Standards used for data and metadata format and content

While several metadata standards are applicable to different project data types, recent studies1, 2 recommend the use of the Genomic Standards Consortium’s (GSC) ‘Minimum information about a marker gene sequence’ MIMARKS, Minimum Information about any (x) Sequence (MIxS - metadata template applicable to sequence data) and Darwin Core metadata standards. In addition to the minimum information checklists, MIxS includes environmental packages. We used these checklists and environmental packages for documenting markers, sequences, and field collection sites. MIMARKS incorporates standards being developed by the Consortium for the Barcode of Life (CBOL), thus the checklist can be universally applied to any marker gene, from small subunit rRNA to cytochrome oxidase I (COI), to all taxa, and to studies ranging from single individuals to complex communities. The metadata for field collection sites includes a unique identifier, a GPS designated location, and a qualitative habitat characterization. Metadata for each field collection includes date and time, collector, processing steps that include filters applied, primers applied, and documentation of controls. Environmental contextual data for each sample obtained at the time of sample collection can include measurements on water temperature, pH, dissolved oxygen, turbidity, and salinity, with possible additional variables as pertinent to the specific project. Detailed procedures and methodological approaches, deviations from protocols, specific equipment, and chemical reagents utilized for this project are documented.

More about the Genomic Standards Consortium (GSC)

1Tedersoo, L., Ramirez, K. S., Nilsson, R. H., Kaljuvee, A., Kõljalg, U., & Abarenkov, K. (2015). Standardizing metadata and taxonomic identification in metabarcoding studies. GigaScience, 4(1), 34.

2Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J. R., Amaral-Zettler, L., Gilbert, J. A., Karsch-Mizrachi, I., Johnston, A., Cochrane, G., Vaughan, R., Hunter, C., Park, J., Morrison, N., Rocca-Serra, P., Sterk, P., Arumugam, M., Bailey, M., Baumgartner, L., … Glöckner, F. O. (2011). Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology, 29(5), 415–420.