Section outline

  • Introduction to Darwin Core and Data Paper

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    Biodiversity data publishing is critical for several reasons, ranging from scientific research and conservation to policy-making and education. Darwin Core, a standardized framework for sharing biodiversity information, plays a crucial role in facilitating the effective use of biodiversity data. We this approach we are responding to:

    WALLACEAN SHORTFALL  – The Wallacean shortfall is named after Alfred Russel Wallace, and refers to lack of knowledge about the geographical distribution of species.

    PRESTONIAN SHORTFALL –  The Prestonian shortfall can be defined as lack of knowledge about the abundance of species and their population dynamics in space and time.

    Importance of Biodiversity Data Publishing includes:

    Data Accessibility: Publishing biodiversity data makes it accessible to researchers worldwide, fostering collaboration and enabling large-scale studies.

    Long-term Studies: Historical data is vital for understanding trends and changes in biodiversity over time.

    Species Distribution and abundance: Data on species distribution and abundance helps in understanding ecological patterns and predicting future changes in ecosystems.

    Importance of Darwin Core includes:

    Standardization.

    Interoperability: Darwin Core provides a common language for biodiversity data, making it easier for different databases and systems to share and integrate information.

    Consistency: Ensures that data collected from various sources are consistent, facilitating accurate analysis and comparisons.

  • Preparatory Materials

    In this section you find a list of Data Paper Useful Links.
    • Darwin Core Quick Reference Guide URL

      At this link you will have access to the explanation of all the Darwin Core fields. This page is not part of the standard, but combines the normative term names and definitions with the non-normative comments and examples that are meant to help people to use the terms consistently. 

    • Online GUID / UUID Generator URL

      GUID (aka UUID) is an acronym for 'Globally Unique Identifier' (or 'Universally Unique Identifier'). It is a 128-bit integer number used to identify resources. The term GUID is generally used by developers working with Microsoft technologies, while UUID is used commonly used elsewhere.

    • GBIF IPT URL
      Integrated Publishing Toolkit. A free, open source software tool used to publish and share biodiversity datasets through the GBIF network.
    • AZORES-BIOTA Collection URL

      The aim of this thematic collection is to collate all the publications dealing with the taxonomic diversity of Azorean terrestrial and marine biota including mostly the categories “Research Article”, “Taxonomic Paper” and “Data Paper”, but also “Alien Species Profiles” and “Species Conservation Profiles”.

    • AZORES BIOPORTAL URL

      The Azores BioPortal (ABP) is a collaborative e-infrastructure for information and research on Biodiversity, which gathers and manages information and resources on the biodiversity of the Azores. This regional e-Infrastructure is dedicated to the organization, mobilization, curation, and dissemination of biodiversity data, on a platform that is connected to the academia, public administration, and civil society.

  • Part One - Explaining the Event Table

    The EVENT Table includes the Darwin Core Fields related with the studied sites/Plots and theie geographical location.

    • Event Table template File

      The following data table includes all the records for which a taxonomic identification of the species was possible. The dataset submitted to GBIF is structured as a sample event dataset that has been published as a Darwin Core Archive (DwCA), which is a standardised format for sharing biodiversity data as a set of one or more data tables. The core data file contains XXX records (eventID). This GBIF IPT (Integrated Publishing Toolkit, Version 2.5.6) archives the data and, thus, serves as the data repository.

    • Explanation of Darwin Core Fields File

      Normative term names and definitions with the non-normative comments and examples that are meant to help people to use the terms consistently.

  • Part Two - Explaining the Occurrence Table

    The OCCURRENCE Table includes the Darwin Core Fields related with species data (abundance and taxonomy).

    • Occurrence Table template File

      The following data table includes all the records for which a taxonomic identification of the species was possible. The dataset submitted to GBIF is structured as an occurrence table that has been published as a Darwin Core Archive (DwCA), which is a standardised format for sharing biodiversity data as a set of one or more data tables. The core data file contains XXX records (occurrenceID). This GBIF IPT (Integrated Publishing Toolkit, Version 2.5.6) archives the data and, thus, serves as the data repository.

    • Metadata for GBIF with Occurrence Data (RTF) File

      Document describing a dataset, published in GBIF IPT.

    • The MATELA DATA PAPER File

      Sousa, M.A., Lamelas-López, L., Elias, R.B., Gabriel, R. & Borges, P.A.V. (2024).  A multitaxa approach to biodiversity inventory in Matela protected area (Terceira, Azores, Portugal). Biodiversity Data Journal, 12: e121884. 

      DOI: 10.3897/BDJ.12.e121884

      https://bdj.pensoft.net/article/121884/list/9/

  • Part Three - Explaining Data Paper

    A data paper is a peer reviewed document describing a dataset, published in a peer reviewed journal. It takes effort to prepare, curate and describe data. Data papers provide recognition for this effort by means of a scholarly article.

    • Checklist in Darwin Core File

      The dataset submitted to GBIF is structured as a Checklist dataset that has been published as a Darwin Core Archive (DwCA), which is a standardised format for sharing biodiversity data as a set of one or more data tables. The Taxon Table contains XXX records. This GBIF IPT (Integrated Publishing Toolkit, Version 2.6.2) archives the data and, thus, serves as the data repository.

    • Distribution of Species File

      The Distribution Table contains XXX records about detailed species distribution data. This GBIF IPT (Integrated Publishing Toolkit, Version 2.6.2) archives the data and, thus, serves as the data repository.

    • Metadata for GBIF with Checklist File

      Document describing a dataset, published in GBIF IPT.

    • Evaluation of Darwin Core by Referee File

      The corrections needed to be performed before publishing the data.

    • Data Paper with Species Checklist File

      Borges, P.A.V., Lamelas-Lopez, L., Andrade, R., Lhoumeau, S., Vieira, V., Soares, A.O., Borges, I., Boieiro, M., Cardoso, P., Crespo, L.C.F., Karsholt, O., Schülke, M., Serrano, A.R.M., Quartau, J.A. & Assing, V. (2022). An updated checklist of Azorean arthropods (Arthropoda). Biodiversity Data Journal, 10: e97682. 

      DOI:  10.3897/BDJ.10.e97682.

      https://bdj.pensoft.net/article/97682/list/9/

  • Additional Resources

  • Credits

    This resource is based on courses developed and delivered by Paulo Alexandre Vieira Borges, PhD.
    Paulo is the current leader of Azorean Biodiversity Group (Center for Ecology, Evolution and Environmental Changes, CE3C) at the University of the Azores (UAc).