Revision as of 09:34, 9 August 2013

In general you can use three options to search our data portal:

1. Browse Taxonomy 2. Search by Fields 3. Search by Citation

Browse Taxonomy

The GGBN/DNA Bank Network's data portal makes currently use of the Catalogue of Life (CoL) as its main taxonomic backbone. We match family and genus of original records provided by our partners with the CoL annual checklist (version 2009). Selecting "Browse Taxonomy" leads you to our Taxonomic Backbone site (figure below).

This site gives you an overview on how many samples and taxa are online available for certain higher taxa and genera (taxa and sample counts bracketed). By clicking on "Show DNA samples" you will be redirected to a query that gives you all records for selected taxon.

Furthermore you can click on the little plus icon to see the next level of taxa.

Search by Fields

The main query form for the data portal can be found at "Search & Preorder". Here you can choose a lot of criteria to filter your results. The upper part contains parameters related to the underlying voucher and collection event and the lower part contains facts about the DNA samples. If you select for example a certain DNA bank you can browse it's whole DNA and tissue collection.

The NCBI Taxonomy ID is often used by the microorganismic community. Right now search does not include synonyms, but will do in the future. Many records are provided with multiple determinations (their determination history). We index all determinations and you can search for all of them. Suggestion lists will help you when entering Family name or Species name.

Furthermore we filter collection year as well as Seas and Oceans out of the raw data. Seas/Oceans and Countries are matched with an existing list, so that also countries like "England" will be recognized as United Kingdom for instance.

We also index related Sequence Accession Numbers (BOLD and GenBank/EMBL/DDBJ) to be available for search.

Dependent parameters

Some parameters are related to each other, e.g. if you select a Continent or an Ocean, the list of Countries or Seas respectively will be reduced to those belonging to the selected Continent/Ocean. The same happens for Family name and Species name/Taxonomy ID. If you select a Family name, the list of suggested Species names and Taxonomy IDs is reduced to the relevant ones.

Getting results

After clicking on "Search" you will receive a hitlist with 50 records per page. The column heading contain small arrows. Clicking on such an arrow will arrange the results in the new order. The green arrow marks the current order (in the figure ordered by Species name from A to Z). The hitlist contains the species name, the country where the specimen/sample was collected, the DNA number as well as the specimen/voucher number. Clicking on the small magnifier or the species name will give you the record details.

Some samples doesn't have a DNA number. This means that DNA was not extracted yet but can be ordered on-demand.

Pre-order samples

Login is required for pre-ordering samples. When you are logged in you can select the required samples (checkboxes on the right) and click on "Add selected DNA/Tissue samples to shopping cart" on top right. Some samples are blocked for the ordering process and marked with a big red X.

Shopping Cart

After putting samples into the shopping cart on top of the website appears the message. Clicking on "Show details" will open you shopping cart and will guide you through the pre-ordering process.