| output | ||||
|---|---|---|---|---|
|
Authors: Kateřina Tschernosterová, Eva Trávníčková, Florencia Grattarola, Clara Rosse, Petr Keil
Contact email: keil@fzp.czu.cz
SPARSE is under CC-BY license (https://creativecommons.org/about/cclicenses/). Users of the Czech bird data in this database should cite the original publications (studies) in which the inventories were first published. A BibTeX file with all the references is in this folder, and can be loaded to common reference managers such as Zotero or JabRef. Users of the SPARSE framework, or those who modify it, should cite Keil et al. (2022) paper in Biodiversity Data Journal.
Folders:
/code- scripts that we use to process the data/code/shapefile_linking- linking shapefiles with database queries/code/study_selection_algorithm- selecting priority studies for digitization/code/taxon harmonization- processing and harmonizing taxonomy/CZ_border_shapefile- shapefile of Czech borders - for plotting purposes/SPARSE_shapefiles- shapefiles of the points, lines, and polygons representing surveyed sites
Files:
/INPUT_data-template-empty- empty .xlsx template that we used during the first step of data digitization. These .xlsx files were then imported to MS Access/INPUT_data-example*- example study (.pdf) and pre-filled template (.xlsx) corresponding to the study/SPARSE.accdb- the main MS Access file with the four core tables/SPARSE_bibliography.bib- BibTeX bibliography with all the digitized studies/SPARSE_definitions.xlsx- detailed descriptions of all fields in the main MC Access file
Hi. This is SPARSE database. It stores data on species composition of sites in space and through time, where multiple species had been recorded during the surveys. Thus, SPARSE does not contain presence-only point observations such as those stored in e.g. GBIF. Examples of data stored in SPARSE are reserve inventories, point surveys, transects, commercial surveys prior to construction activities, checklists and redlists in administrative units such as counties, states, or countries. SPARSE is currently implemented in MS Access, with additional GIS data stored in ESRI shapefiles, and with the original raw data provided as .pdf and .xlsx files.
Full descriptions and details are provided in the Biodiversity Data Journal manuscript.
- To create infrastructure for management of "inventory" data in our research group, with emphasis on temporal change and data heterogeneity.
- The database should have simple structure, so that others can use it or copy it, without a detailed knowledge of databases or spatial data.
- The database structure should work for different groups of organisms, and in different regions of the world.
- For our group, to learn basics of biodiversity databases, standards, and spatial data management.
- To actually have the data for selected groups and regions. The first priority is to digitize data on Central European Birds, so that they can complement other data that we have for this taxon and region.
- To create a backbone for a bigger database of heterogeneous biodiversity data covering Europe, United States, and potentially other regions.
- It is open, free, and simple.
- It is spatially explicit, and can accommodate complex spatial structures and multiple scales, including complex nested sampling designs where multiple sites within a larger area have been surveyed, and this larger area can again be nested in an even larger region.
- It works well with data on temporal change, i.e. with repeated sampling events at a single site.
- It explicitly considers variation in sampling methods and effort, it should work for different regions and taxa.
- It uses a combination of Humboldt core and Darwin core standards.
The very first idea was originally conceived in August 2020, at iDiv, Leipzig, by Petr Keil, and first attempts for implementation were done together with Clara Rosse, with the backing of Jonathan M. Chase. In the fall of 2021, a brand new effort had started at the Department of Spatial Sciences at Czech University of Life Sciences in Prague, where Petr Keil relocated to start his tenure-track position. During summer and fall 2021 we have (with Eva Trávníčková, Kateřina Tschernosterová, and Flo Grattarola) designed a new structure from scratch, matched it with Darwin Core and Humboldt core standards, and implemented it in MS Access.
If you have MS Windows and MS Access
The primary way to open SPARSE is on a MS Windows machine with MS Access installed. We have created SPARSE on MS Access version 2309, so this is the version on which everything works (double checked by several users).
If you have MS Windows but not MS Access
It should be possible to open SPARSE in free LibreOffice BASE. Fire up the program, choose connect to database and choose MS Access.
If you have Ubuntu Linux
You can list and extract individual tables from SPARSE.accdb (tested on Ubuntu 20.04 LTS).
-
install the mdbtools package:
sudo apt install mdbtools -
list all tables in SPARSE:
mdb-tables SPARSE.accdb -
export any table to .csv, for example the 1_DATASET table:
mdb-export SPARSE.accdb 1_DATASET > 1_DATASET.csv
If you have a Mac with no MS Access
We haven't tested this option yet.
SPARSE has been supported by funding from Research Excellence in Evnironmental Sciences (REES) provided by Czech University of Life Sciences. SPARSE has also received funing from the European Union (ERC, BEAST, 101044740). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.