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Institute
Biodiversity research heavily relies on recent and older literature, and the data contained therein. Despite great effort, large parts of the literature and the data it holds are still not available in appropriate formats needed for efficient compilation and analysis. As a part of the current funding strategy of the German Research Council (Deutsche Forschungsgemeinschaft, DFG), and resulting from an extensive dialogue with the scientific community in Germany, a "Specialised Information Service" (Fachinformationsdienst, FID) for Biodiversity Research will be established with the objective of making further segments of literature about biodiversity available in up-to-date formats. This project, starting 2017, is conducted by the University Library Johann Christian Senckenberg (Frankfurt/Main, Germany) together with the Senckenberg Gesellschaft für Naturforschung and the Text Technology Lab of the Goethe University (Frankfurt/Main).
The new Specialised Information Service for Biodiversity Research (FID Biodiversitätsforschung) comprises four core elements: (A) A text mining approach which encompasses advanced text technologies and a large body of 20th century literature; (B) the digitisation of selected German biodiversity literature; (C) a platform für Open Access journals; and (D) Acquisition of specialised print literature.
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.
The Specialized Information Service Biodiversity Research (BIOfid) has been launched to mobilize valuable biological data from printed literature hidden in German libraries for over the past 250 years. In this project, we annotate German texts converted by OCR from historical scientific literature on the biodiversity of plants, birds, moths and butterflies. Our work enables the automatic extraction of biological information previously buried in the mass of papers and volumes. For this purpose, we generated training data for the tasks of Named Entity Recognition (NER) and Taxa Recognition (TR) in biological documents. We use this data to train a number of leading machine learning tools and create a gold standard for TR in biodiversity literature. More specifically, we perform a practical analysis of our newly generated BIOfid dataset through various downstream-task evaluations and establish a new state of the art for TR with 80.23% F-score. In this sense, our paper lays the foundations for future work in the field of information extraction in biology texts.
The Goethe University Frankfurt has updated its APC expenditures, providing data for the 2019 period.
The University Library Johann Christian Senckenberg is in charge of the University’s Open Access Publishing Fund, which is supported under the DFG’s Open Access Publishing Programme.
Contact Person is Roland Wagner.
The Specialised Information Service Performing Arts (SIS PA) is part of a funding programme by the German Research Foundation that enables libraries to develop tailor-made services for individual disciplines in order to provide researchers direct access to relevant materials and resources from their field. For the field of performing arts, the SIS PA is aggregating metadata about theater and dance resources from currently, mostly, German-speaking cultural heritage institutions in a VuFind-based search portal.
In this article, we focus on metadata quality and its impact on the aggregation workflow by describing the different, possibly data provider-specific, process stages of improving data quality in order to achieve a searchable, interlinked knowledge base. We also describe lessons learned and limitations of the process.
Biodiversity information is contained in countless digitized and unprocessed scholarly texts. Although automated extraction of these data has been gaining momentum for years, there are still innumerable text sources that are poorly accessible and require a more advanced range of methods to extract relevant information. To improve the access to semantic biodiversity information, we have launched the BIOfid project (www.biofid.de) and have developed a portal to access the semantics of German language biodiversity texts, mainly from the 19th and 20th century. However, to make such a portal work, a couple of methods had to be developed or adapted first. In particular, text-technological information extraction methods were needed, which extract the required information from the texts. Such methods draw on machine learning techniques, which in turn are trained by learning data. To this end, among others, we gathered the BIOfid text corpus, which is a cooperatively built resource, developed by biologists, text technologists, and linguists. A special feature of BIOfid is its multiple annotation approach, which takes into account both general and biology-specific classifications, and by this means goes beyond previous, typically taxon- or ontology-driven proper name detection. We describe the design decisions and the genuine Annotation Hub Framework underlying the BIOfid annotations and present agreement results. The tools used to create the annotations are introduced, and the use of the data in the semantic portal is described. Finally, some general lessons, in particular with multiple annotation projects, are drawn.
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).
The authors reflect on their experiences as the founding editors of the History of Knowledge blog. Situating the project in its specific institutional, geographical, and historiographical contexts, they highlight its role in scholarly communication and research alongside journals and books in a research domain that is still young, especially when viewed from an international perspective. At the same time, the authors discuss the blog’s role as a tool for classifying and structuring a corpus of work as it grows over time and as new themes and connections emerge from the contributions of its many authors.
Current research on theory and practice of digital libraries: best papers from TPDL 2019 & 2020
(2022)
This volume presents a special issue on selected papers from the 2019 & 2020 editions of the International Conference on Theory and Practice of Digital Libraries (TPDL). They cover different research areas within Digital Libraries, from Ontology and Linked Data to quality in Web Archives and Topic Detection. We first provide a brief overview of both TPDL editions, and we introduce the selected papers.
Current research on theory and practice of digital libraries: best papers from TPDL 2019 & 2020
(2022)
This volume presents a special issue on selected papers from the 2019 & 2020 editions of the International Conference on Theory and Practice of Digital Libraries (TPDL). They cover different research areas within Digital Libraries, from Ontology and Linked Data to quality in Web Archives and Topic Detection. We first provide a brief overview of both TPDL editions, and we introduce the selected papers.
The article discusses the University Library Frankfurt am Main’s current exhibition focusing on the background of and the systematic search for looted assets in the library holdings as part of a wider provenance research project. It offers an overview of various topical areas reaching from initial changes in 1933 to raids throughout Europe by Nazi organisations and restitution procedures during the post-war period. The scope and first findings of the provenance research project will also be addressed.
Die Ausstellung in der Universitätsbibliothek wird noch bis zum 26. Februar 2023 verlängert