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BioDT / uc-CWR

The code base for the Crop-Wild-Relative (CWR) use-case led by UiO
MIT License
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Mobilising more biodiversity data #7

Open ErikKusch opened 5 months ago

ErikKusch commented 5 months ago

Originally an issue in the hackathon repo. Copied here so the other repo can be deleted. Thoughts pasted below were provided by @DesalegnChala and @ICARDAFIGS

ErikKusch commented 5 months ago

What additional data sources can we use for occurrence data? can you please mention them and also if there any function to access them. Additional layers such as protected areas of the world and any function to easily access them.

potential data sources - notes from discussions

Genesys – the accessions in situ – GBIF is more curated – data should be filtered Weighing the data – Filtering by date WIEWS Herbaria – open herbarium – an open data base where major herbaria are digitized and data are made available Symbiota – https://symbiota.org/ The botanical gardens conservation database - can potentially be ex situ conservation - need caution Protected planet.

abiotic stresses

Aridity, Soil Ph, Soil salinity from harmonized data sources

ErikKusch commented 5 months ago

Could we add the websites for these sources and see if scripts exists for pulling data from there by genus?

This the code we have used: install.packages("genesysr") library(genesysr) user_login() musa <- get_accessions(filters = list(taxonomy = list(genus = c('Musa'))), at.least = 1000) lath <- get_accessions(filters = list(taxonomy = list(genus = c('Lathyrus'))))

one needs of course to register first on https://www.genesys-pgr.org/registration as this info is used by user_login() at R. Data is updated yearly by international CGIAR genebanks. Not sure about the other genebanks.