How to collect information on the isolation sources of a collection of different types of bacteria?
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How to get basic isolation source information from ncbi assembly accession
esearch -query [accession] -db assembly | elink -target biosample | esummary | xtract -pattern DocumentSummary -first Title -element Accession -group Attribute -if Attribute@harmonized_name -equals "isolation_source" -element Attribute
You can call this from an Rscript using system()
