Difference between revisions of "GGBN Data Portal Explanations"
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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. | 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. | ||
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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. | 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. | We also index related Sequence Accession Numbers (BOLD and GenBank/EMBL/DDBJ) to be available for search. | ||
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| + | 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. | ||
[[File:Queryform.JPG|500px]] | [[File:Queryform.JPG|500px]] | ||
Revision as of 12:59, 8 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.
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.
