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  1. Book ; Online: Long-term archiving in the NFDI

    Markus, Katharina / Naumann, Kai / Schmalzl, Markus / Watson, Juliane / Triebel, Dagmar

    results of a survey exploring current trends and requirements

    2024  

    Abstract: Long-term archiving (LTA) aims to prevent data and information loss over the long term and intends to ensure sustainable access to information. Failure to correctly implement LTA can put data at risk. Research data holdings in the German science system ... ...

    Institution ZB MED - Informationszentrum Lebenswissenschaften
    Deutsche Forschungsgemeinschaft
    COST Association
    Author's details Katharina Markus, Kai Naumann, Markus Schmalzl, Juliane Watson, Dagmar Triebel ; German National Library of Medicine ; funded by the Deutsche Forschungsgemeinschaft and by EU COST Action
    Abstract Long-term archiving (LTA) aims to prevent data and information loss over the long term and intends to ensure sustainable access to information. Failure to correctly implement LTA can put data at risk. Research data holdings in the German science system are considered vulnerable in this regard, leading to the declaration that LTA is an important task for the German National Research Data Infrastructure e. V. (Nationale Forschungsdateninfrastruktur, NFDI). Yet many aspects remain unclear, including the strategy and targets of LTA in various research disciplines, the status of implementation, and coverage of LTA services in NFDI. To clarify these points, NFDI Working Group Long Term Archiving, which forms part of the Section Common infrastructure has launched a survey in the NFDI consortia. The goal was to determine current status and requirements regarding LTA. One of the survey’s key findings indicated a need for a LTA consultation service, as many consortia and research organisations did not yet approach long-term preservation (i. e. LTA) of data. If they considered LTA at all, they usually did not target preservation beyond bitstream preservation. In general, knowledge gaps in various areas became clear. As a consequence, the consultation service should advise both consortia and institutions on long-term archiving of research data. Survey participants also called for dedicated LTA solutions which are tailored to individual research domains. Therefore, state-of-the-art solutions should be pursued in cooperation with the consortia, their disciplines, and the international LTA community. These solutions should also adopt jointly developed principles, regulations and standards. Other key requirements include improved long-term financial support of consortia and institutions with regard to LTA in accordance with FAIR principles and an increase in LTA-focused certification of existing research data services.
    Subject code 020
    Language English
    Size 1 Online-Ressource (21 Seiten), Diagramme
    Edition Version v1
    Publisher German National Library of Medicine
    Publishing place Cologne
    Publishing country Germany
    Document type Book ; Online
    Note This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0). For material contained in the work other licenses may apply as indicated or all rights are reserved ; funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – NFDI4Microbiota - project number 460129525, NFDI4Biodiversity - project number 442032008 and by EU COST Action CA17106 ; Katharina Markus (ORCID:0000-0002-9316-8982), Kai Naumann (ORCID:0000-0002-2799-1030), Markus Schmalzl (ORCID:0009-0005-7574-2699), Dagmar Triebel (ORCID:0000-0003-1980-3148) ; Open Access
    HBZ-ID HT030744243
    DOI 10.5281/zenodo.11109480
    Database Repository for Life Sciences

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  2. Book ; Online: Langzeitarchivierung in der NFDI

    Markus, Katharina / Naumann, Kai / Schmalzl, Markus / Watson, Juliane / Triebel, Dagmar

    Tendenzen und Bedarfe als Resultat einer Umfrage

    2024  

    Abstract: Langzeitarchivierung (LZA) zielt darauf ab, Daten- und Informationsverlust zu vermeiden und nachhaltigen Zugriff zu Informationen zu ermöglichen. Fehlende oder nicht korrekt durchgeführte LZA kann Daten einer Vielzahl von Risiken aussetzen. Datenbestände ...

    Institution ZB MED - Informationszentrum Lebenswissenschaften
    Deutsche Forschungsgemeinschaft
    COST Association
    Author's details Katharina Markus, Kai Naumann, Markus Schmalzl, Juliane Watson, Dagmar Triebel ; German National Library of Medicine ; gefördert durch die Deutsche Forschungsgemeinschaft (DFG) und durch EU COST Action
    Abstract Langzeitarchivierung (LZA) zielt darauf ab, Daten- und Informationsverlust zu vermeiden und nachhaltigen Zugriff zu Informationen zu ermöglichen. Fehlende oder nicht korrekt durchgeführte LZA kann Daten einer Vielzahl von Risiken aussetzen. Datenbestände im deutschen Wissenschaftssystem sind in dieser Hinsicht gefährdet, was dazu führt, dass Langzeitarchivierung als eine zentrale Aufgabe der Nationalen Forschungsdateninfrastruktur e. V. (NFDI) deklariert wurde. Allerdings sind weiterhin viele Aspekte unklar, wie die Strategie und Ausrichtung von LZA in den Wissenschaftsdisziplinen, der Status der Implementierung und die Abdeckung durch LZA-Services in der NFDI. Um diese Punkte zu klären hat die NFDI Arbeitsgruppe Long Term Archiving der Sektion Common Infrastructures eine Umfrage in den Konsortien gestartet. Das Ziel war, den gegenwärtigen Status von LZA zu ermitteln und entsprechende Bedarfe zu ermitteln. Die Umfrage ergab als zentrale Aussage, dass der Bedarf an Beratung zum Thema LZA groß ist: Viele Konsortien und Forschungsorganisationen haben sich bis jetzt nicht ausreichend mit Lösungen zum langfristigen Erhalt von Daten bzw. LZA befasst. Wenn LZA überhaupt ein Thema war, wurde oft allein der Erhalt auf dem Bitstream Level anvisiert. Generell wurden Wissenslücken in verschiedenen Bereichen deutlich. Als Konsequenz erscheint es sinnvoll, einen LZA-Beratungsservice aufzubauen, der sowohl die NFDI-Konsortien als auch Institutionen hinsichtlich Langzeitarchivierung von Forschungsdaten berät. In der Umfrage haben die meisten Konsortien außerdem einen Bedarf an zielgerichteten LZA-Lösungen geäußert, der auf die spezifischen Forschungscommunities und dort etablierte Lösungen ausgerichtet ist. LZA Lösungen sollten daher in Kooperation mit den Konsortien, deren Fachdisziplin einerseits und der internationalen LZA-Community andererseits verfolgt werden und sollten sich nach gemeinsam entwickelten Prinzipien, Richtlinien und Standards richten. Nicht zuletzt wurde in den Antworten auf die Umfrage deutlich, dass vor allem eine bessere und langfristige finanzielle Unterstützung der Konsortien und von Institutionen bezüglich LZA-Aufgaben entsprechend der FAIR Prinzipien nötig ist und dass die Zertifizierung von Forschungsdatenservices dringend anzustreben ist.
    Subject code 020
    Language German
    Size 1 Online-Ressource (22 Seiten), Diagramme
    Edition Version v1
    Publisher German National Library of Medicine
    Publishing place Köln
    Publishing country Germany
    Document type Book ; Online
    Note Dieses Werk ist lizenziert unter einer Creative Commons Namensnennung 4.0International Lizenz (CC BY 4.0). Für die enthaltenen Materialien gelten, sofern angegeben,andere Lizenzen bzw. sind alle Rechte vorbehalten ; gefördert durch die Deutsche Forschungsgemeinschaft (DFG) als Teil des Projektes ‘Aufbau einer Nationalen Forschungsdateninfrastruktur‘ - NFDI4Microbiota - Projektnummer 460129525, NFDI4Biodiversity - Projektnummer 442032008 und durch EU COST Action CA17106 ; Katharina Markus (ORCID:0000-0002-9316-8982), Kai Naumann (ORCID:0000-0002-2799-1030), Markus Schmalzl (ORCID:0009-0005-7574-2699), Dagmar Triebel (ORCID:0000-0003-1980-3148) ; Open Access
    HBZ-ID HT030743998
    DOI 10.5281/zenodo.10822613
    Database Repository for Life Sciences

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  3. Article ; Online: Software infrastructure and data pipelines established for technical interoperability within a cross-border cooperation for the flora of the Bohemian Forest

    Novotný, Petr / Seifert, Stefan / Rohn, Martin / Diewald, Wolfgang / Štech, Milan / Triebel, Dagmar

    Biodiversity Data Journal. 2022 Oct. 14, v. 10 p.e87254-

    2022  

    Abstract: The timely and geographical resolutions, as well as the quantity and taxon concepts of records on the occurrence of plants near national borders is often ambiguous. This is due to the regional focus and different approaches of the contributing national ... ...

    Abstract The timely and geographical resolutions, as well as the quantity and taxon concepts of records on the occurrence of plants near national borders is often ambiguous. This is due to the regional focus and different approaches of the contributing national and regional databases and networks of the neighbouring countries. Careful data transformation between national data providers is essential for understanding distribution patterns and its dynamics for organisms in areas along the national borders. Sharing occurrence data through the international data aggregator Global Biodiversity Information Facility (GBIF) is also complicated and has to consider that the underlying taxonomic concept and geographic information system of each single GBIF dataset might be different. In addition, some regional data providers have a restrictive (non-cc) licensing policy which does not allow data publication via the GBIF network. Therefore, it is necessary to investigate new ways to make data fit for use for a better and comprehensive understanding of the Flora of the Bohemian Forest. In this paper, we present a bilateral technical interoperability solution for vascular plant occurrence data for the area between the Czech Republic and Bavaria. We describe the initial state of data providers in both countries and the factual and technical challenges in finding a sustainable concept to establish mutual data sharing. The resulting solution for a functional infrastructure and an agreed data pipeline is described in a step-by-step approach. The new distributed infrastructure allows botanists and other stakeholders from both countries to work within the cross-border context of historical and current plants' distribution.
    Keywords biodiversity ; computer software ; data collection ; flora ; forests ; geographic information systems ; infrastructure ; issues and policy ; stakeholders ; vascular plants ; Czech Republic ; Germany ; Flora Silvae Gabretae ; Bohemian Forest ; occurrence data portal ; ABCD occurrence data sources ; taxon names services ; Pladias ; web portal ; Diversity Workbench repositories.
    Language English
    Dates of publication 2022-1014
    Publishing place Pensoft Publishers
    Document type Article ; Online
    ZDB-ID 2736709-5
    ISSN 1314-2828
    ISSN 1314-2828
    DOI 10.3897/BDJ.10.e87254
    Database NAL-Catalogue (AGRICOLA)

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  4. Article: Software infrastructure and data pipelines established for technical interoperability within a cross-border cooperation for the flora of the Bohemian Forest.

    Novotný, Petr / Seifert, Stefan / Rohn, Martin / Diewald, Wolfgang / Štech, Milan / Triebel, Dagmar

    Biodiversity data journal

    2022  Volume 10, Page(s) e87254

    Abstract: Background: The timely and geographical resolutions, as well as the quantity and taxon concepts of records on the occurrence of plants near national borders is often ambiguous. This is due to the regional focus and different approaches of the ... ...

    Abstract Background: The timely and geographical resolutions, as well as the quantity and taxon concepts of records on the occurrence of plants near national borders is often ambiguous. This is due to the regional focus and different approaches of the contributing national and regional databases and networks of the neighbouring countries. Careful data transformation between national data providers is essential for understanding distribution patterns and its dynamics for organisms in areas along the national borders. Sharing occurrence data through the international data aggregator Global Biodiversity Information Facility (GBIF) is also complicated and has to consider that the underlying taxonomic concept and geographic information system of each single GBIF dataset might be different. In addition, some regional data providers have a restrictive (non-cc) licensing policy which does not allow data publication via the GBIF network. Therefore, it is necessary to investigate new ways to make data fit for use for a better and comprehensive understanding of the Flora of the Bohemian Forest.
    New information: In this paper, we present a bilateral technical interoperability solution for vascular plant occurrence data for the area between the Czech Republic and Bavaria. We describe the initial state of data providers in both countries and the factual and technical challenges in finding a sustainable concept to establish mutual data sharing. The resulting solution for a functional infrastructure and an agreed data pipeline is described in a step-by-step approach. The new distributed infrastructure allows botanists and other stakeholders from both countries to work within the cross-border context of historical and current plants' distribution.
    Language English
    Publishing date 2022-10-14
    Publishing country Bulgaria
    Document type Journal Article
    ZDB-ID 2736709-5
    ISSN 1314-2828
    ISSN 1314-2828
    DOI 10.3897/BDJ.10.e87254
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Chemical properties of key metabolites determine the global distribution of lichens

    Schweiger, Andreas H. / Ullmann, G. Matthias / Nürk, Nicolai M. / Triebel, Dagmar / Schobert, Rainer / Rambold, Gerhard

    Ecology letters. 2022 Feb., v. 25, no. 2

    2022  

    Abstract: In lichen symbioses, fungal secondary metabolites provide UV protection on which lichen algae such as trebouxiophycean green algae—the most prominent group of photobionts in lichen symbioses—sensitively depend. These metabolites differ in their UV ... ...

    Abstract In lichen symbioses, fungal secondary metabolites provide UV protection on which lichen algae such as trebouxiophycean green algae—the most prominent group of photobionts in lichen symbioses—sensitively depend. These metabolites differ in their UV absorbance capability and solvability, and thus vary in their propensity of being leached from the lichen body in humid and warm environments, with still unknown implications for the global distribution of lichens. In this study covering more than 10,000 lichenised fungal species, we show that the occurrence of fungal‐derived metabolites in combination with their UV absorbance capability and their probability of being leached in warm and humid environments are important eco‐evolutionary drivers of global lichen distribution. Fungal‐derived UV protection seems to represent an indirect environmental adaptation in which the lichen fungus invests to protect the trebouxiophycean photobiont from high UV radiation in warm and humid climates and, by doing this, secures its carbon source.
    Keywords absorbance ; carbon ; ecology ; fungi ; geographical distribution ; lichens ; probability ; secondary metabolites ; ultraviolet radiation
    Language English
    Dates of publication 2022-02
    Size p. 416-426.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note LETTER
    ZDB-ID 1441608-6
    ISSN 1461-0248 ; 1461-023X
    ISSN (online) 1461-0248
    ISSN 1461-023X
    DOI 10.1111/ele.13930
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: A Rare Glimpse into the Past of the Anthrax Pathogen

    Braun, Peter / Knüpfer, Mandy / Antwerpen, Markus / Triebel, Dagmar / Grass, Gregor

    Microorganisms

    2020  Volume 8, Issue 2

    Abstract: ... The ... ...

    Abstract The bacterium
    Language English
    Publishing date 2020-02-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms8020298
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results.

    Harjes, Janno / Link, Anton / Weibulat, Tanja / Triebel, Dagmar / Rambold, Gerhard

    Database : the journal of biological databases and curation

    2020  Volume 2020

    Abstract: Repeatability of study setups and reproducibility of research results by underlying data are major requirements in science. Until now, abstract models for describing the structural logic of studies in environmental sciences are lacking and tools for data ...

    Abstract Repeatability of study setups and reproducibility of research results by underlying data are major requirements in science. Until now, abstract models for describing the structural logic of studies in environmental sciences are lacking and tools for data management are insufficient. Mandatory for repeatability and reproducibility is the use of sophisticated data management solutions going beyond data file sharing. Particularly, it implies maintenance of coherent data along workflows. Design data concern elements from elementary domains of operations being transformation, measurement and transaction. Operation design elements and method information are specified for each consecutive workflow segment from field to laboratory campaigns. The strict linkage of operation design element values, operation values and objects is essential. For enabling coherence of corresponding objects along consecutive workflow segments, the assignment of unique identifiers and the specification of their relations are mandatory. The abstract model presented here addresses these aspects, and the software DiversityDescriptions (DWB-DD) facilitates the management of thusly connected digital data objects and structures. DWB-DD allows for an individual specification of operation design elements and their linking to objects. Two workflow design use cases, one for DNA barcoding and another for cultivation of fungal isolates, are given. To publish those structured data, standard schema mapping and XML-provision of digital objects are essential. Schemas useful for this mapping include the Ecological Markup Language, the Schema for Meta-omics Data of Collection Objects and the Standard for Structured Descriptive Data. Data pipelines with DWB-DD include the mapping and conversion between schemas and functions for data publishing and archiving according to the Open Archival Information System standard. The setting allows for repeatability of study setups, reproducibility of study results and for supporting work groups to structure and maintain their data from the beginning of a study. The theory of 'FAIR++' digital objects is introduced.
    MeSH term(s) Computational Biology ; Databases, Factual ; Information Dissemination ; Reproducibility of Results ; Research Design ; Software ; Workflow
    Keywords covid19
    Language English
    Publishing date 2020-08-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2496706-3
    ISSN 1758-0463 ; 1758-0463
    ISSN (online) 1758-0463
    ISSN 1758-0463
    DOI 10.1093/database/baaa059
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Chemical properties of key metabolites determine the global distribution of lichens.

    Schweiger, Andreas H / Ullmann, G Matthias / Nürk, Nicolai M / Triebel, Dagmar / Schobert, Rainer / Rambold, Gerhard

    Ecology letters

    2021  Volume 25, Issue 2, Page(s) 416–426

    Abstract: In lichen symbioses, fungal secondary metabolites provide UV protection on which lichen algae such as trebouxiophycean green algae-the most prominent group of photobionts in lichen symbioses-sensitively depend. These metabolites differ in their UV ... ...

    Abstract In lichen symbioses, fungal secondary metabolites provide UV protection on which lichen algae such as trebouxiophycean green algae-the most prominent group of photobionts in lichen symbioses-sensitively depend. These metabolites differ in their UV absorbance capability and solvability, and thus vary in their propensity of being leached from the lichen body in humid and warm environments, with still unknown implications for the global distribution of lichens. In this study covering more than 10,000 lichenised fungal species, we show that the occurrence of fungal-derived metabolites in combination with their UV absorbance capability and their probability of being leached in warm and humid environments are important eco-evolutionary drivers of global lichen distribution. Fungal-derived UV protection seems to represent an indirect environmental adaptation in which the lichen fungus invests to protect the trebouxiophycean photobiont from high UV radiation in warm and humid climates and, by doing this, secures its carbon source.
    MeSH term(s) Biological Evolution ; Chlorophyta ; Climate ; Lichens ; Phylogeny ; Symbiosis
    Language English
    Publishing date 2021-11-16
    Publishing country England
    Document type Letter
    ZDB-ID 1441608-6
    ISSN 1461-0248 ; 1461-023X
    ISSN (online) 1461-0248
    ISSN 1461-023X
    DOI 10.1111/ele.13930
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: A Rare Glimpse into the Past of the Anthrax Pathogen Bacillus anthracis

    Braun, Peter / Knüpfer, Mandy / Antwerpen, Markus / Triebel, Dagmar / Grass, Gregor

    Microorganisms. 2020 Feb. 21, v. 8, no. 2

    2020  

    Abstract: The bacterium Bacillus anthracis is the causative agent of the zoonotic disease anthrax. While genomics of extant B. anthracis isolates established in-depth phylogenomic relationships, there is scarce information on the historic genomics of the pathogen. ...

    Abstract The bacterium Bacillus anthracis is the causative agent of the zoonotic disease anthrax. While genomics of extant B. anthracis isolates established in-depth phylogenomic relationships, there is scarce information on the historic genomics of the pathogen. Here, we characterized the oldest documented B. anthracis specimen. The inactive 142-year-old material originated from a bovine diseased in Chemnitz (Germany) in 1878 and is contemporary with the seminal studies of Robert Koch on B. anthracis. A specifically developed isolation method yielded high-quality DNA from this specimen for genomic sequencing. The bacterial chromosome featuring 242 unique base-characters placed it into a major phylogenetic clade of B. anthracis (B.Branch CNEVA), which is typical for central Europe today. Our results support the notion that the CNEVA-clade represents part of the indigenous genetic lineage of B. anthracis in this part of Europe. This work emphasizes the value of historic specimens as precious resources for reconstructing the past phylogeny of the anthrax pathogen.
    Keywords Bacillus anthracis ; DNA ; anthrax ; bacteria ; cattle ; chromosomes ; genomics ; isolation techniques ; pathogens ; phylogeny ; zoonoses ; Central European region ; Germany
    Language English
    Dates of publication 2020-0221
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms8020298
    Database NAL-Catalogue (AGRICOLA)

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  10. Book: Aufbau des deutschen GBIF-Knotens Mykologie

    Triebel, Dagmar

    Schlussbericht ; Berichtszeitraum: Oktober 2002 bis Juni 2006

    2006  

    Institution Bayern / Generaldirektion der Staatlichen Naturwissenschaftlichen Sammlungen
    Author's details Zuwendungsempfänger: Staatliche Naturwissenschaftliche Sammlungen Bayerns, Botanische Staatssammlung München. Autoren des Schlussberichtes, zugleich Leiter der Teilprojekte: Dagmar Triebel
    Language German
    Size 67 Bl., Ill., graph. Darst., Kt.
    Publishing place München
    Document type Book
    Note Förderkennzeichen BMBF 01LI0202 ; Unterschiede zwischen dem gedruckten Dokument und der elektronischen Ressource können nicht ausgeschlossen werden
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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