Organism Scope is a general term for an organism condition or qualifier that can be at any taxonomic level, from order, through family, genus, species, right down to serotype, but can also be non-taxonomic, e.g. Coagulase-Negative Staphylococcus.
Multiple entities in the system require an organism scope binding to determine to what organisms they should apply, including:
- Breakpoints
- Test Patterns
- Organism Alerts
This article describes the process of selecting an organism scope using a common form page that appears in all add/edit forms for entities (such as the above) that require an organism scope. This page is shown below:
A taxonomic organism scope can be selected starting with Order (the top field on the above page), if the scope is higher than genus, or Genus (the second field on the page), if it's genus or lower in the hierarchy. Once you select the first field, in each case, subsequent fields will appear, reduced in options based on your previous select. For example, if you select Enterobacterales as the Order in the top field, a Family field will appear with options scoped only to Enterobacterales. Similarly, if you select Salmonella from the second field, a Species field will appear, with options scoped only to Salmonella. If the scope you have already selected is what you need it to be, you are finished and can selection Next. However, as you select from each subsequent field, the next down in the taxonomic hierarchy will appear, scoped to your previous selection. For example, if selecting Enterica as the Species under a Genus of Salmonella, a Sub-Species field will appear with options relevant only to Salmonella enterica.
Alternatively, if the organism scope you need is non-taxonomic, use the Organism Group field to select from the available non-taxonomic organism groups already set up in your system.
Finally, if your organism scope is an organism (so a genus or lower) and you simply wish to find it with a text search, click on the Full Organism Search button and follow the menus to enter your organism name and select from the matched list.