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  • 11
    Online Resource
    Online Resource
    The DNA Bank Network: The Start from a German Initiative
    Mary Ann Liebert Inc ; 2011
    In:  Biopreservation and Biobanking Vol. 9, No. 1 ( 2011-03), p. 51-55
    Details
    In: Biopreservation and Biobanking, Mary Ann Liebert Inc, Vol. 9, No. 1 ( 2011-03), p. 51-55
    Type of Medium: Online Resource
    ISSN: 1947-5535 , 1947-5543
    URL: Article
    DOI: 10.1089/bio.2010.0029
    Language: English
    Publisher: Mary Ann Liebert Inc
    Publication Date: 2011
    detail.hit.zdb_id: 2593993-2
    SSG: 12
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  • 12
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    Freier Zugang zu den Informationen der Artenvielfalt - Wie werde ich Teil der Global Biodiversity Information Facility (GBIF)?
    Pensoft Publishers ; 2005
    In:  Beiträge zur Entomologie = Contributions to Entomology Vol. 55, No. 2 ( 2005-12-27), p. 433-444
    Details
    In: Beiträge zur Entomologie = Contributions to Entomology, Pensoft Publishers, Vol. 55, No. 2 ( 2005-12-27), p. 433-444
    Abstract: Die Global Biodiversity Information Facility ist ein internationaler Zusammenschluss von Staaten und Organisationen mit dem Ziel, die weltweit vorhandenen Primärdaten zur Artenvielfalt über das Internet frei verfügbar zu machen. Dieser Artikel gibt einen kurzen Überblick über die Ziele und den Aufbau von GBIF sowie die zugrunde liegenden Prinzipien, erläutert Architektur und Datenströme im Netzwerk und geht auf die verwendeten Standards, Protokolle, Datenschemata und deren Implementierung ein. Im Abschluss werden die notwendigen Schritte zur Anbindung einer bestehenden Sammlungsdatenbank an das GBIF-Netzwerk aufgezeigt sowie die Möglichkeiten einer Hilfestellung durch GBIF-Deutschland.StichwörterBiodiversity, GBIF, GBIF-D, database, network, collection, specimens, observations, XML, ABCD schema, provider software, Python wrapper, BioCASe protocol, mapping, search portal.
    Type of Medium: Online Resource
    ISSN: 2511-6428 , 0005-805X
    URL: Article
    DOI: 10.21248/contrib.entomol.55.2.433-444
    RVK:
    WA 15000
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2005
    detail.hit.zdb_id: 2882838-0
    SSG: 12
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  • 13
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    Caryophyllales 2015 in Berlin and the Global Caryophyllales Initiative
    Wiley ; 2016
    In:  TAXON Vol. 65, No. 2 ( 2016-05), p. 427-428
    Details
    In: TAXON, Wiley, Vol. 65, No. 2 ( 2016-05), p. 427-428
    Type of Medium: Online Resource
    ISSN: 0040-0262 , 1996-8175
    URL: Article
    DOI: 10.12705/652.60
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2081189-5
    detail.hit.zdb_id: 204216-2
    SSG: 12
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  • 14
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    Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens
    Oxford University Press (OUP) ; 2015
    In:  Database Vol. 2015 ( 2015), p. bav094-
    Details
    In: Database, Oxford University Press (OUP), Vol. 2015 ( 2015), p. bav094-
    Type of Medium: Online Resource
    ISSN: 1758-0463
    URL: Article
    DOI: 10.1093/database/bav094
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2015
    detail.hit.zdb_id: 2496706-3
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  • 15
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    AnnoSys - future developments
    Pensoft Publishers ; 2017
    In:  Proceedings of TDWG Vol. 1 ( 2017-08-15), p. e20317-
    Details
    In: Proceedings of TDWG, Pensoft Publishers, Vol. 1 ( 2017-08-15), p. e20317-
    Type of Medium: Online Resource
    ISSN: 2535-0897
    URL: Article
    DOI: 10.3897/tdwgproceedings.1.20317
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2017
    detail.hit.zdb_id: 3028709-1
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  • 16
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    Caught in the concept jungle: developing a format for data contributions to the World Flora Online
    Pensoft Publishers ; 2019
    In:  Biodiversity Information Science and Standards Vol. 3 ( 2019-06-13)
    Details
    In: Biodiversity Information Science and Standards, Pensoft Publishers, Vol. 3 ( 2019-06-13)
    Abstract: The World Flora Online initiative (www.worldfloraonline.org) is a global consortium of many of the world’s leading botanical institutions with the aim to offer a worldwide information resource for plant information (Miller 2019). It aggregates information provided by the botanical community, either through specialized information systems or published taxonomic treatments and floras. WFO distinguishes contributions to the Taxonomic Backbone (i.e. the community-curated consensus system of scientific names, taxa, synonyms and their classification) from Content contributions (i.e. descriptive data, images, distribution, etc.). In the course of writing the guidelines for contributors, a format for the electronic submission of these data had to be developed. The expectation was that this would be a comparatively simple task, drawing on existing TDWG standards and using established formats and tools, i.e. Darwin Core Archive, the Integrated Publishing Toolkit and the DwC-A Validator tool. Actually, it was not that simple, as several problems had to be solved. First of all it was somewhat difficult to find authoritative sources on the web for existing data definitions. That solved, the actual definitions were, in some cases not really adequate for use by the botanical community, or a narrower description had to be given, or our portal software (based on the eMonocot portal system developed by the Royal Botanic Gardens, Kew) required a different controlled vocabulary. A decision was taken to follow the DwC naming conventions for data elements, although in some cases the designations - or at least the applications in a checklist context - were patently wrong (e.g. “taxonID” as the identifier for names, including synonyms). For Content contributions, the DwC-A standard star schema was useful, but it was not appropriate for backbone contributions with their multiple relationships e.g., to literature references. This experience underlines the necessity for a coherent documentation of standards (see Blum et al. (2019)), including user-friendly access to definitions, data validation tools and clear guidelines for extensions/subtyping also at the element-level.
    Type of Medium: Online Resource
    ISSN: 2535-0897
    URL: Article
    DOI: 10.3897/biss.3.35232
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2019
    detail.hit.zdb_id: 3028709-1
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  • 17
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    The Platform for Cybertaxonomy: Standards, services and tools
    Pensoft Publishers ; 2019
    In:  Biodiversity Information Science and Standards Vol. 3 ( 2019-06-18)
    Details
    In: Biodiversity Information Science and Standards, Pensoft Publishers, Vol. 3 ( 2019-06-18)
    Abstract: 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 core of the platform is the Common Data Model (CDM, Müller et al. 2017), offering a comprehensive information model covering all relevant data domains: names and classifications, descriptive data (morphological and molecular), media, geographic information, literature, specimens, types, persons, and external resources. Platform compliant software interacts via services and includes the following components: CDM Server Taxonomic Editor Rich Client Web-based editors Drupal-based and highly configurable portal software Map services and map viewer Xper2 descriptive data editor Specimen search tool Import and export modules CDM Server Taxonomic Editor Rich Client Web-based editors Drupal-based and highly configurable portal software Map services and map viewer Xper2 descriptive data editor Specimen search tool Import and export modules Recent platform-based developments include software components for deriving formal species-level descriptions from measurements on individual specimens (Henning et al. 2018) as well as a registration system for nomenclatural acts of algae (Phycobank, https://www.phycobank.org/). Currently, about 30 portals with regional and taxonomic foci are using the Platform for Cybertaxonomy as their technical basis for capturing, managing, and publishing biodiversity data over the World Wide Web. Prominent examples are the Euro+Med Plantbase, the International Caryophyllales Network, and the Flora of Greece.
    Type of Medium: Online Resource
    ISSN: 2535-0897
    URL: Article
    DOI: 10.3897/biss.3.37177
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2019
    detail.hit.zdb_id: 3028709-1
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  • 18
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    Standardised Globally Unique Specimen Identifiers
    Pensoft Publishers ; 2018
    In:  Biodiversity Information Science and Standards Vol. 2 ( 2018-05-21), p. e26658-
    Details
    In: Biodiversity Information Science and Standards, Pensoft Publishers, Vol. 2 ( 2018-05-21), p. e26658-
    Abstract: 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 al. 2017). CETAF-Identifiers have a Linked Open Data redirection mechanism for both human- and machine-readable access and, if fully implemented, provide Resource Description Framework (RDF) -encoded specimen data following best practices continuously improved by members of the initiative. To date, more than 20 million physical collection objects have been equipped with CETAF Identifiers (Groom et al. 2017). To facilitate the implementation of stable identifiers, simple redirection scripts and guidelines for deciding on the local identifier syntax have been compiled (http://cetafidentifiers.biowikifarm.net/wiki/Main_Page). Furthermore, a capable "CETAF Specimen URI Tester" (http://herbal.rbge.info/) provides an easy-to-use service for testing whether the existing identifiers are operational. For the usability and potential of any identifier system associated with evolving data objects, active links to the source information are critically important. This is particularly true for natural history collections facing the next wave of industrialised mass digitisation, where specimens come online with only basic, but rapidly evolving label data. Specimen identifier systems must therefore have components for monitoring the availability and correct implementation of individual data objects. Our next implementation steps will involve the development of a "Semantic Specimen Catalogue", which has a list of all existing specimen identifiers together with the latest RDF metadata snapshot. The catalogue will be used for semantic inference across collections as well as the basis for periodic testing of identifiers.
    Type of Medium: Online Resource
    ISSN: 2535-0897
    URL: Article
    DOI: 10.3897/biss.2.26658
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2018
    detail.hit.zdb_id: 3028709-1
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  • 19
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    The Additivity Project - Use Cases and User Interface
    Pensoft Publishers ; 2019
    In:  Biodiversity Information Science and Standards Vol. 3 ( 2019-06-19)
    Details
    In: Biodiversity Information Science and Standards, Pensoft Publishers, Vol. 3 ( 2019-06-19)
    Abstract: 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 workflows are needed to support the sustainable collection of this traditional information and maintain the high quality of the morphological data. Data exchange and re-usability requires the use of accepted controlled vocabularies (community approved) that are accessible (web-based ontologies and term vocabularies) and reliable (long-term availability/unique identifiers). The same applies to datasets that must be stored accessibly and sustainably by maintaining all data relationships that would facilitate convenient re-use. This project aims to construct a comprehensive workflow to optimise the delimitation and characterisation (“descriptions”) of taxa (see complementary talk by Plitzner et al.). It is implemented on the open-source software framework of the EDIT Platform for Cybertaxonomy (http://www.cybertaxonomy.org, Ciardelli et al. 2009) extending the workflow for sample data processing developed in a preceding project (Kilian et al. 2015). The principal goals of this new software component are: specimen-level recording and storage of character data in structured character matrices generating taxon characterisations by aggregating the individual specimen-based datasets using and developing community-coordinated, ontology-based exemplar vocabularies persistently linking character datasets with source specimens for high visibility and re-usability specimen-level recording and storage of character data in structured character matrices generating taxon characterisations by aggregating the individual specimen-based datasets using and developing community-coordinated, ontology-based exemplar vocabularies persistently linking character datasets with source specimens for high visibility and re-usability The angiosperm order, Caryophyllales, provides an exemplar use case through cooperation with the Global Caryophyllales Initiative (Borsch et al. 2015). A basic set of morphological terms and vocabularies has been obtained from various online sources (ontologies, glossaries) and can be used, searched and expanded in the EDIT platform. The terms are categorised into: structures, properties and states. Different editors have been developed to combine structure and property terms to characters and assign a customised state vocabulary (categorical) or suitable values and units (numerical) to them. The workflow is built around a data set defining the taxonomic environment of individual use cases. A data set is specified by the characters and a taxonomic group, which can be filtered by area or rank. The dataset can be opened in a tabular representation (character matrix) to enter preselected state terms or values for the individual specimen. The matrix provides several features for basic comparison and analysis and allows the entry of alternative datasets (e.g. literature). Finally, the aggregation of data subsets to potential taxonomic units by adding up the values and summarising character states, allows the convenient test of taxonomic hypotheses. The term additivity is used here to describe this set of workflows and processes adding value to herbarium specimens and accumulating the specimen data for a taxon description.
    Type of Medium: Online Resource
    ISSN: 2535-0897
    URL: Article
    DOI: 10.3897/biss.3.37210
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2019
    detail.hit.zdb_id: 3028709-1
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  • 20
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    Integrating ABCD and DarwinCore: Toward a better foundation for biodiversity information standards
    Pensoft Publishers ; 2019
    In:  Biodiversity Information Science and Standards Vol. 3 ( 2019-07-02)
    Details
    In: Biodiversity Information Science and Standards, Pensoft Publishers, Vol. 3 ( 2019-07-02)
    Abstract: 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 occurrences (also commonly called species occurrence data). ABCD was capable of representing details of more kinds of information, but was necessarily more complicated. DarwinCore, on the other hand, was simpler but more limited in its ability to represent data of different kinds and formats. TDWG endorsed both standards because the different projects and communities that generated them remained dedicated to their different strategies and tool sets, and the Global Biodiversity Information Facility (GBIF) developed the ability to integrate data published in either standard. Since their inceptions, DarwinCore and ABCD have become more similar. DarwinCore has gotten more complicated through the addition of terms and has begun to assign terms to classes. ABCD is now expressed in RDF (Resource Description Framework), potentially enabling re-use of terms with alternative structures among classes. At the same time, methodologies for conceptual modeling and representing complex scientific data have continued to evolve. In particular, a suite of modeling and data representation methods related to linked data and the semantic web, i.e., RDF, SKOS (Simple Knowledge Organization System), and OWL (web Ontology Language), promise to make it easier for us to reconcile shared concepts among different representations or schemas. A mapping between ABCD 2.1 and DarwinCore has existed since before 2005.*1 ABCD 3.0 and DarwinCore are both now represented in RDF. In addition, the BioCollections Ontology (BCO) covers many of the shared concepts and is derived from the Basic Formal Ontology (BFO), an upper level ontology that has oriented many other biomedical ontologies. Reconciling ABCD and DarwinCore through alignment with BCO (in the OBO Foundry; Smith et al. 2007) would better connect TDWG standards to other domains in biology. We appreciate that many working scientists and data managers perceive ontologies as overly complicated. To mitigate the steep learning curve associated with ontologies, we expect to create simpler application profiles or schemas to guide and serve narrower communities of practice within the wider biodiversity domain. We also plan to integrate the current work of the Taxonomic Names and Concepts Interest Group and thereby eliminate the redundancy between DarwinCore and Taxonomic Concepts Transfer Schema (TCS; Kennedy et al. 2006). At the time of this writing, we have only agreements from the authors (i.e., conveners of relevant TDWG Interest Groups and other key stakeholders) to collaborate in pursuit of these common goals. In this presentation we will give a more detailed description of our objectives and products, the methods we are using to achieve them, and our progress to date.
    Type of Medium: Online Resource
    ISSN: 2535-0897
    URL: Article
    DOI: 10.3897/biss.3.37491
    Language: Unknown
    Publisher: Pensoft Publishers
    Publication Date: 2019
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