Publications by authors named "Walter Berendsohn"

8 Publications

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Toward a service-based workflow for automated information extraction from herbarium specimens.

Database (Oxford) 2018 01 1;2018. Epub 2018 Jan 1.

Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Königin-Luise-Str. Berlin, Germany.

Over the past years, herbarium collections worldwide have started to digitize millions of specimens on an industrial scale. Although the imaging costs are steadily falling, capturing the accompanying label information is still predominantly done manually and develops into the principal cost factor. In order to streamline the process of capturing herbarium specimen metadata, we specified a formal extensible workflow integrating a wide range of automated specimen image analysis services. We implemented the workflow on the basis of OpenRefine together with a plugin for handling service calls and responses. The evolving system presently covers the generation of optical character recognition (OCR) from specimen images, the identification of regions of interest in images and the extraction of meaningful information items from OCR. These implementations were developed as part of the Deutsche Forschungsgemeinschaft-funded a standardised and optimised process for data acquisition from digital images of herbarium specimens (StanDAP-Herb) Project.
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http://dx.doi.org/10.1093/database/bay103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6174549PMC
January 2018

PESI - a taxonomic backbone for Europe.

Biodivers Data J 2015 28(3):e5848. Epub 2015 Sep 28.

Muséum national d'Histoire naturelle, Département Systématique & Evolution, UMR 7205 MNHN-CNRS-UPMC-EPHE, (ISyEB), Paris, France.

Background: Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.

New Information: This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.
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http://dx.doi.org/10.3897/BDJ.3.e5848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609752PMC
October 2015

Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens.

Database (Oxford) 2015 30;2015. Epub 2015 Sep 30.

Botanic Garden and Botanical Museum Berlin-Dahlem, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany and.

Unlabelled: We present the model and implementation of a workflow that blazes a trail in systematic biology for the re-usability of character data (data on any kind of characters of pheno- and genotypes of organisms) and their additivity from specimen to taxon level. We take into account that any taxon characterization is based on a limited set of sampled individuals and characters, and that consequently any new individual and any new character may affect the recognition of biological entities and/or the subsequent delimitation and characterization of a taxon. Taxon concepts thus frequently change during the knowledge generation process in systematic biology. Structured character data are therefore not only needed for the knowledge generation process but also for easily adapting characterizations of taxa. We aim to facilitate the construction and reproducibility of taxon characterizations from structured character data of changing sample sets by establishing a stable and unambiguous association between each sampled individual and the data processed from it. Our workflow implementation uses the European Distributed Institute of Taxonomy Platform, a comprehensive taxonomic data management and publication environment to: (i) establish a reproducible connection between sampled individuals and all samples derived from them; (ii) stably link sample-based character data with the metadata of the respective samples; (iii) record and store structured specimen-based character data in formats allowing data exchange; (iv) reversibly assign sample metadata and character datasets to taxa in an editable classification and display them and (v) organize data exchange via standard exchange formats and enable the link between the character datasets and samples in research collections, ensuring high visibility and instant re-usability of the data. The workflow implemented will contribute to organizing the interface between phylogenetic analysis and revisionary taxonomic or monographic work.

Database Url: http://campanula.e-taxonomy.net/.
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http://dx.doi.org/10.1093/database/bav094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589695PMC
May 2016

A decadal view of biodiversity informatics: challenges and priorities.

BMC Ecol 2013 Apr 15;13:16. Epub 2013 Apr 15.

School of Computer Science and Informatics, Cardiff University, Queens Buildings, 5 The Parade, Cardiff, CF24 3AA, UK.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.
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http://dx.doi.org/10.1186/1472-6785-13-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3843378PMC
April 2013

OpenUp! Creating a cross-domain pipeline for natural history data.

Zookeys 2012 20(209):47-54. Epub 2012 Jul 20.

Department of Biodiversity Informatics and Laboratories, Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195 Berlin, Germany.

Multimedia data held by Natural History Museums and Universities are presently not readily accessible, even within the natural history community itself. The EU project OpenUp! is an effort to mobilise scientific biological multimedia resources and open them to a wider audience using the EUROPEANA data standards and portal. The connection between natural history and EUROPEANA is accomplished using well established BioCASe and GBIF technologies. This is complemented with a system for data quality control, data transformation and semantic enrichment. With this approach, OpenUp! will provide at least 1,1 Million multimedia objects to EUROPEANA by 2014. Its lean infrastructure is sustainable within the natural history community and will remain functional and effective in the post-project phase.
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http://dx.doi.org/10.3897/zookeys.209.3179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406465PMC
August 2012

Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information.

Zookeys 2011 28(150):127-49. Epub 2011 Nov 28.

Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Königin-Luise-Str. 19, 14195 Berlin, Germany.

The Creative Commons (CC) licenses are a suite of copyright-based licenses defining terms for the distribution and re-use of creative works. CC provides licenses for different use cases and includes open content licenses such as the Attribution license (CC BY, used by many Open Access scientific publishers) and the Attribution Share Alike license (CC BY-SA, used by Wikipedia, for example). However, the license suite also contains non-free and non-open licenses like those containing a "non-commercial" (NC) condition. Although many people identify "non-commercial" with "non-profit", detailed analysis reveals that significant differences exist and that the license may impose some unexpected re-use limitations on works thus licensed. After providing background information on the concepts of Creative Commons licenses in general, this contribution focuses on the NC condition, its advantages, disadvantages and appropriate scope. Specifically, it contributes material towards a risk analysis for potential re-users of NC-licensed works.
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http://dx.doi.org/10.3897/zookeys.150.2189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234435PMC
August 2012

The DNA bank network: the start from a german initiative.

Biopreserv Biobank 2011 Mar;9(1):51-5

1 Justus-Liebig-Universität Giessen , AG Spezielle Botanik, Giessen, Germany .

The explicit aim of the DNA Bank Network is to close the divide between biological specimen collections and molecular sequence databases. It provides a technically optimized DNA and tissue collection service facility in the interest of all biological research, with access to well-documented DNA-containing samples and voucher specimens as well as to corresponding molecular data stored in public sequence databases. The Network enables scientists to (i) query and order DNA samples of organisms collected from natural habitats via a shared Web portal, (ii) store DNA samples for reference under optimal conditions after project completion or data publication, (iii) obtain DNA material to conduct new studies or to extend and complement previous investigations, and (iv) support good scientific practice as the deposition of DNA samples and related specimens facilitates the verification of published results.
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http://dx.doi.org/10.1089/bio.2010.0029DOI Listing
March 2011

In vitro antiplasmodial investigation of medicinal plants from El Salvador.

Z Naturforsch C J Biosci 2002 Mar-Apr;57(3-4):277-81

Institut für Pharmazie, Freie Universität Berlin, Germany.

In vitro antiplasmodial activities of extracts from Albizia saman, Fabaceae, Calea tenuifolia (C. zacatechichi), Asteraceae, Hymenaea courbaril, Fabaceae, Jatropha curcas, Euphorbiaceae, Momordica charantia, Cucurbitaceae, and Moringa oleifera, Moringaceae were evaluated. From the lipophilic extract of C tenuifolia five active flavones were obtained. 4',5-Dihydroxy-7-methoxyflavone [genkwanin] and 5-hydroxy-4',7-dimethoxyflavone [apigenin 4',7-dimethylether] exhibited the strongest antiplasmodial activity against a chloroquine-sensitive strain (poW) and a chloroquine-resistant strain (Dd2) of Plasmodium falciparum [IC50 values: 17.1-28.5 microM). Furthermore octadeca-9,12-dienoic acid [linoleic acid] [IC50] values of 21.8 microM (poW) and 31.1 microM (Dd2)] and octadeca-9,12,15-trienoic acid (alpha-linolenic acid) were isolated.
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http://dx.doi.org/10.1515/znc-2002-3-413DOI Listing
July 2002
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