0100-simple-quick-start.en.adoc

Simple Quick Start Guide

A Simple Quick Start Guide with minimal explanation.

Important

This guide assumes that you are using the MDT Sandbox (Demo Installation). Please note that datasets in this environment are deleted weekly; therefore, avoid uploading important data without a backup.

This guide uses a minimal dummy dataset – not to be used as a model for real data. The dataset is based on template 1

1. Download Example Dataset 1.

2. (Optional) Explore the structure of the example data in e.g. Microsoft Excel.

   • The Excel Workbook has four sheets: OTU_table, Taxonomy, Samples and Study.

     • OTU_table is the OTU table, with sample IDs as column headers, OTU IDs as row names, and sequence read counts in the cells.

     • Taxonomy links OTU IDs (from OTU_table) to sequence and taxonomic info.

     • Samples links sample IDs (from OTU_table) to sample metadata: e.g. spatiotemporal information, protocols etc.

     • Study holds global values for the dataset, such as barcoding region, primer sequences, and primer names.

Upload data (step 1)

1. Go to MDT Sandbox (Demo Installation) and log in.

2. Press New Dataset in the upper part of the page to go to the first step (Upload data).

3. Drag and drop the dataset OR click and select on your computer.

4. Give it a nickname – e.g. "my_first_test".

5. Press Start Upload.

6. Press Proceed

Map terms (step 2)

The user specifies and verifies how field names of uploaded data (second and third column on the page) correspond to standardized terms (first column on the page).

Note	Example dataset 1 uses standard terms (Darwin Core terms) as field names, and no manual mapping required.

Tip	How to use this form for a guided tour.

Figure 1. The first section (Sample) concerns the mapping of metadata associated with samples. The MDT has automatically mapped four fields from the uploaded Samples table and five fields from the Study table to their identically named Darwin Core counterparts, e.g. the field with sampling dates in the samples table is called eventDate in the uploaded data corresponding exactly (spelling) to the Darwin Core term term:dwc[eventDate], and the field with the term pcr_primer_forward in the Study table is identical to the term term:mixs[pcr_primer_forward].

Figure 2. The second section (Taxon) concerns the mapping of metadata associated with the OTUs, i.e. taxonomy and sequence related information. Similar to above, the MDT has automatically mapped all fields from the uploaded Taxonomy table to identically named Darwin Core terms.

Press Proceed to save mapping and proceed.

Process data (step 3)

1. Press Process data.

Note	Assign taxonomy uses the GBIF Sequence ID tool to assign taxonomy to the sequences. This overwrites any taxonomy provided. We will not use that option here.

Figure 3. Pressing Process data generates standardized intermediate files (in BIOM format) and some data stats/metrics.

2. Press Proceed

Review (step 4)

At this step, data is reviewed to ensure that everything looks OK.

Figure 4. Review and verify that the data looks as expected. E.g.: Check the geolocation in the map (here: northern part on Denmark); Check taxonomic composition in the barcharts; Check ordination plots (PCoA/MDS) for outliers (e.g. control samples not excluded); Select single samples from map, charts or dropdown to explore metadata and taxonomic multilevel piecharts in the panel to the right.

Press Proceed.

Add metadata (step 5)

At this step, information on the dataset is provided.

Figure 5. Dataset information – Notice how the left panel offers several sections of dataset information/metadata. NB: For real datasets it is important to provide rich and meaningful data at this step.

1. Add a title to replace nickname – e.g. “my first simple test dataset”.

2. Select a licence.

3. Add contact information - minimum: email.

4. Leave the other fields empty (as this is just a test).

5. Press Proceed to save the metadata and proceed.

Export (step 6)

At this step, a [dwc-a] file is produced, which can be published to GBIF. In the MDT Sandbox (Demo Installation), the archive can (only!) be published to the GBIF test environment (UAT) for users to preview a potential GBIF.org publication.

1. Press Create Darwin Core Archive.to generate a [dwc-a].

2. Press Publish to GBIF test environment (UAT).

Figure 6. Pressing Create Darwin Core Archive generates a [dwc-a] from the data through several steps – each marked with a green check as successful. Publish to GBIF test environment (UAT) registers ("publishes") the dataset in the GBIF test environment. NB: A notification indicates that it may take a few minutes before the indexing is complete. A link to the "preview" appears next to the Publish button.

3. Click on the hyperlink Dataset at gbif-uat.org.

Figure 7. Pressing Dataset at gbif-uat.org opens the dataset in the GBIF test environment (UAT) where users can see what a real publication would look like and verify that the processed dataset (<dwc-a>) contains all the wanted information for real publication. NB: The dataset is not completely indexed immediately and the dataset may e.g. have 0 occurences and no map compared to this figure, until fully indexed. Notice how the hatched/shaded header and the red "TEST" label indicate that this is a test environment. Explore the dataset and notice how the uploaded data and dataset information/description is presented on the website.

4. Go back to the MDT.

5. Press on Publish (directly in the header with the 7 steps).

Publish (step 7)

You should now have a basic idea of how the MDT works.

If using this quick start guide as suggested, you will be using the MDT Sandbox (Demo Installation). The publishing step (step 7) is not enabled for the this MDT, and step 7 will appear as in the figure below. Read about the publishing step in the [detailed_guidance].

Figure 8. The Publish step is not enabled for the MDT Sandbox (Demo Installation). If you by chance prepared a real dataset using the MDT Sandbox (Demo Installation), it is recommended to redo the processing in a proper MDT installation, unless this would for some reason be too problematic. In that case you can use the link on the page: "Ready to publish a dataset? Reach out to the administrator for assistance".