Linking terms to update your data

This is available for SPARC researchers.

Background

The SciCrunch database for anatomical terminology is used by members of the SPARC consortium and maintained by the SPARC Anatomy Working Group.

• Each term in the database has a unique and ontologically persistent identifier.

• The database is updated frequently with new and revised terms, requested by SPARC investigators and curated by the SPARC Anatomy Working Group.

• If you use an anatomical term in your data (i.e., as a marker, contour, or tree name), and the identical term is added to the SciCrunch database, linking terms using the tools described here will programmatically link the term to its identifier in the database.

• The tools described here will assist in the creation and curation of FAIR data.

Procedure

You can update your data files to link terms to the database and to incorporate terminology revisions one file at a time or multiple files at once using the Link Terms and Batch Link tools, respectively.

	To update a single data file, click the Link Terms button.
	To update multiple data files, click the Batch Link button.

Steps

1. With Neurolucida 360 software in SPARC mode, open or create a data file.

2. Click the Link Terms or Batch Link button on the Trace ribbon in the main (2D) window.

   If you clicked the Batch Link button to update multiple data files, the Select Folder window will open. Navigate to the folder with your data files and click to select it, then click the Select Folder button.

3. The Choose Parcellations dialog opens. The Organ and Species criteria selected previously for association with the current data file are shown. You can select multiple parcellation lists if desired.

   1. Use the drop-down menus to select the Organ and Species of interest.

      The available parcellation lists for the selected organ and species are shown in the window.

   2. Click the checkbox(es) for the parcellation(s) you want to use.

      • If needed, repeat the previous step to display and select parcellation lists for additional Organ(s) and Species.
      • The selected list(s) will download and display in individual tabs in the Link Terms dialog box after you click OK.
      • Note that for many organ/species combinations, the only parcellation choice is Species Independent.
   3. Repeat to load multiple parcellation lists.

4. Click OK. The Link Terms dialog box opens.

5. Select terms from the SciCrunch database on the right to replace terms used in your data file, which are listed on the left.

   1. Click to select a term in the list on the right to replace a term(s) in your data file(s).

      If you loaded more than one parcellation list, choose a tab to view the associated list.

   2. Click the term(s) on the left to be replaced.
      • Tabs for markers and contours will be present if your data file includes them, choose the tab with the term(s) you want to change.
      • Click the checkbox to Maintain colors and the color of the replaced marker or contour will not change when its name updates.
      • You can choose terms to be replaced from either the Unassociated terms list or the Associated terms list.
   3. Click the Replace button and repeat to replace additional terms if needed.