Unterklassen Crustacea, Arachnoidea und Insecta enthielt. Darüber hinaus wird der französische morphologische Begriff „arthropodes“ in der Zoologie seit mindestens 1832 verwendet. Die neue Zitation des Namens wird als „Arthropoda Gravenhorst, 1843“ vorgeschlagen.

10aanatomy10aArthropoda10aDumortier10aGravenhorst10anomenclature10avon Siebold1 aMartínez-Muñoz, Carlos, A. uhttps://bioone.org/journals/integrative-systematics-stuttgart-contributions-to-natural-history/volume-6/issue-1/2023.472723/The-correct-authorship-of-ArthropodaA-reappraisal/10.18476/2023.472723.full02924nas a2200493 4500008004100000022001400041245008000055210007100135260001500206300000900221520141900230653002401649653002601673653002301699653002201722653002201744100002101766700001801787700002701805700002801832700002601860700002301886700002001909700001601929700002101945700001901966700002501985700002502010700003002035700001902065700001702084700002602101700003302127700002302160700001802183700003202201700002602233700002202259700001302281700003502294700002302329700001902352856005902371 2022 eng d a2767-035X00aFrontiers in soil ecology—Insights from the World Biodiversity Forum 20220 aFrontiers in soil ecology—Insights from the World Biodiversity F c11/11/2022 a1-173 a

Global change is affecting soil biodiversity and functioning across all terrestrial ecosystems. Still, much is unknown about how soil biodiversity and function will change in the future in response to simultaneous alterations in climate and land use, as well as other environmental drivers. It is crucial to understand the direct, indirect and interactive effects of global change drivers on soil communities and ecosystems across environmental contexts, not only today but also in the near future. This is particularly relevant for international efforts to tackle climate change like the Paris Agreement, and considering the failure to achieve the 2020 biodiversity targets, especially the target of halting soil degradation. Here, we outline the main frontiers related to soil ecology that were presented and discussed at the thematic sessions of the World Biodiversity Forum 2022 in Davos, Switzerland. We highlight multiple frontiers of knowledge associated with data integration, causal inference, soil biodiversity and function scenarios, critical soil biodiversity facets, underrepresented drivers, global collaboration, knowledge application and transdisciplinarity, as well as policy and public communication. These identified research priorities are not only of immediate interest to the scientific community but may also be considered in research priority programmes and calls for funding.

10abiodiversity change10aecosystem functioning10ascenario modelling10asoil biodiversity10asoil macroecology1 aEisenhauer, Nico1 aBender, Franz1 aCalderón-Sanou, Irene1 ade Vries, Franciska, T.1 aLembrechts, Jonas, J.1 aThuiller, Wilfried1 aWall, Diana, H.1 aZeiss, Romy1 aBahram, Mohammad1 aBeugnon, Rémy1 aBurton, Victoria, J.1 aCrowther, Thomas, W.1 aDelgado-Baquerizo, Manuel1 aGeisen, Stefan1 aKardol, Paul1 aKrashevska, Valentyna1 aMartínez-Muñoz, Carlos, A.1 aPatoine, Guillaume1 aSeeber, Julia1 aSoudzilovskaia, Nadejda, A.1 aSteinwandter, Michael1 aSünnemann, Marie1 aSun, Xin1 avan der Heijden, Marcel, G. A.1 aGuerra, Carlos, A.1 aPotapov, Anton uhttps://onlinelibrary.wiley.com/doi/10.1002/sae2.1203101950nas a2200169 4500008004100000245008100041210006900122520137000191100002101561700002101582700002301603700001901626700002201645700003301667700002101700856005901721 2022 eng d00aApplication of BIOfid tools for extracting data from biodiversity literature0 aApplication of BIOfid tools for extracting data from biodiversit3 a

In an ideal world, extraction of machine-readable data and knowledge from natural-language biodiversity literature would be done automatically, but not so currently. The BIOfid project has developed some tools that can help with important parts of this highly demanding task, while certain parts of the workflow cannot be automated yet. BIOfid focuses on the 20th century legacy literature, a large part of which is only available in printed form. In this workshop, we will present the current state of the art in mobilisation of data from our corpus, as well as some challenges ahead of us. Together with the participants, we will exercise or explain the following tasks (some of which can be performed by the participants themselves, while other tasks currently require execution by our specialists with special equipment): Preparation of text files as an input; pre-processing with TextImager/TextAnnotator; semiautomated annotation and linking of named entities; generation of output in various formats; evaluation of the output. The workshop will also provide an outlook for further developments regarding extraction of statements from natural-language literature, with the long-term aim to produce machine-readable data from literature that can extend biodiversity databases and knowledge graphs.

Publication date: 09/06/2022

1 aKasperek, Gerwin1 aAbrami, Giuseppe1 aDriller, Christine1 aLücking, Andy1 aMehler, Alexander1 aMartínez-Muñoz, Carlos, A.1 aPachzelt, Adrian uhttps://nbn-resolving.org/urn:nbn:de:hebis:30:3-69677702221nas a2200157 4500008004100000245008300041210006900124520168100193100003301874700002301907700003001930700002601960700002001986700001902006856003802025 2022 eng d00aDomain Ontologies to Explore and Manage Functional Soil-invertebrate Diversity0 aDomain Ontologies to Explore and Manage Functional Soilinvertebr3 a

Due to their high structural and functional diversity, soil invertebrates are crucial for ecosystem functioning and its stability. This diversity is reflected not only in the multitude of quantitative and qualitative studies, but also in the range of existing vocabularies of characters and character states for functional soil biodiversity. Data mining and text mining are increasingly used to scour large data resources and systematically extract relevant information in a machine-based manner. Controlled vocabularies play a central role in applying these methods to represent implicit and explicit knowledge in so-called knowledge graphs in a structured and machine- and human-readable way. The Specialized Information Service Biodiversity Research (BIOfid) aims at this method of data mobilization from Central European biodiversity literature. In cooperation with the European Soil-Biology Data Warehouse for Soil Protection (EUdaphobase), differing vocabularies on the taxonomy, anatomy, ecology and traits of soil invertebrates are currently being harmonized and mapped onto domain-specific ontologies. In addition to data extraction, these ontologies should also support the interoperable and sustainable management of pan-European soil biodiversity data.

Recommended citation: Martínez-Muñoz, C. A., Driller, C., Aldana-Martín, J. F., Navas-Delgado, I., Hedde, M., & Russell, D. (2022): Domain Ontologies to Explore and Manage Functional Soil-invertebrate Diversity. World Biodiversity Forum 2022 (WBF 2022), Davos, Switzerland. Zenodo. https://doi.org/10.5281/zenodo.7074617

1 aMartínez-Muñoz, Carlos, A.1 aDriller, Christine1 aAldana-Martín, José, F.1 aNavas-Delgado, Ismael1 aHedde, Mickaël1 aRussell, David uhttps://zenodo.org/record/707461703182nas a2200217 4500008004100000022001400041245010700055210006900162260001500231300000800246490000600254520250900260653002902769653001502798653001402813653002202827653001502849100002302864700003302887856004402920 2022 eng d a2535-089700aBIOfid Steps Up to Provide Introduced Species Information: The case of myriapods in German greenhouses0 aBIOfid Steps Up to Provide Introduced Species Information The ca c23/08/2022 a1-30 v63 a

The German Specialized Information Service Biodiversity Research (BIOfid) is an infrastructure that provides scientists with information tailored to the specific needs of biodiversity research and related disciplines (Koch et al. 2017). The service, in particular, promotes digital access to legacy literature and enables the retrieval of research-relevant data using natural language processing (NLP) and machine learning (ML) techniques (Hemati et al. 2016, Abrami et al. 2020, Lücking et al. 2021), and provides a customized semantic search engine (Pachzelt et al. 2021). Thus, historical species records can be found and help to estimate past and present species distributions as well as potential range shifts. Future BIOfid services are planned to specifically address interoperability and linking of research data for rapid integration into national and international databases such as the German Federation for Biological Data (GFBio) and the Global Biodiversity Information Facility (GBIF). To this end, for example, BIOfid will contribute to further developing the open-source virtual research environment (VRE) Scratchpads (Smith et al. 2011) and promote its usage in the scientific community. Based on a use case on myriapods, we will test the ability of the two tools mentioned above to accelerate information retrieval and knowledge sharing by professional data mobilization and management methods. Certain myriapod species are known to have been introduced from tropical and subtropical environments to Germany, a country that lies in the north temperate zone. In this regard, we will scour BIOfid´s legacy literature for these species to find spatio-temporal evidence. Moreover, we will explore the usefulness of Myriatrix, a Scratchpads instance specialized on Myriapoda and Onychophora, to collate information on millipede and centipede species introduced to German greenhouses. Data on 35 diplopod and 18 chilopod species in German greenhouses (Decker et al. 2014) have been integrated into Myriatrix using the "Taxon Description" content type provided by Scratchpads. Subsequently, more comprehensive, recent information on the millipede Cylindrodesmus hirsutus Pocock, 1889 (Martínez-Muñoz 2020 onwards) has been incorporated. Finally, we will show how this compiled information can be integrated into GBIF through the Scratchpads' Darwin Core Archive (DwC-A) export.

10abiodiversity informatics10acentipedes10aFAIR data10alegacy literature10amillipedes1 aDriller, Christine1 aMartínez-Muñoz, Carlos, A. uhttps://biss.pensoft.net/article/93666/04243nas a2200229 4500008004100000022001400041245010600055210006900161260001500230300000800245490000600253520352600259653002903785653001403814653001403828653003303842100003303875700001903908700001903927700002303946856004403969 2022 eng d a2535-089700aMobilizing and Enhancing Legacy Biodiversity Data: The case of Karl Wilhelm Verhoeff's correspondence0 aMobilizing and Enhancing Legacy Biodiversity Data The case of Ka c23/08/2022 a1-30 v63 a

A considerable amount of biological data is preserved as physical documents, the legacy of former explorers, collectors, researchers, and others. Mobilizing data from handwritten documents has been considered particularly challenging, with well-known cases such as the manual transcription of specimen labels and herbarium sheets by museum staff, or crowdsourced transcription of data card collections through online platforms. Here we present a pipeline of open-source software that can be used to automatically transcribe handwritten text, make it publicly available, annotate it with e.g., scientific names, extract names in Darwin Core Archive (DwC-A) for third-party reuse, and automatically recognize named entities in the machine-readable text. automatically transcribe handwritten text, make it publicly available, annotate it with e.g., scientific names, extract names in Darwin Core Archive (DwC-A) for third-party reuse, and automatically recognize named entities in the machine-readable text. We based our use case on the correspondence of the German zoologist Karl Wilhelm Verhoeff, related to the Myriapoda collection held at the Musée Zoologique de Strasbourg. The documents were processed with Transkribus (Muehlberger et al. 2019), a mostly open-source virtual research environment (OS VRE), which allows text in images to be converted into machine-readable text amenable to semantic enrichment. We achieved a character error rate as low as 5%, a remarkable result for handwritten material, as an accuracy higher than 95% for printed material is acceptable (Deutsche Forschungsgemeinschaft 2016). We then used Myriatrix (Martínez-Muñoz 2019), an instance of the Scratchpads OS VRE (Smith et al. 2011), to create bibliographic references, publish the full text, and annotate the correspondence with scientific names of myriapods. During the process, we added new scientific name spellings and combinations to the taxonomic backbone of Myriatrix and exported the full taxon classification in DwC-A via the Global Biodiversity Information Facility (GBIF) for reuse by the Global Names Architecture and its open-source tools (Patterson et al. 2016, Mozzherin et al. 2017). As a next step we are planning to subject the corrected text from Transkribus to a specific text-preprocessing workflow combining natural language processing (NLP) and machine learning (ML) techniques (Lücking et al. 2021). This includes, inter alia, a multiple annotation approach for general and bioscientific term classification in order to detect the respective entities automatically. The workflow has been developed in the framework of the Specialized Information Service Biodiversity Research (Koch et al. 2017) to make biodiversity information available via a customized and (bio-)ontology-based semantic search engine (Pachzelt et al. 2021). We recommend our comprehensive approach to natural history institutions seeking to efficiently digitize and mobilize the rich biological data present in their archival documents.

10abiodiversity informatics10aChilopoda10aDiplopoda10ahandwritten text recognition1 aMartínez-Muñoz, Carlos, A.1 aHuff, Dorothee1 aMeister, Marie1 aDriller, Christine uhttps://biss.pensoft.net/article/93679/