Step by step guide to GeoFRESH

Upload your data

This tutorial walks though the single steps of GeoFRESH using the test data set (random selection of fish occurrences, drawn from the Harmonised freshwater fish occurrence and abundance data for 12 federal states in Germany, downloaded from GBIF.

Point data coordinates need to be uploaded as a comma-separated table (.csv) with the three columns ID, latitude and longitude (column names are flexible). Latitude and longitude coordinates are required to be in the WGS84 coordinate reference system.

The points are instantly visualized on the map.

You can select different backround layers from the right-hand side, including the stream segment map. The uploaded table is also displayed and can be cross-checked and queried prior to the next steps.

Snap coordinates to the stream network

After the upload, the points need to be assigned to the corresponding sub-catchments and stream segments of the Hydrography90m dataset. This assignment, called “point snapping”, moves the point to the closest stream segment.

When the snapping is completed, the snapped points (yellow icons) are shown on the map. If you zoom in, you can observe that each point has been moved to the closest location of the stream segment within the sub-catchment the point falls into. This is the default option for snapping.

The new coordinates of the snapped points are also displayed in the table as additional columns.

Select environmental variables

Afterwards, you can annotate the point data with environmental information across the sub-catchment of each point. You can select from a suite of 48 variables related to topography and hydrography, 19 climate variables, (i.e., current bioclimatic variables), 15 soil variables and 22 land cover variables.

Extract local environmental information

Click on “Start query” on the bottom to initiate the computation. For each selected environmental variable, you will receive local, i.e., ., within-sub-catchment summary statistics (mean, minimum, maximum, range, standard deviation) for each point location as a table.

Extract upstream environmental information

Additionally, you can obtain the summary statistics (mean, min, max, sd) for the upstream catchment of each point for each of the selected environmental variables is calculated and displayed in a table. Again, click on “Start query”:

Finally, you can download the data as multiple comma-separated tables in a zip-file by clicking on ““Download ZIP”.

Plot data

After obtaining the local and / or upstream environemntal information, you can visualize the results in a histogram and box-plots (for categorical land-cover data). Move the slider to change the number of bins in the histogram:

After closing the browser window, all data is removed, meaning that no data is stored permanently on the platform.

References

GBIF.org (24 April 2023) GBIF Occurrence Download https://doi.org/10.15468/dl.xbuqe5

GeoFRESH in a nutshell

Freshwater water bodies are highly connected with each other and with their terrestrial catchments. In the light of climate and land use changes as well as feedback mechanisms between earth systems, the integration of earth system data into freshwater research is long-overdue to assess those interdependencies. However, freshwater-specific characteristics like spatial connectivity and fragmentation as well as legacy effects require a specialized workflow. Within the first pilot project “GeoFRESH: Getting freshwater spatio-temporal data on track”, the aim was to built a prototype for a new online platform, called GeoFRESH. The platform provides the integration, processing, management and visualization of various standardized spatiotemporal freshwater-related earth system data. The platform is built around IGBs GeoNode using RShiny and includes the newly created Hydrography90m dataset. The second pilot project “Connecting rivers and lakes FAIRly” we integrated lakes into GeoFRESH, currently based on the Hydrolakes dataset and planned to be replaced by the NASA SWOT data. The aim for the third pilot project “The seamless interoperability of geospatial freshwater tools” is an improved interoperability and user experience of the GeoFRESH platform, including interactive point snapping, an improved visualization, a connection to the hydrographr R-package, and the integration of dam / barriers.

Development team: Vanessa Bremerich, Yusdiel Torres-Cambas, Afroditi Grigoropoulou, Jaime R. Garcia Marquez, Sami Domisch, Thomas Tomiczek, Merret Buurman
Proposal team: Sami Domisch, Giuseppe Amatulli, Luc De Meester, Hans-Peter Grossart, Mark Gessner, Thomas Mehner, Vanessa Bremerich, Rita Adrian
Contact information: sami.domisch@igb-berlin.de
Bug reports and feature requests: https://github.com/glowabio/geofresh/issues

Project duration:
Pilot 1: 01.04.2022 - 31.03.2023
Pilot 2: 01.10.2023 - 30.09.2024
Pilot 3: 01.03.2025 - 28.02.2026

Project funding: NFDI4Earth (DFG)

This work has been funded by the German Research Foundation (DFG) through the project NFDI4Earth (TA1 M1.1, DFG project no. 460036893, https://www.nfdi4earth.de/) within the German National Research Data Infrastructure (NFDI, https://www.nfdi.de/).

Citation

Please cite the GeoFRESH platform as follows:

Domisch, S., Bremerich, V., Buurman, M., Kaminke, B., Tomiczek, T., Torres-Cambas, Y., Grigoropoulou, A., Garcia Marquez, J. R., Amatulli, G., Grossart, H. P., Gessner, M. O., Mehner, T., Adrian, R. & De Meester, L. (2024). GeoFRESH – an online platform for freshwater geospatial data processing. International Journal of Digital Earth, 17(1). https://doi.org/10.1080/17538947.2024.2391033

In addition, GeoFRESH relies on a number of external data sources regarding the environmental data and we ask you to please use the following citations depending on your analysis:

Topography (Hydrography90m)
Amatulli, G., Marquez, J.G., Sethi, T., Kiesel, J., Grigoropoulou, A., Ublacker, M. M., Shen, L. Q., & Domisch, S. (2022). Hydrography90m: a new high-resolution global hydrographic dataset. Earth System Science Data, 14(10), 4525-4550. https://doi.org/10.5194/essd-14-4525-2022

Climate (CHELSA v2.1)
Karger, D.N., Conrad, O., Böhner, J., Kawohl, T., Kreft, H., Soria-Auza, R.W., Zimmermann, N.E., Linder, P., Kessler, M. (2017): Climatologies at high resolution for the Earth land surface areas. Scientific Data, 4 170122. https://doi.org/10.1038/sdata.2017.122
Karger, D.N., Conrad, O., Böhner, J., Kawohl, T., Kreft, H., Soria-Auza, R.W., Zimmermann, N.E., Linder, H.P. & Kessler, M. (2021) Climatologies at high resolution for the earth’s land surface areas. EnviDat. https://doi.org/10.16904/envidat.228.v2.1

Soil (SoilGrids250m)
Hengl, T., Mendes de Jesus, J., Heuvelink, G.B.M., Ruiperez Gonzalez, M., Kilibarda, M., Blagotić, A., Shangguan, W., Wright, M.N., Geng, X., Bauer-Marschallinger, B., Guevara, M.A., Vargas, R., MacMillan, R.A., Batjes, N.H., Leenaars, J.G.B., Ribeiro, E., Wheeler, I., Mantel, S., & Kempen, B. (2017). SoilGrids250m: Global gridded soil information based on machine learning. PLOS ONE, 12(2), e0169748. https://doi.org/10.1371/journal.pone.0169748

Landcover (ESA CCI LC)
ESA. Land Cover CCI Product User Guide Version 2. Tech. Rep. (2017). Available at: http://maps.elie.ucl.ac.be/CCI/viewer/download/ESACCI-LC-Ph2-PUGv2_2.0.pdf

Lakes (HydroLAKES v1.0)
Messager, M.L., Lehner, B., Grill, G., Nedeva, I., Schmitt, O. (2016). Estimating the volume and age of water stored in global lakes using a geo-statistical approach. Nature Communications, 7: 13603. https://doi.org/10.1038/ncomms13603

NFDI4Earth

NFDI4Earth addresses digital needs of Earth System Sciences. Earth System scientists cooperate in international and interdisciplinary networks with the overarching aim to understand the functioning and interactions within the Earth system and address the multiple challenges of global change. NFDI4Earth is a community-driven process providing researchers with FAIR, coherent, and open access to all relevant Earth System data, to innovative research data management and data science methods.

GeoFRESH was initiated as part of the first cohort of 1-year pilot projects: in a first round in 2020, 14 pilots out of 38 were selected and started in April 2022.