THE GBIF DATABASE [download]
The GBIF database is presented by its developers as “an international open data infrastructure, funded by governments that allows anyone, anywhere to access data about all types of life on Earth, shared across national boundaries via the Internet. By encouraging and helping institutions to publish data according to common standards, GBIF enables research not possible before, and informs better decisions to conserve and sustainably use the biological resources of the planet.” (source). The idea of developing a free database centralizing all the biodiversity information available around the globe emerged almost 20 years ago. After years of development and data acquisition, collation and formatting, the database now contains more than 920 million georeferenced records (July 2018, mainly of animals (716 millions) and plants (182 millions) distributed across all terrestrial and oceanic realms around the world. The earliest georeferenced presence records in the database goes back to the beginning of the 17th century, but the vast majority of the records (>811 million, >98% of the total database) were retrieved after 1950 with the beginning of a strong diversification and exponential increase during the 70s-80s. The database is still regularly updated with new records.
Screenshot of all the presence records (all taxa) stored in the GBIF database (02/08/2018).
Of particular interest to palaeoclimatology, GBIF contains the distributions of a large number of the commonly used palaeo-indicators, such as pollen-producing plants (conifers and flowering plants are represented by 413 families, 11,585 genera and 220,605 species [1-5]), beetles (245 families, 13,111 genera and 71,082 species [6]), foraminifera (329 families, 1,657 genera and 9,158 species [7]), diatoms (102 families, 537 genera and 6,501 species [8]) and, to a lesser degree, chironimidae (334 genus and 1,896 species [9-10]).
Spatial distribution of the number of georeferenced records stored in GBIF for five common palaeo-indicators
(A: spermatophytes (plants producing pollen), B: beetles, C: Foraminifers, D: Chironomids and E: Diatoms).
The coordinates of all the records have been upscaled at a 2° resolution for graphical purposes.
All these data have been stored in one unique relational database. Two distribution tables coexist in the database: one with the original coordinates as reported in the GBIF database (DISTRIB), and another one with the same data points but homogenised at a quarter-degree grid cell resolution (DISTRIB_QDGC). Only one data point per grid cell has been retained. This database also contains the 19 bioclimatic variables of the Worldclim 2 database [11] as well as the annual aridity index [12] for the terrestrial realm (WC_QDGC). Elevation information has also been included in the database (ELEV_QDGC, [13]). All these variables have been extracted at the same spatial resolution. The list of variables can and will be expanded in the future, especially in regards to the marine realm (e.g. sea-surface temperatures and salinities) based on users’ specific needs and requests. To facilitate the reduction of the database to specific regions, all the grid cells have been assigned to a country and a continent (GEO_QDGC).
DOWNLOAD
The CREST-formatted GBIF database comes in as a SQLite3 format. This format was preferred because SQLite3 files are stand alone, portable databases and, as a consequence, are easier to use for non-experts. Many database viewers exist (e.g. SQLite Browser). SQLite3 databases can also be accessed and queried directly from R (RSQLite package) and python (sqlite3 library, native in the latest versions of python).
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PS: A PostGreSQL dump can be provided upon request.
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If you are using this dataset, please cite the following paper and dataset references.
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Chevalier, M., 2019. Enabling possibilities to quantify past climate from fossil assemblages at a global scale. Glob. Planet. Change 175, 27–35. DOI: 10.1016/j.gloplacha.2019.01.016
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Chevalier, M., GBIF for CREST database v1.1.0. DOI: 10.6084/m9.figshare.6743207
[1] GBIF.org, 2018a. Gnetopsidae occurrence data downloaded on March 30th, 2018. doi:10.15468/dl.prwbxf
[2] GBIF.org, 2018b. Gingkoopsidae occurrence data downloaded on March 30th, 2018. doi:10.15468/dl.mvduln
[3] GBIF.org, 2018c. Pinopsidae occurrence data downloaded on March 30th, 2018. doi:10.15468/dl.rldwzj
[4] GBIF.org, 2018d. Magnoliopsida occurrence data downloaded on March 30th, 2018. doi:10.15468/dl.wamwmk
[5] GBIF.org, 2018e. Cycadopsidae occurrence data downloaded on March 30th, 2018. doi:10.15468/dl.lnzrov
[6] GBIF.org, 2018f. Beetles occurrence data downloaded on March 30th, 2018. doi:10.15468/dl.dsxp44
[7] GBIF.org, 2018g. Foraminifera occurrence data downloaded on March 30th, 2018. doi:10.15468/dl.jt5rea
[8] GBIF.org, 2018h. Diatoms occurrence data downloaded on March 30th, 2018. doi:10.15468/dl.d5iodp
[9] GBIF.org, 2018i. Chironomids occurrence data downloaded on March 30th, 2018. doi:10.15468/dl.8h2ymo
[10] Catalogue of Life, 2016. The Catalogue of Life Partnership. Checklist Dataset http://doi.org/10.15468/rffz4x accessed via GBIF.org on 2017-05-05.
[11] Fick, S.E., Hijmans, R.J., 2017. WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315. doi:10.1002/joc.5086
[12] Trabucco, A., Zomer, R.J., 2009. Global Aridity Index (Global-Aridity) and Global Potential Evapo-Transpiration (Global-PET) Geospatial Database. CGIAR.
Consortium for Spatial Information. Published online, available from the CGIAR-CSI GeoPortal at http://www.cgiar-csi.org/.
[13] Amante, C., Eakins, B.W., 2009. Etopo1 1 Arc-Minute Global Relief Model: Procedures, Data Sources and Analysis. NOAA Tech. Memo. NESDIS NGDC-24. Natl.
Geophys. Data Center, NOAA. doi:10.7289/V5C8276M
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