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Institute
Buchbesprechungen
(2023)
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.
Buchbesprechungen
(2022)
Es werden folgende Publikationen rezensiert: Jansen W. & T. Gregor 2021: Rubi hassici – die Brombeeren Hessens; Schmidt M. & P. Meyer (Gesamtredaktion) 2019: Hessische Naturwaldreservate im Portrait. Waldgebiet östlich Oppershofen; Schmidt M. & P. Meyer (Gesamtredaktion) 2020: Hessische Naturwaldreservate im Portrait. Schloßberg; Schmidt M., J. Evers, T. Hövelmann, K. Lorenz, U. Paar, R. Starke & P. Meyer 2021: Hessische Naturwaldreservate im Portrait. Niestehänge; Stützel T. 2021: Botanische Bestimmungsübungen. 4. Auflage; Ssymank A., G. Ellwanger, M. Ersfeld, J. Ferner, S. Lehrke, C. Müller, U. Raths, M. Röhling & M. Vischer-Leopold 2021: Das europäische Schutzgebietssystem Natura 2000. BfN-Handbuch zur Umsetzung der Fauna-Flora-Habitat-Richtlinie (92/43/EWG) und der Vogelschutzrichtlinie (2009/147/EG). Zweite, erweiterte und geänderte Auflage. Band 2.1: Lebensraumtypen der Meere und Küsten, der Binnengewässer sowie der Heiden und Gebüsche; Tietze A., C. Hepting, V. Hollmann, L. Jeske, I. Leyer, S. Liepelt, A. Peters & J. Weise 2020: Wilde Arnika – Ein Leitfaden für die Praxis; Verband Botanischer Gärten (2021): Neue Wilde – Globalisierung in der Pflanzenwelt.
Die Fundmeldungen in Band 33 von Botanik und Naturschutz in Hessen stammen von: Dirk Bönsel, Martin de Jong, Wolfgang Ehmke, Peter Emrich, Benjamin Feller, Brunhilde Göbel, Thomas Gregor, Arthur Händler, Sylvain Hodvina, Gerwin Kasperek, Egbert Korte, Ute Lange, Stefan Meyer, Hasko Friedrich Nesemann, Uwe Raabe, Bernd Sauerwein, Marco Schmidt, Christof Nikolaus Schröder, Antje Schwab, Rainer Stoodt und Michael Uebeler.
In 23 survey areas with woodland vegetation or woodland succession in Frankfurt/Main with a total size of 134 hectares, woody species were surveyed (excluding species only occurring as planted individuals). We found 149 woody taxa; 42% of them indigenous, and 58% non-native. Out of the 86 non-native taxa, 49 were naturalized in Frankfurt while 37 were considered as casual. Among non-native taxa, East Asian taxa formed the largest phytogeographic group. We found taxa originating from horticulture (cultigens) to be an important part of the woody flora of Frankfurt/Main. The most common taxa were Acer pseudoplatanus, A. platanoides, Betula pendula, and Sambucus nigra; the two Acer species were regarded as naturalized. Non-native woody species were generally common (with percentages ranging from 24% to 79% in individual areas).
Im Jahr 2008 wurden im Hochtaunus zwei Vorkommen der für diesen Bereich in der Literatur bisher nicht erwähnten Süßdolde (Myrrhis odorata) entdeckt. Beide haben sich bis heute (2017) in dicht geschlossenen, einmal im Jahr gemähten Pflanzenbeständen gehalten. Die Art besitzt also offensichtlich das Potential zur Einbürgerung, wobei man angesichts der relativ geringen Bestandesgröße noch nicht von einem gesicherten Trend zur Einbürgerung sprechen darf. Beide Pflanzenbestände sind saumartig ausgebildet, wobei der Aspekt auch von typischen Saumarten bestimmt wird. Der für Saumgesellschaften auffallend hohe Anteil an Wiesenarten dürfte darauf zurückzuführen sein, dass beide Säume einmal im Jahr gemäht werden.
BIOfid is a specialized information service currently being developed to mobilize biodiversity data dormant in printed historical and modern literature and to offer a platform for open access journals on the science of biodiversity. Our team of librarians, computer scientists and biologists produce high-quality text digitizations, develop new text-mining tools and generate detailed ontologies enabling semantic text analysis and semantic search by means of user-specific queries. In a pilot project we focus on German publications on the distribution and ecology of vascular plants, birds, moths and butterflies extending back to the Linnaeus period about 250 years ago. The three organism groups have been selected according to current demands of the relevant research community in Germany. The text corpus defined for this purpose comprises over 400 volumes with more than 100,000 pages to be digitized and will be complemented by journals from other digitization projects, copyright-free and project-related literature. With TextImager (Natural Language Processing & Text Visualization) and TextAnnotator (Discourse Semantic Annotation) we have already extended and launched tools that focus on the text-analytical section of our project. Furthermore, taxonomic and anatomical ontologies elaborated by us for the taxa prioritized by the project’s target group - German institutions and scientists active in biodiversity research - are constantly improved and expanded to maximize scientific data output. Our poster describes the general workflow of our project ranging from literature acquisition via software development, to data availability on the BIOfid web portal (http://biofid.de/), and the implementation into existing platforms which serve to promote global accessibility of biodiversity data.
With the ongoing loss of global biodiversity, long-term recordings of species distribution patterns are increasingly becoming important to investigate the causes and consequences for their change. Therefore, the digitization of scientific literature, both modern and historical, has been attracting growing attention in recent years. To meet this growing demand the Specialised Information Service for Biodiversity Research (BIOfid) was launched in 2017 with the aim of increasing the availability and accessibility of biodiversity information. Closely tied to the research community the interdisciplinary BIOfid team is digitizing data sources of biodiversity related research and provides a modern and professional infrastructure for hosting and sharing them. As a pilot project, German publications on the distribution and ecology of vascular plants, birds, moths and butterflies covering the past 250 years are prioritized. Large parts of the text corpus defined in accordance with the needs of the relevant German research community have already been transferred to a machine-readable format and will be publicly accessible soon. Software tools for text mining, semantic annotation and analysis with respect to the current trends in machine learning are developed to maximize bioscientific data output through user-specific queries that can be created via the BIOfid web portal (https://www.biofid.de/). To boost knowledge discovery, specific ontologies focusing on morphological traits and taxonomy are being prepared and will continuously be extended to keep up with an ever-expanding volume of literature sources.
In order to promote the accessibility of biodiversity data in historic and contemporary literature, we introduce a new interdisciplinary project called BIOfid (FID=Fachinformationsdienst, a service for providing specialized information). The project aims at a mobilization of data available in print only by combining digitization of scientific biodiversity literature with the development of innovative text mining tools for complex, eventually semantic searches throughout the complete text corpus. A major prerequisite for the development of such search tools is the provision of sophisticated anatomy ontologies on the one hand, and of complete lists of species names (currently considered valid as well as all synonyms) at a global scale on the other hand. In the initial stage, we chose examples from German publications of the past 250 years dealing with the geographic distribution and ecology of vascular plants (Tracheophyta), birds (Aves), as well as moths and butterflies (Lepidoptera) in Germany. These taxa have been prioritized according to current demands of German research groups (about 50 sites) aiming at analyses and modeling of distribution patterns and their changes through time. In the long term, we aim at providing data and open source software applicable for any taxon and geographic region. For this purpose, a platform for open access journals for long-term availability of professional e-journals will be established. All generated data will also be made accessible through GFBio (German Federation for Biological Data). BIOfid is supported by the LIS-Scientific Library Services and Information Systems program of the German Research Foundation (DFG).