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The Opportunistic Database of Databases (ODD) for Biodiversity and Global Change
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The worksheets here represent opportunistically-collated sources for:
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* Biodiversity data (specimens, observations, etc.)
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* Georeferencing resources
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* Taxonomic name resolution
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* Useful R packages related to biogeography, macroecology, spatial analysis, etc.
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* And others (in progress... including environmental data)
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Given that they are opportunistic, they do not represent an attempt to be thorough, complete, or even precisely accurate. Rather, they represent a useful tool we wanted to share with others. If you have additions, corrections, or comments, please contact us. The database is available as a Google Sheet linked from www.earthSkySea.org. To ensure integrity, the sheets are locked except for comments. The easiest way to work with the database is probably to download it (File --> Download...) and work with it locally.
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The Biodiversity Information Projects of the World project has a much larger list of biodiversity portals, although it ceased to be updated around 2015 and ~50% of its projects now have inactive links. Please see:
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http://old.tdwg.org/biodiv-projects/
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https://doi.org/10.3897/BDJ.8.e32765
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Last update to any sheet:
2021-10-19
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Database maintainers:
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Adam B. Smith, PhD
Anna Willoughby, PhD Student
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Associate Scientist in Global Change Conservation
Odum School of Ecology
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Missouri Botanical Garden, Saint Louis MO 63110 USA
University of Georgia, Athens GA 30602
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adam.smith@mobot.org
anna.willoughby@uga.edu
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www.earthSkySea.org
https://www.ecology.uga.edu/directory/anna-willoughby/
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+01 1-314-577-9473 extension 76314
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The ODD FAQ
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How do I find data on XYZ?
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For specimen data, we recommend looking at the GBIF database first since it's intended to be the global meta-repository of all specimen data. Nonetheless, not all biodiversity data is on GBIF, and records that are served to GBIF from other databases do not necessarily contain all of the information available in the original database. Thus, it's often necessary to look at the primary databases where the original data is stored. If you download the DarwinCore format of data from GBIF you can find columns in that which will help you track down the primary databases.
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How do I download data from XYZ?
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Every database is different--if given the option, though, we recommend downloading the fullest version of the data that is available. This said, it's worth checking out our recomendations for downloading data from GBIF (and maybe any other portal using DarwinCore) and iDigBio.
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http://www.earthskysea.org/working-with-gbif-data/
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http://www.earthskysea.org/working-with-idigbio-data/
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What other databases do you recommend?
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It really depends on what you are looking for and where the taxa in which you're interested reside. For specimen/observational data, other than suggesting GBIF as a "starting" place, we've decided not to strongly recommend specific databases. However, here are a few suggestions based on our experience, which is limited to the taxa on which we have conducted research.
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Marine species: OBIS
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New World plants: BIEN
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North American birds: eBird (also available on GBIF)
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North American anything: BISON
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What R packges do I need?
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Assuming you want to do biogeographic analyses, the most basic R packages you need are:
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raster (or terra, the updated version of raster--still in development as of April 2020)
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sp or sf (to deal with shapefiles and similar polygon/line/point data)
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dismo (for species distribution modeling)
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geosphere (useful calculations for spatial things on globes)
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rgeos (useful operations for spatial polygon/line/point data)
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