Workflow and current achievements of BIOfid, an information service mobilizing biodiversity data from literature sources

  • 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 (, and the implementation into existing platforms which serve to promote global accessibility of biodiversity data.

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Author:Christine DrillerORCiDGND, Markus KochORCiDGND, Marco SchmidtORCiDGND, Claus WeilandORCiDGND, Thomas HörnschemeyerORCiDGND, Thomas HicklerORCiD, Giuseppe AbramiORCiD, Sajawel AhmedGND, Rüdiger Gleim, Wahed Hemati, Tolga UsluGND, Alexander MehlerORCiDGND, Adrian PachzeltORCiDGND, Jashar Rexhepi, Thomas RisseORCiDGND, Janina Schuster, Gerwin KasperekORCiDGND, Angela HausingerORCiDGND
Parent Title (English):Biodiversity information science and standards
Publisher:Pensoft Publishers
Place of publication:Sofia
Document Type:Article
Year of Completion:2018
Date of first Publication:2018/04/16
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2020/06/24
Tag:Biodiversity; Ontologies; Specialized Information Service; Text mining
Page Number:2
First Page:1
Last Page:2
© Driller C et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Institutes:Sprach- und Kulturwissenschaften / Kulturwissenschaften
Geowissenschaften / Geographie / Geographie
Informatik und Mathematik / Informatik
Zentrale Einrichtung / Universitätsbibliothek
Angeschlossene und kooperierende Institutionen / Senckenbergische Naturforschende Gesellschaft
Fachübergreifende Einrichtungen / Biodiversität und Klima Forschungszentrum (BiK-F)
Dewey Decimal Classification:0 Informatik, Informationswissenschaft, allgemeine Werke / 02 Bibliotheks- und Informationswissenschaften / 020 Bibliotheks- und Informationswissenschaften
5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Licence (German):License LogoCreative Commons - Namensnennung 4.0