posted this on August 07, 2012 05:22 pm
Finders are available to help facilitate selections and control vocabulary usage, thus improving result outputs. At times the potential list of selections can be quite extensive, and the finders help users make selections from large lists. Multiple selections can be made when utilizing finders during a query.
The organism finder is used to facilitate the selection of a species or virus from the NCBI Taxonomy Database. Common selections are displayed initially to speed the selection of the usual suspects, as seen in Figure 1. To view the entire NCBI taxonomy data set click NCBI Taxonomy Tree in the accordion slider. The Common Selection bar will move down to reveal the taxonomy tree.
Figure 1. Common selections in Organism finder
An Allergen tree has also been provided. The Allergen tree consists of species from the NCBI taxonomy, but is organized to help allergists locate common allergen selections more easily. To use the Allergen tree click the Allergen Tree heading in the accordion slider. The Allergen tree displays only nodes referenced by curated data. In addition, all nodes in the Allergen tree are selectable. Figure 2 shows the result of searching for "birch". Synonyms are incorporated into the nodes of the tree, so the common name of birch returns its corresponding scientific name of betula.
Figure 2. Searching for "birch" in the Allergen Tree results with finding "Betula" in the Organism Finder
The Organism finder will allow the user to find species using their name or taxonomy identifier (assigned by NCBI). When the user performs a search, the system will display the first match then allow the user to move forward and backward through the matching records using Next and Previous buttons as in Figure 3. When the user provides a name, any species name or synonym that contains the name provided will be considered a match. Search results will always appear in the NCBI Taxonomy tree, not the Allergen Tree or Common Selections.
The selections in the organism finder are displayed in a tree (Figure 3). The taxonomy identifier is displayed next to each node of the tree in square brackets. For example, the taxonomy identifier for the selection of Dengue Virus 2 in the example below is 11060. To see the synonyms for a selection, users can place their computer mouse over the scientific name.
Figure 3. NCBI Taxonomy Tree within the Organism Finder.