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  1. Article: Ecological data in Darwin Core: the case of earthworm surveys.

    Shashkov, Maxim / Ivanova, Natalya / Wieczorek, John

    Biodiversity data journal

    2021  Volume 9, Page(s) e71292

    Abstract: Background: This sampling-event dataset provides primary data about species diversity, age structure, abundance (in terms of biomass and density) and seasonal activity of earthworms (Lumbricidae). The study was carried out in old-growth broad-leaved and ...

    Abstract Background: This sampling-event dataset provides primary data about species diversity, age structure, abundance (in terms of biomass and density) and seasonal activity of earthworms (Lumbricidae). The study was carried out in old-growth broad-leaved and young forests of two protected areas ("Kaluzhskiye Zaseki" Nature Reserve and Ugra National Park) of Kaluga Oblast (Russia).
    New information: The published dataset provides new data about earthworm communities in European Russia. We propose a new schema according to Darwin Core for the standardisation of the soil invertebrates survey data.
    Language English
    Publishing date 2021-12-08
    Publishing country Bulgaria
    Document type Journal Article
    ZDB-ID 2736709-5
    ISSN 1314-2828
    ISSN 1314-2828
    DOI 10.3897/BDJ.9.e71292
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Ecological data in Darwin Core: the case of earthworm surveys

    Shashkov, Maxim / Ivanova, Natalya / Wieczorek, John

    Biodiversity data journal. 2021 Dec. 08, v. 9

    2021  

    Abstract: This sampling-event dataset provides primary data about species diversity, age structure, abundance (in terms of biomass and density) and seasonal activity of earthworms (Lumbricidae). The study was carried out in old-growth broad-leaved and young ... ...

    Abstract This sampling-event dataset provides primary data about species diversity, age structure, abundance (in terms of biomass and density) and seasonal activity of earthworms (Lumbricidae). The study was carried out in old-growth broad-leaved and young forests of two protected areas ("Kaluzhskiye Zaseki" Nature Reserve and Ugra National Park) of Kaluga Oblast (Russia). The published dataset provides new data about earthworm communities in European Russia. We propose a new schema according to Darwin Core for the standardisation of the soil invertebrates survey data.
    Keywords Lumbricidae ; Russia ; age structure ; biomass ; conservation areas ; data collection ; earthworms ; national parks ; soil ; species diversity ; surveys
    Language English
    Dates of publication 2021-1208
    Publishing place Pensoft Publishers
    Document type Article
    ZDB-ID 2736709-5
    ISSN 1314-2828
    ISSN 1314-2828
    DOI 10.3897/BDJ.9.e71292
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: Uncertainty matters: ascertaining where specimens in natural history collections come from and its implications for predicting species distributions

    Marcer, Arnald / Chapman, Arthur D. / Wieczorek, John R. / Xavier Picó, F. / Uribe, Francesc / Waller, John / Ariño, Arturo H.

    Ecography. 2022 Sept., v. 2022, no. 9

    2022  

    Abstract: Natural history collections (NHCs) represent an enormous and largely untapped wealth of information on the Earth's biota, made available through GBIF as digital preserved specimen records. Precise knowledge of where the specimens were collected is ... ...

    Abstract Natural history collections (NHCs) represent an enormous and largely untapped wealth of information on the Earth's biota, made available through GBIF as digital preserved specimen records. Precise knowledge of where the specimens were collected is paramount to rigorous ecological studies, especially in the field of species distribution modelling. Here, we present a first comprehensive analysis of georeferencing quality for all preserved specimen records served by GBIF, and illustrate the impact that coordinate uncertainty may have on predicted potential distributions. We used all GBIF preserved specimen records to analyse the availability of coordinates and associated spatial uncertainty across geography, spatial resolution, taxonomy, publishing institutions and collection time. We used three plant species across their native ranges in different parts of the world to show the impact of uncertainty on predicted potential distributions. We found that 38% of the 180+ million records provide coordinates only and 18% coordinates and uncertainty. Georeferencing quality is determined more by country of collection and publishing than by taxonomic group. Distinct georeferencing practices are more determinant than implicit characteristics and georeferencing difficulty of specimens. Availability and quality of records contrasts across world regions. Uncertainty values are not normally distributed but peak at very distinct values, which can be traced back to specific regions of the world. Uncertainty leads to a wide spectrum of range sizes when modelling species distributions, potentially affecting conclusions in biogeographical and climate change studies. In summary, the digitised fraction of the world's NHCs are far from optimal in terms of georeferencing and quality mainly depends on where the collections are hosted. A collective effort between communities around NHC institutions, ecological research and data infrastructure is needed to bring the data on a par with its importance and relevance for ecological research.
    Keywords climate change ; geographical distribution ; georeferencing ; infrastructure ; natural history ; taxonomy ; uncertainty
    Language English
    Dates of publication 2022-09
    Publishing place Blackwell Publishing Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 1112659-0
    ISSN 0906-7590
    ISSN 0906-7590
    DOI 10.1111/ecog.06025
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: A community-developed extension to Darwin Core for reporting the chronometric age of specimens.

    Brenskelle, Laura / Wieczorek, John / Davis, Edward / Wallis, Neill J / Emery, Kitty / LeFebvre, Michelle J / Guralnick, Rob

    PloS one

    2022  Volume 17, Issue 9, Page(s) e0261044

    Abstract: Darwin Core, the data standard used for sharing modern biodiversity and paleodiversity occurrence records, has previously lacked proper mechanisms for reporting what is known about the estimated age range of specimens from deep time. This has led to data ...

    Abstract Darwin Core, the data standard used for sharing modern biodiversity and paleodiversity occurrence records, has previously lacked proper mechanisms for reporting what is known about the estimated age range of specimens from deep time. This has led to data providers putting these data in fields where they cannot easily be found by users, which impedes the reuse and improvement of these data by other researchers. Here we describe the development of the Chronometric Age Extension to Darwin Core, a ratified, community-developed extension that enables the reporting of ages of specimens from deeper time and the evidence supporting these estimates. The extension standardizes reporting about the methods or assays used to determine an age and other critical information like uncertainty. It gives data providers flexibility about the level of detail reported, focusing on the minimum information needed for reuse while still allowing for significant detail if providers have it. Providing a standardized format for reporting these data will make them easier to find and search and enable researchers to pinpoint specimens of interest for data improvement or accumulate more data for broad temporal studies. The Chronometric Age Extension was also the first community-managed vocabulary to undergo the new Biodiversity Informatics Standards (TDWG) review and ratification process, thus providing a blueprint for future Darwin Core extension development.
    MeSH term(s) Biodiversity ; Data Collection
    Language English
    Publishing date 2022-09-15
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0261044
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Building community-specific standards and vocabularies: prospects and challenges for linking to the broader community - The SINP Case

    Jomier, Remy / Zermoglio, Paula F / Wieczorek, John

    Biodiversity Information Science and Standards. 2017 Aug. 14, v. 1 p.e20297-

    2017  

    Abstract: Biodiversity data may come from myriad sources. From data capture in the field through digitization processes, each source may choose distinctive ways to capture data. When it comes to sharing data more broadly at national or regional levels, it is ... ...

    Abstract Biodiversity data may come from myriad sources. From data capture in the field through digitization processes, each source may choose distinctive ways to capture data. When it comes to sharing data more broadly at national or regional levels, it is imperative that data is presented in ways that encourage understanding both by humans and machines, allowing aggregation and serving the data back to the community. This implies two levels of agreement, one at a structural level, where data is organized under certain terms or fields, and another related to the actual values contained in such fields. Since its ratification in 2009, the Darwin Core standard Wieczorek et al. (2012) has been increasingly used across the community to respond to the first need, providing a relatively simple means to organize shared data. Nonetheless, despite its broad acceptance, efforts to develop different standards to answer the same problems are not uncommon among some stakeholders, and may introduce yet another issue: reconciling the data shared under different standards. The second level of agreement, at the value level, constitutes a much more complex issue, partly given the nature of biodiversity data and partly due to social constraints. Many potential, partial solutions involving the development of dictionaries and controlled vocabularies are found scattered across the community. As the lack of homogeneity renders data less discoverable (Zermoglio et al. 2016) and therefore less usable for research and decision making, there exists a growing need for unifying such efforts. As part of the Biodiversity Information System on Nature and Landscapes (SINP), the French National Museum of Natural History was appointed to develop biodiversity data exchange standards, with the goal of sharing French marine and terrestrial data at the national level, meeting national and European requirements (e.g., the European INSPIRE Directive European Commission 2017). The French data providers include a broad range of people with diverse backgrounds. While some stakeholders can provide data under very specific constraints and formats, others lack the capabilities or resources to do so. The variability in the data provided therefore extends through both the structure and the value levels. In order to integrate the data in a coherent national system, a dedicated working group was assembled, mobilizing a range of biodiversity stakeholders and experts. Existing standards were compared, existing vocabularies gathered and compiled for review by experts, and then presented to the working group. As a result, a set of terms and associated controlled vocabularies was established. Finally, the set was released to the public to test and amended as needed. The results of the French initiative proved useful to compile and share data at the national level, bringing together data providers that otherwise would have been excluded. However, at a global scale, it faces some challenges that still need to be fully addressed. For instance, the standards created do not have an exact correspondence with Darwin Core, and so a complex mapping is required in order to integrate the data with that of the rest of the community. A serious mapping effort is being carried out as the national standards progress and has already rendered good results (Jomier and Pamerlon 2016). Regardless of the problems that remain to be solved, some lessons can be learnt from this effort. Getting actively involved in the broader, global community can help identify available tools, resources and expertise, and avoid repeated efforts that can be costly and time-consuming. Furthermore, re-using elements that already have been proven to work, prevents the need for reconciliations and makes data integration easier. With the ultimate goal of making biodiversity data readily available, these lessons should be kept in mind for future initiatives.
    Keywords biodiversity ; information systems ; stakeholders ; biodiversity data standards ; controlled vocabularies ; SINP ; community engagement
    Language English
    Dates of publication 2017-0814
    Publishing place Pensoft Publishers
    Document type Article ; Online
    ISSN 2535-0897
    DOI 10.3897/tdwgproceedings.1.20297
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  6. Article ; Online: A Standardized Reference Data Set for Vertebrate Taxon Name Resolution.

    Zermoglio, Paula F / Guralnick, Robert P / Wieczorek, John R

    PloS one

    2016  Volume 11, Issue 1, Page(s) e0146894

    Abstract: Taxonomic names associated with digitized biocollections labels have flooded into repositories such as GBIF, iDigBio and VertNet. The names on these labels are often misspelled, out of date, or present other problems, as they were often captured only ... ...

    Abstract Taxonomic names associated with digitized biocollections labels have flooded into repositories such as GBIF, iDigBio and VertNet. The names on these labels are often misspelled, out of date, or present other problems, as they were often captured only once during accessioning of specimens, or have a history of label changes without clear provenance. Before records are reliably usable in research, it is critical that these issues be addressed. However, still missing is an assessment of the scope of the problem, the effort needed to solve it, and a way to improve effectiveness of tools developed to aid the process. We present a carefully human-vetted analysis of 1000 verbatim scientific names taken at random from those published via the data aggregator VertNet, providing the first rigorously reviewed, reference validation data set. In addition to characterizing formatting problems, human vetting focused on detecting misspelling, synonymy, and the incorrect use of Darwin Core. Our results reveal a sobering view of the challenge ahead, as less than 47% of name strings were found to be currently valid. More optimistically, nearly 97% of name combinations could be resolved to a currently valid name, suggesting that computer-aided approaches may provide feasible means to improve digitized content. Finally, we associated names back to biocollections records and fit logistic models to test potential drivers of issues. A set of candidate variables (geographic region, year collected, higher-level clade, and the institutional digitally accessible data volume) and their 2-way interactions all predict the probability of records having taxon name issues, based on model selection approaches. We strongly encourage further experiments to use this reference data set as a means to compare automated or computer-aided taxon name tools for their ability to resolve and improve the existing wealth of legacy data.
    MeSH term(s) Algorithms ; Animals ; Biodiversity ; Classification/methods ; Databases, Factual ; Datasets as Topic ; Geography ; Probability ; Reference Values ; Reproducibility of Results ; Terminology as Topic ; Vertebrates/classification
    Language English
    Publishing date 2016-01-13
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0146894
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: A globally integrated structure of taxonomy to support biodiversity science and conservation.

    Sandall, Emily L / Maureaud, Aurore A / Guralnick, Robert / McGeoch, Melodie A / Sica, Yanina V / Rogan, Matthew S / Booher, Douglas B / Edwards, Robert / Franz, Nico / Ingenloff, Kate / Lucas, Maisha / Marsh, Charles J / McGowan, Jennifer / Pinkert, Stefan / Ranipeta, Ajay / Uetz, Peter / Wieczorek, John / Jetz, Walter

    Trends in ecology & evolution

    2023  Volume 38, Issue 12, Page(s) 1143–1153

    Abstract: All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on the coordination and organization of taxonomic data. We ... ...

    Abstract All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on the coordination and organization of taxonomic data. We assess current efforts and find that even key applications for well-studied taxa still lack commonality in taxonomic information required for integration. We identify essential taxonomic elements from our interoperability assessment to support improved access and integration of taxonomic data. A stronger focus on these elements has the potential to involve taxonomic communities in biodiversity science and overcome broken linkages currently limiting research capacity. We encourage a community effort to democratize taxonomic expertise and language in order to facilitate maximum interoperability and integration.
    MeSH term(s) Biodiversity ; Classification ; Conservation of Natural Resources
    Language English
    Publishing date 2023-09-06
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 284965-3
    ISSN 1872-8383 ; 0169-5347
    ISSN (online) 1872-8383
    ISSN 0169-5347
    DOI 10.1016/j.tree.2023.08.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Data Leakage and Loss in Biodiversity Informatics.

    Peterson, A Townsend / Asase, Alex / Canhos, Dora Ann Lange / de Souza, Sidnei / Wieczorek, John

    Biodiversity data journal

    2018  , Issue 6, Page(s) e26826

    Abstract: The field of biodiversity informatics is in a massive, "grow-out" phase of creating and enabling large-scale biodiversity data resources. Because perhaps 90% of existing biodiversity data nonetheless remains unavailable for science and policy ... ...

    Abstract The field of biodiversity informatics is in a massive, "grow-out" phase of creating and enabling large-scale biodiversity data resources. Because perhaps 90% of existing biodiversity data nonetheless remains unavailable for science and policy applications, the question arises as to how these existing and available data records can be mobilized most efficiently and effectively. This situation led to our analysis of several large-scale biodiversity datasets regarding birds and plants, detecting information gaps and documenting data "leakage" or attrition, in terms of data on taxon, time, and place, in each data record. We documented significant data leakage in each data dimension in each dataset. That is, significant numbers of data records are lacking crucial information in terms of taxon, time, and/or place; information on place was consistently the least complete, such that geographic referencing presently represents the most significant factor in degradation of usability of information from biodiversity information resources. Although the full process of digital capture, quality control, and enrichment is important to developing a complete digital record of existing biodiversity information, payoffs in terms of immediate data usability will be greatest with attention paid to the georeferencing challenge.
    Language English
    Publishing date 2018-11-07
    Publishing country Bulgaria
    Document type Journal Article
    ZDB-ID 2736709-5
    ISSN 1314-2828
    ISSN 1314-2828
    DOI 10.3897/BDJ.6.e26826
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: A globally integrated structure of taxonomy to support biodiversity science and conservation

    Sandall, Emily L. / Maureaud, Aurore A. / Guralnick, Robert / McGeoch, Melodie A. / Sica, Yanina V. / Rogan, Matthew S. / Booher, Douglas B. / Edwards, Robert / Franz, Nico / Ingenloff, Kate / Lucas, Maisha / Marsh, Charles J. / McGowan, Jennifer / Pinkert, Stefan / Ranipeta, Ajay / Uetz, Peter / Wieczorek, John / Jetz, Walter

    Trends in Ecology & Evolution.

    2023  

    Abstract: All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on coordination and organization of taxonomic data. We assess ... ...

    Abstract All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on coordination and organization of taxonomic data. We assess current efforts and find that even key applications for well-studied taxa still lack commonality in taxonomic information required for integration. We identify essential taxonomic elements from our interoperability assessment to support improved access and integration of taxonomic data. A stronger focus on these elements has the potential to involve taxonomic communities in biodiversity science and overcome broken linkages currently limiting research capacity. We encourage a community effort to democratize taxonomic expertise and language in order to facilitate maximum interoperability and integration.
    Keywords biodiversity ; evolution ; taxonomy ; taxonomic backbone ; integrative science ; data linkage ; social infrastructure ; biodiversity conservation
    Language English
    Publishing place Elsevier Ltd
    Document type Article ; Online
    Note Pre-press version
    ZDB-ID 284965-3
    ISSN 1872-8383 ; 0169-5347
    ISSN (online) 1872-8383
    ISSN 0169-5347
    DOI 10.1016/j.tree.2023.08.004
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  10. Article ; Online: Standards in Action: The Darwin Core Hour

    Paul, Deborah L / Zermoglio, Paula F / Wieczorek, John / Motz, Gary J / Krimmel, Erica

    Biodiversity Information Science and Standards. 2017 Aug. 14, v. 1 p.e20280-

    2017  

    Abstract: Darwin Core Wieczorek et al. 2012 has become broadly used for biodiversity data sharing since its ratification as a standard in 2009. Despite its popularity, or perhaps because of it, questions about Darwin Core, its definitions, and its applications ... ...

    Abstract Darwin Core Wieczorek et al. 2012 has become broadly used for biodiversity data sharing since its ratification as a standard in 2009. Despite its popularity, or perhaps because of it, questions about Darwin Core, its definitions, and its applications continue to arise. However, no easy mechanism previously existed for the users of the standard to ask their questions and to have them answered and documented in a strategic and timely way. In order to close this gap, a double-initiative was developed: the Darwin Core Hour (DHC) Darwin Core Hour Team 2017a and the Darwin Core Questions & Answers SiteDarwin Core Hour Team 2017b. The Darwin Core HourZermoglio et al. 2017 is a webinar series in which particular topics concerning the Darwin Core standard and its use are presented by more experienced and vested community members for the benefit of and discussion amongst the community as a whole. All webinars are recorded for broader accessibility. The Darwin Core Questions & Answers Site is a GitHub repository where questions from the community are submitted as issues, then discussed and answered in the repository as a means of building up documentation. These two instances are tightly linked and feed each other Fig. 1.Questions from the community, some arising during the webinars, turn into issues and are then answered and shaped into documentation, while some questions give birth to new webinar topics for further discussion. So far, this double-initiative model has proved useful in bringing together communities from different geographic locales, levels of expertise, and degrees of involvement in open dialogue for the collaborative evolution of the standard. At the time of this presentation, the group has produced nine webinar sessions and provided a corpus of documentation on several topics. We will discuss its current status, origins and potential of the double-initiative model, community feedback, and future directions, in addition to inviting the TDWG community to join efforts to keep the Darwin Core standard "in action".
    Keywords biodiversity ; evolution ; information science ; models ; Darwin Core standard ; Darwin Core Hour ; capacity building ; community engagement
    Language English
    Dates of publication 2017-0814
    Publishing place Pensoft Publishers
    Document type Article ; Online
    ISSN 2535-0897
    DOI 10.3897/tdwgproceedings.1.20280
    Database NAL-Catalogue (AGRICOLA)

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