Anton Güntsch

The DNA Bank Network: The Start from a German Initiative

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.

Fauna Europaea – all European animal species on the web

Abstract Fauna Europaea is Europes main zoological taxonomic index, making the scientific names and distributions of all living, currently known, multicellular, European land and freshwater animals species integrally available in one authoritative database. Fauna Europaea covers about 260,000 taxon names, including 145,000 accepted (sub)species, assembled by a large network of (>400) leading specialists, using advanced electronic tools for data collations with data quality assured through sophisticated validation routines. Fauna Europaea started in 2000 as an EC funded FP5 project and provides a unique taxonomic reference for many user-groups such as scientists, governments, industries, nature conservation communities and educational programs. Fauna Europaea was formally accepted as an INSPIRE standard for Europe, as part of the European Taxonomic Backbone established in PESI. Fauna Europaea provides a public web portal at faunaeur.org with links to other key biodiversity services, is installed as a taxonomic backbone in wide range of biodiversity services and actively contributes to biodiversity informatics innovations in various initiatives and EC programs.

Biodiversity information platforms: From standards to interoperability

Abstract One of the most serious bottlenecks in the scientific workflows of biodiversity sciences is the need to integrate data from different sources, software applications, and services for analysis, visualisation and publication. For more than a quarter of a century the TDWG Biodiversity Information Standards organisation has a central role in defining and promoting data standards and protocols supporting interoperability between disparate and locally distributed systems.Although often not sufficiently recognized, TDWG standards are the foundation of many popular Biodiversity Informatics applications and infrastructures ranging from small desktop software solutions to large scale international data networks. However, individual scientists and groups of collaborating scientist have difficulties in fully exploiting the potential of standards that are often notoriously complex, lack non-technical documentations, and use different representations and underlying technologies. In the last few years, a series of initiatives such as Scratchpads, the EDIT Platform for Cybertaxonomy, and biowikifarm have started to implement and set up virtual work platforms for biodiversity sciences which shield their users from the complexity of the underlying standards. Apart from being practical work-horses for numerous working processes related to biodiversity sciences, they can be seen as information brokers mediating information between multiple data standards and protocols.The ViBRANT project will further strengthen the flexibility and power of virtual biodiversity working platforms by building software interfaces between them, thus facilitating essential information flows needed for comprehensive data exchange, data indexing, web-publication, and versioning. This work will make an important contribution to the shaping of an international, interoperable, and user-oriented biodiversity information infrastructure.

Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects

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 organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals. Database URL: http://cetaf.org/cetaf-stable-identifiers

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

Abstract 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.

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

BackgroundMaking 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 analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as “Web services”) and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust “in silico” science. However, use of this approach in biodiversity science and ecology has thus far been quite limited.ResultsBioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible ‘virtual laboratory’, free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity.ConclusionsOur work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.

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

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/

AnnoSys—implementation of a generic annotation system for schema-based data using the example of biodiversity collection data

Abstract 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 documentation and data quality control is broken. In order to create an online annotation system, we analysed, modeled and adapted traditional specimen annotation workflows. The AnnoSys system accesses collection data from either conventional web resources or the Biological Collection Access Service (BioCASe) and accepts XML-based data standards like ABCD or DarwinCore. It comprises a searchable annotation data repository, a user interface, and a subscription based message system. We describe the main components of AnnoSys and its current and planned interoperability with biodiversity data portals and networks. Details are given on the underlying architectural model, which implements the W3C OpenAnnotation model and allows the adaptation of AnnoSys to different problem domains. Advantages and disadvantages of different digital annotation and feedback approaches are discussed. For the biodiversity domain, AnnoSys proposes best practice procedures for digital annotations of complex records. Database URL: https://annosys.bgbm.fu-berlin.de/AnnoSys/AnnoSys

Marine long-term biodiversity assessment suggests loss of rare species in the Skagerrak and Kattegat region

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 the same methods in the early twentieth century. We generated comparable datasets from our own investigation and the historical data to compare species richness, abundance, and geographic distribution of diversity. Our analysis indicates that the benthic ecosystems in the region have lost a large part of its original species richness over the last seven decades. We find evidence that especially rare species have disappeared. This process has caused a more homogenized community structure in the region and diminished historical biodiversity hotspots. We argue that the contemporary lack of rare species in the benthic ecosystems of the Kattegat and Skagerrak offers less opportunity to respond to environmental perturbations in the future and suggest improving the poor representation of rare species in the region. The study shows the value of biodiversity inventories as well as natural history collections in investigations of accumulated effects of anthropogenic activities and for re-establishing species-rich, productive, and resilient ecosystems.

Building compatible and dynamic character matrices – Current and future use of specimen-based character data

Abstract Herbarium specimens have always played a central role in plant sciences and constitute the cornerstone for systematic 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 sustainable handling of specimen data not only in new scientific uses correlated with the digitisation, but also by modern workflows applied to the traditional purpose of specimens. A crucial step in the comparative analyses of organisms is the preparation of a character matrix to observe and assess the morphological extent and variability of taxa on the basis of individual specimens. This process and the resulting matrix often are of ephemeral nature since only its results are published in a condensed form. The data relationships are usually not stored, making a re-use impossible and a new analysis inevitable. To overcome the limitations of conventional taxonomy, we here introduce a comprehensive workflow that is currently being implemented on the EDIT Platform for Cybertaxonomy.