0
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Characterizing the Vector Data Ecosystem

      discussion

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          A growing body of information on vector-borne diseases has arisen as increasing research focus has been directed towards the need for anticipating risk, optimizing surveillance, and understanding the fundamental biology of vector-borne diseases to direct control and mitigation efforts. The scope and scale of this information, in the form of data, comprising database efforts, data storage, and serving approaches, means that it is distributed across many formats and data types. Data ranges from collections records to molecular characterization, geospatial data to interactions of vectors and traits, infection experiments to field trials. New initiatives arise, often spanning the effort traditionally siloed in specific research disciplines, and other efforts wane, perhaps in response to funding declines, different research directions, or lack of sustained interest. Thusly, the world of vector data – the Vector Data Ecosystem – can become unclear in scope, and the flows of data through these various efforts can become stymied by obsolescence, or simply by gaps in access and interoperability. As increasing attention is paid to creating FAIR (Findable Accessible Interoperable, and Reusable) data, simply characterizing what is ‘out there’, and how these existing data aggregation and collection efforts interact, or interoperate with each other, is a useful exercise. This study presents a snapshot of current vector data efforts, reporting on level of accessibility, and commenting on interoperability using an illustration to track a specimen through the data ecosystem to understand where it occurs for the database efforts anticipated to describe it (or parts of its extended specimen data).

          Related collections

          Most cited references34

          • Record: found
          • Abstract: not found
          • Article: not found

          spThin: an R package for spatial thinning of species occurrence records for use in ecological niche models

            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            The Value of Museum Collections for Research and Society

              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

              The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org ) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.
                Bookmark

                Author and article information

                Contributors
                Role: Subject Editor
                Journal
                J Med Entomol
                J Med Entomol
                jme
                Journal of Medical Entomology
                Oxford University Press (US )
                0022-2585
                1938-2928
                March 2023
                08 February 2023
                08 February 2023
                : 60
                : 2
                : 247-254
                Affiliations
                Quantitative Disease Ecology and Conservation (QDEC) Lab Group, Department of Geography, University of Florida , Gainesville, FL 32611, USA
                Emerging Pathogens Institute, University of Florida , Gainesville, FL 32610, USA
                Center for Research Computing, Department of Biological Sciences, & Eck Institute for Global HealthUniversity of Notre Dame , Notre Dame, IN 46556, USA
                Quantitative Disease Ecology and Conservation (QDEC) Lab Group, Department of Geography, University of Florida , Gainesville, FL 32611, USA
                Emerging Pathogens Institute, University of Florida , Gainesville, FL 32610, USA
                Author notes
                Corresponding author, e-mail: sjryan@ 123456ufl.edu
                Author information
                https://orcid.org/0000-0002-7988-0324
                https://orcid.org/0000-0002-1701-7787
                https://orcid.org/0000-0002-4308-6321
                Article
                tjad009
                10.1093/jme/tjad009
                9989832
                36752771
                1c47d326-9d13-46a7-a534-a850e5c8193f
                © The Author(s) 2023. Published by Oxford University Press on behalf of Entomological Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence ( https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                : 29 September 2022
                : 03 January 2023
                Page count
                Pages: 8
                Funding
                Funded by: VectorByte;
                Award ID: NSF DBI 2016265
                Award ID: NSF-DBI-2016282
                Funded by: Verena;
                Award ID: NSF BII 2021909
                Award ID: NSF BII 2213854
                Categories
                Forum
                AcademicSubjects/SCI01382
                AcademicSubjects/MED00860

                vector-borne disease,mosquito,database,interoperability,ecoinformatics

                Comments

                Comment on this article