Aperio Scanning Request - Entering Taxonomic Strings
Some types of scanning requests will require you to enter taxonomic information for each slide you are submitting.
Requests That Require Taxonomy Information
Any slide scanned into the Residency Education folder must be appended with a taxonomic string. This includes:
- Surgical Pathology Unknowns
- CK Chang
- Curriculum Boxes
- Specific courses (e.g. interesting liver cases)
Entering Taxonomy Information
Before you can enter any taxonomy information, you need to have set the form to “Education” at the top of the request form. For each slide, fill out the rest of the request form as described in the the appropriate document on submitting a scanning request form.
- Submitting a Scanning Request - CK Chang
- Submitting a Scanning Request - SP Unknowns
- Submitting a Scanning Request - Curriculum Boxes
Once the slide's case number is entered in the "Case" field, a "taxonomy" field will become visible beneath the slide ID field. It will look something like the image below. If you don't see the "Taxonomy" field, you haven't selected "Education" as your "Request Type" at the top of the form, or you haven't entered a "Case" for the slide. Go back and check that you've filled everything out correctly.
There are two different ways of entering the taxonomy information.
- Start by selecting clicking the first "Taxonomy" drop down menu and selecting "Human". After making your selection, the next drop down menu will automatically appear and the list will populate with options corresponding to your previous selections.
- Click the new drop down menu and select the organ system. Please note that if this is a soft tissue, hematopoietic, or bony lesion, it may be listed under one of those three options, not under the actual organ. For example, angiosarcoma of the jaw will be listed under “Bone,” not “Oropharynx,” and large B-cell lymphoma affecting the colon will be listed under “Hematopoietic” rather than “Colon and Rectum.”
- Click the new drop down menu and select the term that best describes the process on the slide. Repeat this step until no more drop down menus appear, indicating that you have reached the end of this particular taxonomic string.
- The “clinical data field” corresponds to “Other Tax Notes” on the slide scan request submission form. Only enter something in the "Other Tax Notes" field if prompted to by the taxonomic string. Ex: Human -> THYROID -> Infectious -> Septic embolus -> Bacterial: specify name of bacterium, if pertinent, in clinical data field
- Repeat this process for each slide on your request form. Be sure to enter taxonomic information for each slide, or you won't be able to submit the form.
(See below, “What if No Appropriate Term Exists?", if you cannot identify an appropriate taxonomic string.)
- Click the "Tax Search" button at the far right end of this slide's line.
- A window will pop up. Enter the term you wish to search for in the "Taxonomy Search" field (Ex. collagen polyp), and click the "Search" button.
- The window will populate with a list of taxonomic strings that contain your search term.
- If no results are found, none will be displayed.
- If you searched for a very common term (Ex. breast), the search could take several seconds and return hundreds of results. The more specific your term, the better.
- If a results ends in an arrow (->), that means there are several possible ways the taxonomic string could be completed. If you select an incomplete string, you will need to manually complete it after selection. See method 1 for instructions on manual selection.
- Click the radio button for the taxonomic string you wish to use, and click the "Select" button. The taxonomy drop down fields for this slide will be automatically filled in with the string you selected.
If you selected an incomplete term (as indicated by a blank field at the end of the string), you will need to finish the string by clicking the drop down box and selecting a term as per the instructions for method 1 above.
- Repeat this process for each slide on in your request form. Be sure to enter taxonomic information for each slide, or you won't be able to submit the form.
You will not be able to submit the form without entering taxonomy information for each slide. If you encounter a slide for which you believe there is no appropriate existing term, do the following.
- Select "Human" for the first taxonomic term, then select "Unclassified" for the second term. (Ex. Human -> Unclassified)
- Contact Dr. Loeffler. You will need to work with her to determine what term or terms need to be added to the taxonomy.
- Once the additions have been decided on, email firstname.lastname@example.org with the changes, as well the request # and slide ID to which this new string applies. We will need to go back and enter it into Aperio.
In order to maintain the integrity and utility of these education slides, they must all have the correct taxonomic string associated with them. If the string does not exist, please do your part and alert Dr. Loeffler right away. Send her an email with the diagnosis you think is best for the slide and the slide ID number you entered into Aperio. Please keep in mind that the taxonomy spreadsheet from which the taxonomic strings are pulled contains 5,000+ rows: it is invariable that we will have missed some or made mistakes as we built the system. Future generations of residents are relying on you to make sure that what is entered into the system is as correct and complete as possible. We have no systematic way of identifying incorrect information after the slide is submitted. If we do identify an incorrect submission, we will simply delete the entry, and the educational value of the slide will be lost forever. When you submit a slide with the string of Human -> Unclassified, we will be following up with you to make sure that you and Dr. Loeffler are able to figure out what term(s) is appropriate for the unclassified slide. We will periodically run reports so that no unclassified slides slip through.