Terminology labels and file location

Support
1

We are creating a custom terminology for vertebrate musculoskeletal system by extracting the relevant terms from the Uberon ontology. I have encountered a few things that I can’t find the answers to.

  1. When I custom terminology is successfully imported to Slicer, where is it saved? I removed the original JSON file that was imported, but the terminology is still there. I searched for files modified under Slicer install tree, but wasn’t able to find. As I am testing more and more files are being added, and I would like clear them.
  2. Is there field that controls the value of the displayed value? AFAIT the label comes from “CodeMeaning” field. There is a field called “3dSlicerLabel” but that does’t seem to affect the displayed value.

The issue is some of the terms from Uberon is too long to use as the actual name.
E.g., upper first primary molar tooth

Instead we would like this to be displayed something like UM1.

Here is the section of terminology we are using…

"SegmentationCategoryTypeContextName": "Murat",
    "@schema": "https://raw.githubusercontent.com/qiicr/dcmqi/master/doc/schemas/segment-context-schema.json#",
    "SegmentationCodes": {
        "Category": [
            {
                "CodeMeaning": "Dentition",
                "CodingSchemeDesignator": "UBERON",
                "showAnatomy": true,
                "cid": "7150",
                "CodeValue": "0018588",
                "contextGroupName": "SegmentationPropertyCategories",
                "Type": [
                    {
                        "recommendedDisplayRGBValue": [
                            0,
                            179,
                            92
                        ],
                        "CodeMeaning": "upper first primary molar tooth",
                        "CodingSchemeDesignator": "UBERON",
                        "3dSlicerLabel": "UM1",
                        "3dSlicerIntegerLabel": 1,
                        "CodeValue": "0018588",
                        "contextGroupName": "CommonTissueSegmentationTypes",
                        "paired": "Y",
                        "Modifier": [
                            {
                                "recommendedDisplayRGBValue": [
                                    0,
                                    179,
                                    92
                                ],
                                "CodeMeaning": "Right",
                                "CodingSchemeDesignator": "SCT",
                                "3dSlicerLabel": "right UM1",
                                "3dSlicerIntegerLabel": 2,
                                "cid": "244",
                                "UMLSConceptUID": "C0205090",
                                "CodeValue": "24028007",
                                "contextGroupName": "Laterality",
                                "SNOMEDCTConceptID": "24028007"
                            },
                            {
                                "recommendedDisplayRGBValue": [
                                    0,
                                    179,
                                    92
                                ],
                                "CodeMeaning": "Left",
                                "CodingSchemeDesignator": "SCT",
                                "3dSlicerLabel": "left UM1",
                                "3dSlicerIntegerLabel": 3,
                                "cid": "244",
                                "UMLSConceptUID": "C0205091",
                                "CodeValue": "7771000",
                                "contextGroupName": "Laterality",
                                "SNOMEDCTConceptID": "7771000"
                            }
                        ]
                    },
                    {
                        "recommendedDisplayRGBValue": [
                            144,
                            16,
                            49
                        ],
2
  1. When you import the terminology, currently it is not even saved in the scene, but the Terminology module logic stores and handles the new terminology data. So you need to load the json after every restart (from script or manually) if you want to use it. No need to delete it (I am not even sure the current API supports it), all you need to do is restart Slicer and you won’t have any custom terminology loaded.
  2. 3dSlicerLabal as I understand is just a way to connect any entry to the current GeneralAnatomyColors color table, just establishing correspondence. It is not needed for a custom terminology. The CodeMeaning field is what the displayed terminology type will be.

Why do you say it is too long? I work with terminology type names of similar length and did not have problems.

3

That’s not the behavior I am observing. The imported terminology is persistent after multiple restarts.

It makes it harder to distinguish between consecutive segments:
e.g.

upper first primary molar tooth
upper second primary molar tooth
upper third primary molar tooth
upper fourth primary molar tooth
upper first secondary molar tooth
upper second seconday molar tooth
upper third secondary molar tooth
upper fourth secondary molar tooth
vs
UdM1
UdM2
UdM3
UdM4
UM1
UM2
UM3
UM4

(UdM1 stands for upper deciduous molar #1)

4

“3sSlicerLabel” field specifies the default segment name (see orange arrow):

image
image1116×797 24.5 KB

This label gives more flexibility in how a name appears, which can be particularly useful if there are modifiers, because then automatically generated names are not always the best.

          {
            "CodingSchemeDesignator": "SCT",
            "CodeValue": "46027005",
            "CodeMeaning": "Common iliac vein",
            "Modifier": [
              {
                "3dSlicerLabel": "right common iliac vein",
                "recommendedDisplayRGBValue": [ 0, 151, 206 ],
                "CodingSchemeDesignator": "SCT",
                "CodeValue": "24028007",
                "CodeMeaning": "Right"
              },
              {
                "3dSlicerLabel": "left common iliac vein",
                "recommendedDisplayRGBValue": [ 0, 151, 206 ],
                "CodingSchemeDesignator": "SCT",
                "CodeValue": "7771000",
                "CodeMeaning": "Left"
              },
              {
                "CodingSchemeDesignator": "SCT",
                "CodeValue": "51440002",
                "CodeMeaning": "Right and left"
              }
            ]
          },

However, you don’t have to use 3dSlicerLabel. You can change CodeMeaning value instead. A term is specified only by coding scheme designator and code value; code meaning is for convenience only (for example to provide some user-friendly displayable string).

1 Like
5

I’m surprised, I need to import the terminology every time. @lassoan do you know what is the expected behavior?

About the long code meanings, we also have a terminology for teeth, this is how we created it:
image
I guess the teeth do not have numbering for animals…
Anyway you can edit the code meaning as you wish.

6

Yes, that’s human specific. Varying number of teeth and dental formula in different organisms makes it impossible to use such a numbering scheme.