Abstract
Molecular identification methods, such as DNA barcoding, rely on centralized databases populated with morphologically identified individuals and their referential nucleotide sequence records. As molecular identification approaches have expanded in use to fields such as food fraud, environmental surveys, and border surveillance, there is a need for diverse international data sets. Although central data repositories, like the Barcode of Life Datasystems (BOLD), provided workarounds for formatting data for upload, these workarounds can be taxing on researchers with few resources and limited funding. To address these concerns, we present the Molecular Data Organization for Publication (MDOP) R package to assist researchers in uploading data to public databases. To illustrate the use of these scripts, we use the BOLD system as an example. The main intent of this writing is to assist in the movement of data, from academic, governmental, and other institutional computer systems, to public locations. The movement of these data can then better contribute to the global DNA barcoding initiative and other global molecular data efforts.
Highlights
The use of molecular identification techniques on biological samples has been in practice for some time and includes methods like restriction fragment length polymorphisms (Magee et al 1987), denaturing gradient gel electrophoresis (Muyzer et al 1995), temperature gradient gel electrophoresis (Ogier et al 2002), and analytical methods using molecular DNA sequence data (Bartlett and Davidson 1992)
Technological advancements in DNA sequencing have reduced the cost, and by extension, increased the accessibility of obtaining nucleotide sequences from biological samples. Such advancements have led to an increase in the production of molecular sequence data resulting in the establishment and maintenance of large data repositories to house and share these data
We present the package Molecular Data Organization for Publication (MDOP) (R Ver. 3.5.1; R Core Team 2018) to assist users in the standardization and upload of molecular sequence data and associated metadata files to centralized data repositories
Summary
The use of molecular identification techniques on biological samples has been in practice for some time and includes methods like restriction fragment length polymorphisms (Magee et al 1987), denaturing gradient gel electrophoresis (Muyzer et al 1995), temperature gradient gel electrophoresis (Ogier et al 2002), and analytical methods using molecular DNA sequence data (Bartlett and Davidson 1992). We present the package Molecular Data Organization for Publication (MDOP) (R Ver. 3.5.1; R Core Team 2018) to assist users in the standardization and upload of molecular sequence data and associated metadata files to centralized data repositories.
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