OBIS sequence data

[humbleflowers]

Hello @pieterprovoost

Is there a way i can download underlying nucleotide fasta database from OBIS to do analysis?

Thank you.

[pieterprovoost]

@humbleflowers This can be done using the robis R package, but it can be fairly slow to get the entire database. Let me know if you would like to have a full export.

This is an example for just the most recent data (2022 onwards):

library(robis)

occ <- occurrence(hasextensions = "DNADerivedData", extensions = "DNADerivedData", startdate = "2022-01-01")
dna <- unnest_extension(occ, "DNADerivedData", fields = c("scientificName", "decimalLongitude", "decimalLatitude", "eventDate", "datasetName", "materialSampleID"))

[humbleflowers]

Hello @pieterprovoost , Thanks for the reply. I would like to have a full export. Do you have FTP? and Any idea how big will be the FASTA file?

Thank you.

[humbleflowers]

@pieterprovoost , i got the files i needed through R commands. Thank you.