mariyad/openbiodiving: Linking the Open Biodiversity Knowledge Management System With BOLD Systems to Retrieve Specimen Voucher Metadata

Uses the packages ropenbio and rdf4r to generate Turtle files from xmls. Identifiers from BOLD Systems like BINs, record ids, process ids, etc. are found within the xml (if present) and added to the article-meta section.A Curl request to BOLD Systems is made and additional information about each id is retrieved. Metadata includes fields like catalog number, holding institution, nucleotide sequence, etc. for each voucher. The generated Turtle file is enhanced with triples describing the metadata retrieved from BOLD. There is an option to upload the triples to a GraphDB repo.

install.packages("remotes")
remotes::install_github("mariyad/openbiodiving")