3D Macromolecular Structures
 
 
 
 
How to retrieve all structures from a particular source organism or taxon
 
 

The source organism of each 3D structure is noted in its database record, and is linked to the organism's taxonomic lineage in the NCBI Taxonomy database. It is therefore possible to retrieve 3D structure records for a specific organism, or for all organisms that fall within a taxonomic node, in the following ways:

 
  Method 1:   Start on the Entrez Structure page:
  • Open the Limits folder tab, select the Organism search field, enter the common (e.g., sheep) or scientific (e.g., Ovis aries) name of the organism, or the name of the taxonomic node of interest (e.g., Bovidae), in the search box and press "Go".


  • OR, simply enter your term and the search field specifier in the format: term[field] directly into the query box on the Entrez Structure page, without using the Limits folder tab. For example, any one of the following searches will work: sheep[Organism] or Ovis aries[Organism] or bovidae[Organism].
 
 
  Method 2:   Start on the NCBI Taxonomy Database page:
  • Enter the common (e.g., sheep) or scientific (e.g., Ovis aries) name of the organism, or the name of the taxonomic node of interest (e.g., Bovidae), in the search box and press "Go"


  • Click on the search result of interest to view it in the Taxonomy Browser, which shows the organism or taxon's lineage as well as taxonomic nodes that fall under it, if any.


  • Click on the organism or taxon name in that view to open a page that summarizes the data available for that organism/taxon. In the "Entrez Records" summary table, click on the number of structure records shown in the "Subtree Links" column to retrieve the 3D structure records for that taxon and all nodes that fall under it. (The "Direct Links" column will only retrieve the subset of records which list that exact taxonomic node as the source organism, and will not retrieve data from lower taxonomic nodes. For example, the "Direct Links" column of the Bovidae summary table shows 38 direct links (as of 14 July 2009) to nucleotide sequence records that list "Bovidae" as the source organism, whereas the "Subtree Links" column retrieves those 38 records plus any records that have Bovidae as part of their taxonomic lineage.)
 
 
 
 
Revised 05 February 2015