@article {1996, title = {The correct authorship of Arthropoda{\textemdash}A reappraisal}, journal = {Integrative Systematics}, volume = {6}, year = {2023}, month = {04/05/2023}, pages = {1-8}, type = {Research Article}, abstract = {

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 \überpr\üft und die \„korrekte Zitierung\“ auf der Grundlage der verf\ügbaren Literatur mit \„Arthropoda von Siebold, 1848\“ best\ätigt. Hier wird die Recherche historischer Literatur um zus\ätzliche 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. Dar\über hinaus wird der franz\ösische morphologische Begriff \„arthropodes\“ in der Zoologie seit mindestens 1832 verwendet. Die neue Zitation des Namens wird als \„Arthropoda Gravenhorst, 1843\“ vorgeschlagen.

}, keywords = {anatomy, Arthropoda, Dumortier, Gravenhorst, nomenclature, von Siebold}, issn = {2628-2380}, doi = {https://doi.org/10.18476/2023.472723}, url = {https://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.full}, author = {Mart{\'\i}nez-Mu{\~n}oz, Carlos A.} } @article {1767, title = {Frontiers in soil ecology{\textemdash}Insights from the World Biodiversity Forum 2022}, journal = {Journal of Sustainable Agriculture and Environment}, year = {2022}, month = {11/11/2022}, pages = {1-17}, type = {Opinion}, abstract = {

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.

}, keywords = {biodiversity change, ecosystem functioning, scenario modelling, soil biodiversity, soil macroecology}, issn = {2767-035X}, doi = {https://doi.org/10.1002/sae2.12031}, url = {https://onlinelibrary.wiley.com/doi/10.1002/sae2.12031}, author = {Eisenhauer, Nico and Bender, S. Franz and Calder{\'o}n-Sanou, Irene and de Vries, Franciska T. and Lembrechts, Jonas J. and Thuiller, Wilfried and Wall, Diana H. and Zeiss, Romy and Bahram, Mohammad and Beugnon, R{\'e}my and Burton, Victoria J. and Crowther, Thomas W. and Delgado-Baquerizo, Manuel and Geisen, Stefan and Kardol, Paul and Krashevska, Valentyna and Mart{\'\i}nez-Mu{\~n}oz, Carlos A. and Patoine, Guillaume and Seeber, Julia and Soudzilovskaia, Nadejda A. and Steinwandter, Michael and S{\"u}nnemann, Marie and Sun, Xin and van der Heijden, Marcel G. A. and Guerra, Carlos A. and Potapov, Anton} } @booklet {1611, title = {Application of BIOfid tools for extracting data from biodiversity literature}, year = {2022}, abstract = {

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

}, doi = {https://doi.org/10.21248/gups.69677}, url = {https://nbn-resolving.org/urn:nbn:de:hebis:30:3-696777}, author = {Kasperek, Gerwin and Abrami, Giuseppe and Driller, Christine and L{\"u}cking, Andy and Mehler, Alexander and Mart{\'\i}nez-Mu{\~n}oz, Carlos A. and Pachzelt, Adrian} } @booklet {1609, title = {Domain Ontologies to Explore and Manage Functional Soil-invertebrate Diversity}, year = {2022}, abstract = {

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: Mart\ínez-Mu\ñoz, C. A., Driller, C., Aldana-Mart\ín, 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

}, doi = {https://doi.org/10.5281/zenodo.7074617}, url = {https://zenodo.org/record/7074617}, author = {Mart{\'\i}nez-Mu{\~n}oz, Carlos A. and Driller, Christine and Aldana-Mart{\'\i}n, Jos{\'e} F. and Navas-Delgado, Ismael and Hedde, Micka{\"e}l and Russell, David} } @article {1602, title = {BIOfid Steps Up to Provide Introduced Species Information: The case of myriapods in German greenhouses}, journal = {Biodiversity Information Science and Standards}, volume = {6}, year = {2022}, month = {23/08/2022}, pages = {1-3}, type = {Abstract}, abstract = {

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, L\ücking 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 (Mart\ínez-Mu\ñoz 2020 onwards) has been incorporated. Finally, we will show how this compiled information can be integrated into GBIF through the Scratchpads\&$\#$39; Darwin Core Archive (DwC-A) export.

}, keywords = {biodiversity informatics, centipedes, FAIR data, legacy literature, millipedes}, issn = {2535-0897}, doi = {https://doi.org/10.3897/biss.6.93666}, url = {https://biss.pensoft.net/article/93666/}, author = {Driller, Christine and Mart{\'\i}nez-Mu{\~n}oz, Carlos A.} } @article {1601, title = {Mobilizing and Enhancing Legacy Biodiversity Data: The case of Karl Wilhelm Verhoeff{\textquoteright}s correspondence}, journal = {Biodiversity Information Science and Standards}, volume = {6}, year = {2022}, month = {23/08/2022}, pages = {1-3}, type = {Abstract}, abstract = {

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 Mus\ée 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 (Mart\ínez-Mu\ñoz 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 (L\ücking 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.

}, keywords = {biodiversity informatics, Chilopoda, Diplopoda, handwritten text recognition}, issn = {2535-0897}, doi = {https://doi.org/10.3897/biss.6.93679}, url = {https://biss.pensoft.net/article/93679/}, author = {Mart{\'\i}nez-Mu{\~n}oz, Carlos A. and Huff, Dorothee and Meister, Marie and Driller, Christine} }