The ABCD of primary biodiversity data access

Holetschek, Jörg; Dröge, Gabriele; Güntsch, Anton; Berendsohn, Walter G.

doi:10.1080/11263504.2012.740085

Cited by 60 publications

(41 citation statements)

References 8 publications

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“…It is used by the Global Biodiversity Information Facility (GBIF) and the Biological Collection Access Service for Europe network (BioCASe: [20]). The schema is strongly hierarchically organized capturing e.g.…”

Section: The Frameworkmentioning

confidence: 99%

Essential Annotation Schema for Ecology (EASE)—A framework supporting the efficient data annotation and faceted navigation in ecology

et al. 2017

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Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.

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Section: The Frameworkmentioning

confidence: 99%

Essential Annotation Schema for Ecology (EASE)—A framework supporting the efficient data annotation and faceted navigation in ecology

et al. 2017

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“…The construction of a national vegetation database and primary biodiver sity data, which had raised high attention and made much progress in European countries and worldwide (Martellos et al 2011;Basset & Los 2012;Holetschek et al 2012;Landucci et al 2012), should also be strengthened for public education and participation in invasive species management.…”

Section: Discussionmentioning

confidence: 99%

Challenge of weed risk assessment (WRA) for ecological restoration in China: The case ofRhus typhinaL. and the new officially released weed risk assessment system

Wang

Yang

Jiang

et al. 2013

Plant Biosystems - An International Journal Dealing with all As

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Challenge of weed risk assessment (WRA) for ecological restoration in China: The case of Rhus typhina L. and the new officially released weed risk assessment system, AbstractChina has conducted many ecological restoration projects to alleviate environmental degradation, with numerous alien species having good adaptability widely used for fast effect. However, unsuitable plant selection may bring negative impacts and even cause biological invasion. Weed risk assessment (WRA) is therefore indispensable, yet it is often contentious especially concerning those species that has been widely utilized before weedy attributes were noted. In this paper, we take Rhus typhina L. as an example to illustrate how scientific researches and social factors can influence the evaluation of alien species and cause challenge to WRA. The evaluation of this species is not only a pure scientific issue but also influenced by many factors such as the introduction history, current utilization status in afforestation, and divergent underlying values varying through persons and sectors. These factors determined the kind of data to be assessed, which lead to different evaluations, therefore, causing challenge to its WRA. We further examined newly officially released WRA system in China from the invasion biology viewpoint, arguing that it had some major flaws in design and validation and need much improvement. Considering the human dimension and biological characters together, we suggest that the "black list" and "green list" approaches with rigorous expert assessment should be adopted simultaneously in alien species management in China.

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“…Zhong et al, 1996;Berendsohn, 1997;Pullan et al, 2000), followed by software development that demonstrated the practicability of such models for taxonomic data (e. g. Pullan et al, 2000;Gradstein, 2001;Berendsohn et al, 2003;Berendsohn and Geoffroy, 2007). In parallel, a number of projects drove standardisation of data items, especially in the context of the organisation for Biodiversity Data (ABCD; Berendsohn, 2007, Holetschek et al 2012 and Darwin Core (DwC; Wieczorek et al, 2009). This development culminated in the definition of an object-oriented Common Data Model for taxonomic information (CDM) that was devised for and forms the basis of the EDIT Platform for Cybertaxonomy (Berendsohn, 2010;Berendsohn et al, 2011).…”

Section: Standards and Tools For Managing Integrative Concept-based Cmentioning

confidence: 97%

“…Most of the current technical reports and opinion papers focus on either the development of information standards, data base and portal systems Holetschek et al, 2012) or the information needs for conservation (Paton, 2009;Nic Lughadha and Miller, 2009;Hardisty and Roberts, 2013). Only few studies address the taxonomic or monographic workflow as such (e.g., Stuessy and Lack, 2011;Marhold and Stuessy, 2013).…”

Section: Introductionmentioning

confidence: 98%

An integrative and dynamic approach for monographing species-rich plant groups – Building the global synthesis of the angiosperm order Caryophyllales

Borsch

Hernández‐Ledesma

Berendsohn

et al. 2015

Perspectives in Plant Ecology, Evolution and Systematics

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and dynamic approach for monographing species-rich plant groups ndash building the global synthesis of the angiosperm order Caryophyllales, Perspectives in Plant Ecology, Evolution and Systematics (2015), http://dx. AbstractOne of the major goals of systematics is to provide a synthesis of knowledge on the diversity of a group of organisms, such as flowering plants. Biodiversity conservation and management call for rapid and accurate global assessments at the species level. At the same time the rapid development of evolutionary biology with a spectrum of approaches to test species relationships and species limits, has revolutionized and is still revolutionizing the science of plant systematics including taxonomy. We explore the relevant scientific and technological developments, but also organizational and logistic requirements, with the aim to suggest a conceptual framework for an integrated monographic synthesis of species diversity which can reach global coverage. Our exemplar group are the Caryophyllales, as an example of a globally distributedwhich are a plant lineage of worldwide distribution,, comprising approx. 5% of flowering plant species diversity. The current situation of organism classification is marked by a transition from pre-phylogenetic treatments to taxonomic treatments increasingly evaluated in an evolutionary context. Structured data (both molecular and morphological), linked to well-documented specimens will be important as fundamental entities of information that can be subjected to evolutionary analysis. As a result, taxon concepts are established as hypotheses which then can be used as basis for a classification system in a second step. The process of generating knowledge and subsequent classification of the recognized entities is step by step, including processes of reciprocal illumination. Global syntheses need to provide information and use a classification system that reflects the current state of knowledge. , they need to be dynamic Iin order to accommodate the constantly improved understanding of the organisms, eventually also resulting in the change of taxon concepts, the treatments need to be dynamic. The workflow for a global monographic synthesis as outlined here is supported by currently available biodiversity informatics tools such as the EDIT Platform for Cybertaxonomy. Based on these conceptual findings we outline the practical implementation steps towards a synthesis of the Caryophyllales, as an example of a globally distributed plant lineage, comprising approx. 5% of flowering plant species diversity. While the actualThe availability of electronic sources (names, protologues, type images, literature) greatly facilitates the access to information, but as our case shows, considerable efforts for data curation and research are still needed. Tthe implementation of a global monographic synthesis such as the Caryophyllales requires the involvement of the global scientific community.

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The ABCD of primary biodiversity data access

Cited by 60 publications

References 8 publications

Essential Annotation Schema for Ecology (EASE)—A framework supporting the efficient data annotation and faceted navigation in ecology

Essential Annotation Schema for Ecology (EASE)—A framework supporting the efficient data annotation and faceted navigation in ecology

Challenge of weed risk assessment (WRA) for ecological restoration in China: The case ofRhus typhinaL. and the new officially released weed risk assessment system

An integrative and dynamic approach for monographing species-rich plant groups – Building the global synthesis of the angiosperm order Caryophyllales

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