Workflow and Current Achievements of BIOfid, an Information Service Mobilizing Biodiversity Data from Literature Sources

By

Driller, Christine
Koch, Markus, 1967-
Schmidt, Marco
Weiland, Claus
Hörnschemeyer, Thomas
Hickler, Thomas
Abrami, Giuseppe
Ahmed, Sajawel
Gleim, Rüdiger
Hemati, Wahed
Uslu, Tolga
Mehler, Alexander
Pachzelt, Adrian
Rexhepi, Jashar
Risse, Thomas
Schuster, Janina
Kasperek, Gerwin
Hausinger, Angela

Type

Article

Date of Publication

2018-4-16

Original Publication

Metabarcoding and metagenomics

Volume

2

Pages

1--2

Subjects

Biodiversity , ontologies , Specialized Information Service , text mining

Contributed by

Pensoft Publishers

Language

English

Published by

Bulgaria Pensoft Publishers 2017-

Identifiers

DOI: https://doi.org/10.3897/biss.2.25876

 

Abstract

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.