Darwin Core: An Evolving Community-Developed Biodiversity Data Standard

Wieczorek, John; Bloom, David; Guralnick, Robert; Blum, Stan; Döring, Markus; Giovanni, Renato De; Robertson, Tim; Vieglais, Dave

doi:10.1371/journal.pone.0029715

Cited by 824 publications

(704 citation statements)

References 29 publications

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“…Both voucher records and observations (collectively termed occurrences) have been subject to the development and adoption of useful standards for publishing and exchanging biodiversity information (the group known as Biodiversity Information Standards (BIS), formerly called the Taxonomic Databases Working Group or TDWG) [6]. One of the BIS standards is the set of terms named the Darwin Core, which contain 'clearly defined semantics that can be understood by people or interpreted by machines, making it possible to determine appropriate uses of the data encoded therein' [7]. The purpose of the Darwin Core terms is to allow biodiversity data to be published and integrated [7].…”

Section: Semantics In Biodiversity Informaticsmentioning

confidence: 99%

“…One of the BIS standards is the set of terms named the Darwin Core, which contain 'clearly defined semantics that can be understood by people or interpreted by machines, making it possible to determine appropriate uses of the data encoded therein' [7]. The purpose of the Darwin Core terms is to allow biodiversity data to be published and integrated [7].…”

Section: Semantics In Biodiversity Informaticsmentioning

confidence: 99%

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A Case-Study of Ontology-Driven Semantic Mediation of Flower-Visiting Data from Heterogeneous Data-Stores in Three South African Natural History Collections

Coetzer

Moodley

Gerber

2013

Advanced Information Systems Engineering

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Abstract. The domain complexity and structural-and semantic heterogeneity of biodiversity data, as well as idiosyncratic legacy data-creation processes, present significant integration and interoperability challenges. In this paper we describe a casestudy of ontology-driven semantic mediation using records of flower-visiting insects from three natural history collections in South Africa. We establish a conceptual domain model for flower-visiting, expressed in an OWL ontology, and use it to semantically enrich the three data-stores. We show how this enrichment allows for the creation of an integrated flower visiting data set. We discuss how this ontology captures both implicit and explicit knowledge, how it can be used to identify and analyze highlevel flower-visiting behaviour, and ultimately to construct flower-visiting and pollination networks.Keywords: biodiversity information, semantic mediation, ontology, plant-insect interactions, pollination IntroductionThe challenges of integrating, or making interoperable, distributed, heterogeneous sources of biodiversity-and ecological data have been described. Biodiversity is a complex domain and is no different from other domains in that users encode different definitions of the same concepts [3], which frustrates efforts to integrate data.We present a case study of three data-stores of flower-visiting insect specimens. All three data-stores consistently contained the names of the plant species, termed hostplants, with which both flower-visiting and non-flower-visiting insect specimens were associated. Whereas flower-visiting records were not explicit in most records of two data-stores, most records of the third data-store contained explicit, easily distinguishable flower-visiting data. To develop a semantic mediation solution, we created the first version of an OWL ontology containing concepts related to flower-visiting and the utilization of flower products, as well as the bearing of pollen by insect vectors. Our work will facilitate the construction of a system to bring about interoperability between distributed and heterogeneous biodiversity data-stores and systems. This will enable biodiversity scientists to more easily extract and analyze the behaviour of flower-visiting insects. Such a system would allow flower-visiting and pollination networks to be automatically assembled and compared.Outline. In Section 2 we sketch the background against which the need for our study emerged, discuss previous work in biodiversity semantics, and introduce our casestudy of interoperability of flower-visiting data. Section 3 begins by describing the domain of flower-visiting and pollination, including our scope, before explaining the process of ontology construction. Expert-and implicit knowledge is highlighted. The usefulness of the concepts in the ontology is discussed in Section 4, by linking data from the data-stores to classes in the ontology. Finally we discuss our approach to a potential solution, including areas where future work is required, and conclude. Background 2

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Section: Semantics In Biodiversity Informaticsmentioning

confidence: 99%

Section: Semantics In Biodiversity Informaticsmentioning

confidence: 99%

A Case-Study of Ontology-Driven Semantic Mediation of Flower-Visiting Data from Heterogeneous Data-Stores in Three South African Natural History Collections

Coetzer

Moodley

Gerber

2013

Advanced Information Systems Engineering

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“…We are not addressing the numerous additional GUID values that might appear in a single specimen record. Based on Darwin Core (DwC; Wieczorek et al., 2012; Biodiversity Information Standards [TDWG], 2018) terminology, records might also include GUID values for locationID, eventID, collectorID, taxonID, and others. These additional GUID values allow a specimen record to be linked to information about where a specimen was collected, when it was collected, and who collected it, as well as information about the taxon the specimen is presumed to represent.…”

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confidence: 99%

Use of globally unique identifiers (GUIDs) to link herbarium specimen records to physical specimens

2018

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With the advent of the U.S. National Science Foundation's Advancing Digitization of Biodiversity Collections program and related worldwide digitization initiatives, the rate of herbarium specimen digitization in the United States has expanded exponentially. As the number of electronic herbarium records proliferates, the importance of linking these records to the physical specimens they represent as well as to related records from other sources will intensify. Although a rich and diverse literature has developed over the past decade that addresses the use of specimen identifiers for facilitating linking across the internet, few implementable guidelines or recommended practices for herbaria have been advanced. Here we review this literature with the express purpose of distilling a specific set of recommendations especially tailored to herbarium specimen digitization, curation, and management. We argue that associating globally unique identifiers (GUIDs) with physical herbarium specimens and including these identifiers in all electronic records about those specimens is essential to effective digital data curation. We also address practical applications for ensuring these associations.

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“…В связи с этим интенсивно развиваются компьютерные методы описания образцов, создаются системы баз данных (БД) для хра нения информации и быстрого доступа к ней (Bea man, Cellinese, 2012; Guralnick et al, 2016), разрабатываются форматы, протоколы и технологии открытого доступа к информации по биологическому разнообразию (Ло банов и др., 2008; Wieczorek et al, 2012;Robertson et al, 2014). В результате обеспечивается быстрый доступ к информации о биологическом разнообразии в мировом масштабе.…”

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An Integrated Information System on Bioresource Collections of the Faso of Russia

Lashin¹,

Afonnikov²,

Genaev³

et al. 2018

Vestn. VOGiS

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Biological collections play a huge role in studying biological diversity as systematic storages of biological materials in all combinations and forms. Collection materials have generally been formed over hundreds of years and may describe a vast number of samples counted by billions. Great efforts are made to preserve these materials, as well as to obtain more and more samples. The Russian Federation occupies a huge land area, has a long coastline and huge natural resources, a variety of natural and ecological zones. In this regard, its territory is unique from the viewpoint of biodiversity and development of biological collections. Currently, a large number of collec tions are being developed in Russia, but there are a number of problems associated, first of all, with the lack of an integrated information resource on bioresource collections (BRC). In order to support the development of scientific infrastructure, the Federal Agency for Scientific Organizations (FASO of Russia) has been working on the development of unified approaches to the use of existing bioresource collections and the estab lishment of the integrated information system. The paper presents an information portal designed to provide uniform methods of work for all BRC organizations of the FASO of Russia: input, storage, updating and differentiated access to specific information about storage units and their character istics. The information system "Bioresource Collections of Scientific Organizations" (IS BRC) has been developed as a Web portal (www.biores.cytogen.ru) integrating databases on bioresource collections of the FASO of Russia and graphical user interface. Access control to the databases integrated into the IS BRC is performed through authorized program access for viewing records, their creation and editing on the basis of REST technology. The graphical user interface (GUI) provides the following features in accordance with the access rights: authorized access to the BRC database; viewing BRC database records; editing BRC database records; creating and deleting BRC database records; statistical data analysis in the BRC da tabase; generation of summary reports on the BRC database; export of records content in PDF/RTF/JSON format. The graphi cal user interface was implemented using the DRUPAL 7.0 tool kit. Architecturally, the portal is concerned as a central node При изучении живого разнообразия большую роль играют биоресурсные коллекции -систематизированные храни лища биологического материала в любых комбинациях и формах. Содержимое коллекций, как правило, формирова лось в течение нескольких сотен лет и описывает огромное количество образцов, исчисляемое миллиардами. Большие усилия направлены на сохранение этого материала, а так же получение новых образцов. Российская Федерация занимает огромную территорию суши, имеет протяженную береговую линию и богатые природные ресурсы, разнооб разие природно экологических зон. В связи c этим ее тер ритория является уникальной для сбора материала биоло гических коллекций. В настоящее время в России...

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Darwin Core: An Evolving Community-Developed Biodiversity Data Standard

Cited by 824 publications

References 29 publications

A Case-Study of Ontology-Driven Semantic Mediation of Flower-Visiting Data from Heterogeneous Data-Stores in Three South African Natural History Collections

A Case-Study of Ontology-Driven Semantic Mediation of Flower-Visiting Data from Heterogeneous Data-Stores in Three South African Natural History Collections

Use of globally unique identifiers (GUIDs) to link herbarium specimen records to physical specimens

An Integrated Information System on Bioresource Collections of the Faso of Russia

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