Anton Güntsch

Anton Güntsch
Freie Universität Berlin | FUB · Botanischer Garten und Botanisches Museum

MSc Computer Science

About

142
Publications
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1,524
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Publications

Publications (142)
Article
Full-text available
ABCD (Access to Biological Collection Data, Holetschek et al. 2012) 2.06 was ratified by Biodiversity Information Standards (TDWG) in September 2005. In 2017, TDWG ratified the Standards Documentation Standard (SDS, Vocabulary Maintenance Specification Task Group 2017), which is a set of regulations and guidelines on how TDWG standards should be st...
Article
Full-text available
Digital data have become an indispensable basis for biodiversity research. Sustainable curation, archiving, accessibility and integrability according to the FAIR principles ("Findable, Accessible, Interoperable and Reusable", Wilkinson et al. 2016) are essential for re-use to answer pressing questions in a rapidly changing environment. As part of t...
Article
The International Code of Nomenclature (ICN) for algae, fungi, and plants calls for indexing of names in nomenclatural repositories (Turland 2018, Art. 42). Scientific names, new combinations, validations, and typifications of algae are novelties tracked by PhycoBank, the registration system for algae. PhycoBank was established and institutionalize...
Article
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BiCIKL is an European Union Horizon 2020 project that will initiate and build a new European starting community of key research infrastructures, establishing open science practices in the domain of biodiversity through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle. BiCIKL wi...
Article
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Natural history collection data available digitally on the web have so far only made limited use of the potential of semantic links among themselves and with cross-disciplinary resources. In a pilot study, botanical collections of the Consortium of European Taxonomic Facilities (CETAF) have therefore begun to semantically annotate their collection...
Conference Paper
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With the increasing amount of interdisciplinary and international networks dedicated to long-term persistence and interoperability of research data, the demand for semantic linking of environmental research data has grown. Data related to organisms frequently inherit a major obstacle. Organisms often are ambiguously identified by using only the sci...
Conference Paper
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Biodiversity research data often reference individual organisms, populations, or other taxonomic contexts by using scientific names. Scientific names, however, are unstable, ambiguous, and no precise identifier for the specific taxonomic concept that has been used implicitly. Using identifiers for taxonomic concepts instead does not fully solve the...
Article
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The Horizon 2020 project Bi odiversity C ommunity I ntegrated K nowledge L ibrary (BiCIKL) (started 1st of May 2021, duration 3 years) will build a new European community of key research infrastructures, researchers, citizen scientists and other stakeholders in biodiversity and life sciences. Together, the BiCIKL 14 partners will solidify open scie...
Article
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Persistent identifiers (PID) to identify digital representations of physical specimens in natural science collections (i.e., digital specimens) unambiguously and uniquely on the Internet are one of the mechanisms for digitally transforming collections-based science. Digital Specimen PIDs contribute to building and maintaining long-term community tr...
Article
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People are one of the best known and most stable entities in the biodiversity knowledge graph. The wealth of public information associated with people and the ability to identify them uniquely open up the possibility to make more use of these data in biodiversity science. Person data are almost always associated with entities such as specimens, mol...
Article
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ABCD (Access to Biological Collection Data, Holetschek et al. 2012) and DwC (Darwin Core, Wieczorek et al. 2012), are TDWG standards for documenting the occurrence of organisms in nature and/or collections, whether as specimens or observations (i.e., unit-level data), and are used for a wide range of applications. Since 2019, the working group has...
Article
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Plants, fungi and algae are important components of global biodiversity and are fundamental to all ecosystems. They are the basis for human well-being, providing food, materials and medicines. Specimens of all three groups of organisms are accommodated in herbaria, where they are commonly referred to as botanical specimens. The large number of spec...
Poster
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The EDIT Platform for Cybertaxonomy was initially developed as part of the EU Network of Excellence project EDIT (European Distributed Institute of Taxonomy, 2006-2011) aimed at a concertation of different taxonomic computing platforms applied in Europe. For example, it incorporated the ideas about taxon concept handling that were a core feature of...
Article
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1.Trait‐based approaches are widespread throughout ecological research as they offer great potential to achieve a general understanding of a wide range of ecological and evolutionary mechanisms. Accordingly, a wealth of trait data is available for many organism groups, but this data is underexploited due to a lack of standardisation and heterogenei...
Conference Paper
Full-text available
For the last 15 years, Biodiversity Information Standards (TDWG) has recognized two competing standards for organism occurrence data, ABCD (Access to Biological Collections Data; Holetschek et al. 2012) and DarwinCore (Wieczorek et al. 2012). These two representations emerged from contrasting strategies for mobilizing information about organism occ...
Article
Full-text available
Trait-based research spans from evolutionary studies of individual-level properties to global patterns of biodiversity and ecosystem functioning. An increasing number of trait data is available for many different organism groups, published as open access data on a variety of file hosting services. Thus, standardization between datasets is generally...
Article
Full-text available
The International Code of Nomenclature (ICN) for algae, fungi, and plants provides for nomenclatural indexing through nomenclatural repositories (Turland et al. 2018, Art. 42). Registering nomenclatural novelties and nomenclatural acts means that repositories will keep track of names (species names and names at all ranks, replacement names, names p...
Conference Paper
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The TDWG standard ABCD (Access to Biological Collections Data task group 2007) was aimed at harmonizing terminologies used for modelling biological collection information and is used as a comprehensive data format for transferring collection and observation data between software components. The project ABCD 3.0 (A community platform for the develop...
Article
Full-text available
Herbarium specimens are central to botanical science and of rising importance thanks to increasing accessibility and broadened usability. Alongside the many new uses of specimen data, sit a range of traditional uses supporting the collection of morphological data and their application to taxonomy and systematics. (Henning et al. 2018). Technical wo...
Article
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In the ABCD 3.0 Project the ABCD (Access to Biological Collection Data) Standard (Access to Biological Collections Data task group 2007) was transformed from a classic XML Schema into an OWL (Web Ontology Language) ontology (along side an updated semantic-aware XML version). While it was initially planned to use the established TDWG Terms wiki as t...
Article
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The Platform for Cybertaxonomy (http://www.cybertaxonomy.org) is a standards-based open-source software framework covering the breadth of the taxonomic workflow, from fieldwork to publication (Ciardelli et al. 2009). It provides coupled tools for full, customized access to taxonomic data, editing and management, and collaborative team work. At the...
Article
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Herbarium specimens have always played a central role in the classical disciplines of plant sciences and the global digitisation efforts now open new horizons. To make full use of the inherent possibilities of specimen based taxonomic descriptions corresponding workflows are needed. A crucial step in the comparative analyses of organisms is the pre...
Article
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Botanic gardens are an invaluable refuge for plant diversity for conservation, education and research. Worldwide, they manage over 100,000 species, roughly 30% of all plant species diversity, and over 41% of known threatened species; the botanic gardens in Germany house approximately 50,000 different species (Marquardt et al. in press). Scientists...
Article
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Herbarium specimens have been digitized at the Botanical Garden and Botanical Museum, Berlin (BGBM) since the year 2000. As part of the digitization process, specimen data have been recorded manually for specific basic data elements. Additional elements were usually added later based on the digital images. During the last twenty years, data were tr...
Article
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More and more herbaria are digitising their collections. Images of specimens are made available online to facilitate access to them and allow extraction of information from them. Transcription of the data written on specimens is critical for general discoverability and enables incorporation into large aggregated research datasets. Different methods...
Data
R script used to map data from FinBIF API to DwC
Data
Python script to upload the dataset to Zenodo
Data
Taxonomic coverage (interactive HTML file)
Article
Full-text available
The Caryophyllales Network strives to assemble an online dynamic synthesis of the order Caryophyllales, uniting the current knowledge about the phylogeny of the order with up-to-date information on the individual taxa contained. Capturing taxonomic data and the decision processes involved in the definition and circumscription of the taxa requires h...
Article
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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 he...
Preprint
Full-text available
1. Trait-based approaches are widespread throughout ecological research, offering great potential for trait data to deliver general and mechanistic conclusions. Accordingly, a wealth of trait data is available for many organism groups, but, due to a lack of standardisation, these data come in heterogeneous formats. 2. We review current initiatives...
Article
Full-text available
On herbarium sheets, data elements such as plant name, collection site, collector, barcode and accession number are found mostly on labels glued to the sheet. The data are thus visible on specimen images. With continuously improving technologies for collection mass-digitisation it has become easier and easier to produce high quality images of herba...
Article
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A simple, permanent and reliable specimen identifier system is needed to take the informatics of collections into a new era of interoperability. A system of identifiers based on HTTP URI (Uniform Resource Identifiers), endorsed by the Consortium of European Taxonomic Facilities (CETAF), has now been rolled out to 14 member organisations (Güntsch et...
Article
Herbarium specimens have always played a central role in plant sciences and constitute the cornerstone for systematics and taxonomy. This role is further strengthened with the ongoing digitisation and growing online-availability of collections all over the globe. The increasing usability of specimens demands, however, an improved use and sustainabl...
Conference Paper
Using the angiosperm order Caryophyllales, we will provide an ex-emplar use case on optimizing the taxonomic research process with respect to delimitation and characterisation ("description") of taxa using the the European Distributed Institute of Taxonomy (EDIT) Platform for Cybertaxonomy. The workflow for sample data handling of the EDIT platform...
Conference Paper
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One of the major design features of the Common Data Model (CDM) is the ability to store and handle taxonomic concepts (a.k.a. “potential taxa” -Berendsohn 1995 , “taxonyme” - Koperski et al. 2000, "Assertions" - Pyle 2004, "taxonomic entities" -Kennedy et al. 2005 “taxon circumscriptions”, etc.). A major driver of the critical appreciation of the...
Conference Paper
Full-text available
The EDIT Platform for Cybertaxonomy has come a long way towards providing a complete, standards-based and reliable set of tools and services supporting the taxonomic workflow (Ciardelli et al. 2009). The Platform is firmly grounded in the organisational structure of the BGBM, with several positions directly dedicated to maintenance and further deve...
Conference Paper
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Specimens form the falsifiable evidence used in plant systematics. Derivatives of specimens (including the specimen as the organism in the field) such as tissue and DNA samples play an increasing role in research. The EDIT Platform for Cybertaxonomy is a specialist's tool that allows to document and sustainably store all data that are used in the t...
Conference Paper
Full-text available
The EDIT Common Data Model (CDM) (FUB, BGBM 2008) is the centrepiece of the EDIT Platform for Cybertaxonomy (FUB, BGBM 2011, Ciardelli et al. 2009). Building on modelling efforts reaching back to the 1990ies, it aims to combine existing standards relevant to the taxonomic domain (but often designed for data exchange) with requirements of modern tax...
Conference Paper
Full-text available
The Platform for Cybertaxonomy (FUB, BGBM 2011) is an open-source software framework covering the full breadth of the taxonomic workflow, from fieldwork to data publication. It provides a set of tools for editing and management of taxonomic data (individually or collaboratively), fully customizable on-line access to that data, and other means of da...
Conference Paper
Full-text available
The EDIT Platform for Cybertaxonomy is a standards based suite of software components supporting the taxonomic research workflow from field work to publication in journals and dynamic web portals (FUB, BGBM 2011). The underlying Common Data Model (CDM) covers the main biodiversity informatics foci such as names, classifications, descriptions, liter...
Conference Paper
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In many research projects, much more data are created than made publicly available. Keeping research data deliberately closed or publishing only selected subsections of the gathered data are unfortunately common practices in academia. Fortunately, such problems have been getting more and more attention in the past years. However, another issue that...
Article
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Studies of cumulative and long-term effects of human activities in the ocean are essential for developing realistic conservation targets. Here, we report the results of a recent national marine biodiversity inventory along the Swedish West coast between 2004 and 2009. The expedition revisited many historical localities that have been sampled with t...
Article
Members of the Consortium of European Taxonomic Facilities have adopted a consistent citation system for an estimated 20 million biological and geological specimens from European collections. We encourage researchers, publishers and other institutions to engage with this initiative by citing the full specimen identifier in their publications and da...
Article
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Biological research collections holding billions of specimens world-wide provide the most important baseline information for systematic biodiversity research. Increasingly, specimen data records become available in virtual herbaria and data portals. The traditional (physical) annotation procedure fails here, so that an important pathway of research...
Article
Full-text available
With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member or...
Presentation
Full-text available
Describing a tool for managing taxonomic concepts and their relations in the case of Red Lists of endangered species
Conference Paper
The TDWG standard ABCD (Access to Biological Collection Data) has been developed between 2001 and 2006. It was aimed at harmonising terminologies used for modelling biological collection information. Furthermore, it is used as a comprehensive data format for transferring collection and observational data between software components facilitating sea...
Technical Report
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The goal of the deliverable is to provide a technical summary of web services providing a harmonised and unified access layer to taxonomic information resources defined by Appendix 3 of the INSPIRE Directive. We describe the basic web service architecture, the unified access protocol, the harmonisation of contributing databases, integration into th...
Article
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Background Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced...
Article
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Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs t...
Article
Research has become more data-intensive over the last few decades. Sharing research data is often a challenge, especially for interdisciplinary collaborative projects. One primary goal of a research infrastructure for data management should be to enable efficient data discovery and integration of heterogeneous data. In order to enable such interope...
Article
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Europe is building its Open Science Cloud; a set of robust and interoperable e-infrastructures with the capacity to provide data and computational solutions through cloud-based services. The development and sustainable operation of such e-infrastructures are at the forefront of European funding priorities. The research community, however, is still...
Conference Paper
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OUT OF STORAGE - ONTO THE WEB OPENING UP NATURAL HISTORY COLLECTIONS TO THE PUBLIC VIA EUROPEANA Gisela Baumann, Wolf-Henning Kusber, Jörg Holetschek, Anton Güntsch, Walter G. Berendsohn Freie Universität Berlin, Botanic Garden and Botanical Museum Berlin-Dahlem Corresponding author: g.baumann@bgbm.org Natural history institutions increasingly...
Article
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With the rapidly growing number of data publishers, the process of harvesting and indexing information to offer advanced search and discovery becomes a critical bottleneck in globally distributed primary biodiversity data infrastructures. The Global Biodiversity Information Facility (GBIF) implemented a Harvesting and Indexing Toolkit (HIT), which...
Article
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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 indi...