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Example datasets

Example dataset 1: ITS fungi – fictional minimal dataset

A simple dataset is used in the [simple_quick_start]. It is based on template 1 (Excel workbook with four sheets).

Download file(s): example_dataset_1.

Comments

  • A very minimal dataset to exemplify the overall structure of such datasets.

  • For real datasets, we recommend to get inspiration from some of the richer datasets.

  • See more detail the walk-through here: [simple_quick_start]

Example dataset 2: COI marine water – a richly formatted dataset

A real dataset with COI metabarcoding of DNA extracted from sea water. The dataset has rich metadata and is a good example of a well-documented dataset. This example version has been modified slightly from the original dataset. It is based on template 1.

Download file(s): Example Dataset 2.

Comments

  • The OTU_table file 159 samples and 24.744 OTUs.

  • The Samples file includes links to the corresponding "GenBank" (SRA) sequence and sample records in fields that already carry DwC term names: term:dwc[associatedSequences], term:dwc[materialSampleID].

  • Several fields carry names not corresponding to DwC terms and need manual mapping during processing: Sample_Name, Latitude, Longitude, temperature, salinity, sequence, lsid, rank.

    • As the current dataset was formatted for indexing by OBIS, the dataset follows the recommendations from the DNA guide and includes the scientific name ID of the detected taxa as per the WoRMS database in the field lsid. During processing the lsid field should be mapped to term:dwc[scientificNameID] (or renamed in the file before upload). Likewise NCBI taxon IDs are given in the field taxonConceptID (which will be automatically mapped to term:dwc[taxonConceptID]).

  • The Study file includes 29 terms with global values, adding to the richness of the dataset.

  • Also take a look at the dataset description, etc of the published dataset for inspiration on which information can be added in the "Add metadata step".

  • NB: This modified version has 93.908 occurrences (compare to the original datasets 160.114)