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uva.nl
Institute for Biodiversity and Ecosystem Dynamics null

Dr. J. (Johannes) De Groeve PhD

I am the data manager at the Institute for Biodiversity and Ecosystem Dynamics, and one of the four members of the recently established computational support team. I am working on several topics that involve dedicated data management, database development and data visualisation. I am also supporting a faculty-broad initiative set up to facilitate good data management practices.
Faculty of Science
Institute for Biodiversity and Ecosystem Dynamics
Visiting address
  • Science Park 904
  • Room number: C4.204
Postal address
  • Postbus 94240
    1090 GE Amsterdam
Contact details
  • Profile

    I am the data manager, part of the Computational Support Unit of the Institute for Biodiversity and Ecosystem Dynamics at the University of Amsterdam. My main interest is to support researchers in developing and setting up database platforms for wide variety of ecological datasets. I like to think along about all the steps, from building a database model (data structure, normalization, standardization), implementation (development, optimalization, automatic data population) to integration (linking databases to analysis software, developing data visualization apps). With the boom of data generated in recent years and increasing needs on guidance in data management an important task as data manager is to help researchers with setting up data management plans and to provide advice and encourage best-practices in data management. Documentation on best practices in data management and helpful templates are currently available in Teams (IBED/General information/Data Management). 

    Research

    I have background in Archaeology, Geography and Animal Ecology and gradually roled into Data Science. With my background in research I like to remain connected to the actual science behind a project. Currently, I am involved in various research projects in which my expertise is used to support and guide scientists, postdocs and PhD-students from IBED. Among other tasks, I can be involved in a project to think along about data standardization (e.g., developing metadata standards), database development and data visualization.


    Education

    During my PhD I realized that helping and teaching colleagues and students provided me the most satisfaction. As IBED data manager, researchers can contact me for hands-on course on Structured Query Language (SQL), R-programming and for presentations on best-practices in data management.

  • Publications

    2024

    • van Erp, J. A., van Loon, E. E., De Groeve, J., Bradarić, M., & Shamoun-Baranes, J. (2024). A framework for post-processing bird tracks from automated tracking radar systems. Methods in Ecology and Evolution, 15(1), 130-143. https://doi.org/10.1111/2041-210X.14249
      • Related datasets
        • van Erp, J. A., De Groeve, J., van Loon, E., Shamoun-Baranes, J. & Bradarić, M. (23-10-2023). Data and script for "A framework for post-processing bird tracks from automated tracking radar systems". Universiteit van Amsterdam. https://doi.org/10.21942/uva.22567918.v1

    2023

    • De Groeve, J., Van de Weghe, N., Ranc, N., Morellet, N., Bonnot, N. C., Gehr, B., Heurich, M., Hewison, A. J. M., Kroeschel, M., Linnell, J. D. C., Mysterud, A., Sandfort, R., & Cagnacci, F. (2023). Back and forth: day–night alternation between cover types reveals complementary use of habitats in a large herbivore. Landscape Ecology. https://doi.org/10.1007/s10980-023-01594-1
    • Mumme, S., Middleton, A. D., Ciucci, P., De Groeve, J., Corradini, A., Aikens, E. O., Ossi, F., Atwood, P., Balkenhol, N., Cole, E. K., Debeffe, L., Dewey, S. R., Fischer, C., Gude, J., Heurich, M., Hurley, M. A., Jarnemo, A., Kauffman, M. J., Licoppe, A., ... Cagnacci, F. (2023). Wherever I may roam—Human activity alters movements of red deer (Cervus elaphus) and elk (Cervus canadensis) across two continents. Global Change Biology, 29(20), 5788-5801. https://doi.org/10.1111/gcb.16769

    2022

    • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, A. C., Hoeksema, B. W., Yasuhara, M., Norder, S. J., Cahyarini, S. Y., van der Geer, A., Meijer, H. J. M., Kubota, Y., & Rijsdijk, K. F. (2022). Global raster dataset on historical coastline positions and shelf sea extents since the Last Glacial Maximum. Global Ecology and Biogeography, 31(11), 2162-2171. https://doi.org/10.1111/geb.13573 [details]
      • Related datasets
        • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, H., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Historic coastline age raster (AGE 2019). Universiteit van Amsterdam. https://doi.org/10.21942/uva.17215094.v1
        • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, A. C., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Historic coastline age raster (AGE 2021). Universiteit van Amsterdam. https://doi.org/10.21942/uva.20029304.v1
        • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, H., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Resampled Bathymetry (GEBCO 2019). Universiteit van Amsterdam. https://doi.org/10.21942/uva.17218484.v1
        • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, A. C., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Shelf sea extent rasters (SLW140 2019). Universiteit van Amsterdam. https://doi.org/10.21942/uva.17216081.v1
        • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, A. C., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Shelf sea extent rasters (SLW140 2021). Universiteit van Amsterdam. https://doi.org/10.21942/uva.20029220.v1
        • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, A. C., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Spatial polygons for Sunda, Timor, and Caribbean regions.. Universiteit van Amsterdam. https://doi.org/10.21942/uva.17218724.v1
        • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, A. C., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A. A. E., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Spatio-Temporal Relative Sea Level Curve (RSL). Universiteit van Amsterdam. https://doi.org/10.21942/uva.20029991.v1
    • Salvatori, M., De Groeve, J., van Loon, E., De Baets, B., Morellet, N., Focardi, S., Bonnot, N. C., Gehr, B., Griggio, M., Heurich, M., Kroeschel, M., Licoppe, A., Moorcroft, P., Pedrotti, L., Signer, J., Van de Weghe, N., & Cagnacci, F. (2022). Day versus night use of forest by red and roe deer as determined by Corine Land Cover and Copernicus Tree Cover Density: Assessing use of geographic layers in movement ecology. Landscape Ecology, 37(5), 1453–1468. https://doi.org/10.1007/s10980-022-01416-w [details]
      • Related datasets
        • De Groeve, J., Salvatori, M., van Loon, E., De Baets , B., Morellet, N., Focardi, S., Griggio, M., Moorcroft, P., Bonnot, N. C., Gehr, B., Heurich, M., Kroeschel, M., Licoppe, A., Pedrotti, L., Signer, J., Van de Weghe, N. & Cagnacci, F. (2023). Data from: Day versus night use of forest by red and roe deer as determined by Corine Land Cover and Copernicus Tree Cover Density: assessing use of geographic layers in movement ecology. Zenodo. https://doi.org/10.5281/zenodo.7625970

    2021

    • Bergvall, U. A., Morellet, N., Kjellander, P., Rauset, G. R., De Groeve, J., Borowik, T., Brieger, F., Gehr, B., Heurich, M., Hewison, A. J. M., Kröschel, M., Pellerin, M., Saïd, S., Soennichsen, L., Sunde, P., & Cagnacci, F. (2021). Settle down! ranging behaviour responses of roe deer to different capture and release methods. Animals, 11(11), Article 3299. https://doi.org/10.3390/ani11113299
    • Leontidou, K., Vokou, D., Sandionigi, A., Bruno, A., Lazarina, M., De Groeve, J., Li, M., Varotto, C., Girardi, M., Casiraghi, M., & Cristofori, A. (2021). Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps). Scientific Reports, 11(1), Article 18226. https://doi.org/10.1038/s41598-021-97619-3

    2020

    • Aikens, E. O., Mysterud, A., Merkle, J. A., Cagnacci, F., Rivrud, I. M., Hebblewhite, M., Hurley, M. A., Peters, W., Bergen, S., De Groeve, J., Dwinnell, S. P. H., Gehr, B., Heurich, M., Hewison, A. J. M., Jarnemo, A., Kjellander, P., Kröschel, M., Licoppe, A., Linnell, J. D. C., ... Kauffman, M. J. (2020). Wave-like Patterns of Plant Phenology Determine Ungulate Movement Tactics. Current Biology, 30(17), 3444-3449.e4. https://doi.org/10.1016/j.cub.2020.06.032
    • Bonnot, N. C., Couriot, O., Berger, A., Cagnacci, F., Ciuti, S., De Groeve, J. E., Gehr, B., Heurich, M., Kjellander, P., Kröschel, M., Morellet, N., Sönnichsen, L., & Hewison, A. J. M. (2020). Fear of the dark? Contrasting impacts of humans versus lynx on diel activity of roe deer across Europe. Journal of Animal Ecology, 89(1), 132-145. https://doi.org/10.1111/1365-2656.13161
    • De Groeve, J., Cagnacci, F., Ranc, N., Bonnot, N. C., Gehr, B., Heurich, M., Hewison, A. J. M., Kroeschel, M., Linnell, J. D. C., Morellet, N., Mysterud, A., Sandfort, R., & Van De Weghe, N. (2020). Individual Movement - Sequence Analysis Method (IM-SAM): characterizing spatio-temporal patterns of animal habitat use across landscapes. International Journal of Geographical Information Science, 34(8), 1530-1551. https://doi.org/10.1080/13658816.2019.1594822

    2019

    • Peters, W., Hebblewhite, M., Mysterud, A., Eacker, D., Hewison, A. J. M., Linnell, J. D. C., Focardi, S., Urbano, F., De Groeve, J., Gehr, B., Heurich, M., Jarnemo, A., Kjellander, P., Kröschel, M., Morellet, N., Pedrotti, L., Reinecke, H., Sandfort, R., Sönnichsen, L., ... Cagnacci, F. (2019). Large herbivore migration plasticity along environmental gradients in Europe: life-history traits modulate forage effects. Oikos, 128(3), 416-429. https://doi.org/10.1111/oik.05588

    2018

    • Leontidou, K., Vernesi, C., De Groeve, J., Cristofolini, F., Vokou, D., & Cristofori, A. (2018). DNA metabarcoding of airborne pollen: new protocols for improved taxonomic identification of environmental samples. Aerobiologia, 34(1), 63-74. https://doi.org/10.1007/s10453-017-9497-z

    2016

    • De Groeve, J., Van de Weghe, N., Ranc, N., Neutens, T., Ometto, L., Rota-Stabelli, O., & Cagnacci, F. (2016). Extracting spatio-temporal patterns in animal trajectories: An ecological application of sequence analysis methods. Methods in Ecology and Evolution, 7(3), 369-379. https://doi.org/10.1111/2041-210X.12453

    2024

    2023

    • van Erp, J. A., De Groeve, J., van Loon, E., Shamoun-Baranes, J. & Bradarić, M. (23-10-2023). Data and script for "A framework for post-processing bird tracks from automated tracking radar systems". Universiteit van Amsterdam. https://doi.org/10.21942/uva.22567918.v1
    • Kalb, S., Rijsdijk, K., De Groeve, J., Denkers, L., van Loon, E. & Foufopoulos, J. (18-9-2023). Present day and paleo ecological distributions of reptiles in the Aegean and Ionian seas. Universiteit van Amsterdam. https://doi.org/10.21942/uva.23284868.v1
    • Kalb, S., Rijsdijk, K., Denkers, L. M., van Loon, E. E., Foufopoulos, J. & De Groeve, J. (18-9-2023). Reproduction Package Kalb et al. 2023. Universiteit van Amsterdam. https://doi.org/10.21942/uva.23284787.v3
    • De Groeve, J., Norder, S. & Rijsdijk, K. (8-5-2023). island reference dataset. Universiteit van Amsterdam. https://doi.org/10.21942/uva.22140113.v1
    • Haest, B., Hertner, F., Schmid, B., Preatoni, D., De Groeve, J. & Liechti, F. (2023). birdscanR: Migration Traffic Rate Calculation Package for Birdscan MR1 Radars. CRAN. https://doi.org/10.5281/zenodo.7665531
    • De Groeve, J., Salvatori, M., van Loon, E., De Baets , B., Morellet, N., Focardi, S., Griggio, M., Moorcroft, P., Bonnot, N. C., Gehr, B., Heurich, M., Kroeschel, M., Licoppe, A., Pedrotti, L., Signer, J., Van de Weghe, N. & Cagnacci, F. (2023). Data from: Day versus night use of forest by red and roe deer as determined by Corine Land Cover and Copernicus Tree Cover Density: assessing use of geographic layers in movement ecology. Zenodo. https://doi.org/10.5281/zenodo.7625970

    2022

    • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, A. C., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Spatial polygons for Sunda, Timor, and Caribbean regions.. Universiteit van Amsterdam. https://doi.org/10.21942/uva.17218724.v1
    • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, H., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Historic coastline age raster (AGE 2019). Universiteit van Amsterdam. https://doi.org/10.21942/uva.17215094.v1
    • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, H., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Resampled Bathymetry (GEBCO 2019). Universiteit van Amsterdam. https://doi.org/10.21942/uva.17218484.v1
    • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, A. C., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Shelf sea extent rasters (SLW140 2019). Universiteit van Amsterdam. https://doi.org/10.21942/uva.17216081.v1
    • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, A. C., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A. A. E., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Spatio-Temporal Relative Sea Level Curve (RSL). Universiteit van Amsterdam. https://doi.org/10.21942/uva.20029991.v1
    • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, A. C., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Shelf sea extent rasters (SLW140 2021). Universiteit van Amsterdam. https://doi.org/10.21942/uva.20029220.v1
    • De Groeve, J., Kusumoto, B., Koene, E., Kissling, W. D., Seijmonsbergen, A. C., Hoeksema, B. W., Yasuhara, M., Norder, S., Cahyarini, S., van der Geer, A., Meijer, H. J. M., Kubota, Y. & Rijsdijk, K. (12-7-2022). Historic coastline age raster (AGE 2021). Universiteit van Amsterdam. https://doi.org/10.21942/uva.20029304.v1
    • De Groeve, J. (10-6-2022). Untitled Item. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20051978.v1

    2020

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