Searching for codes outside DICOM

To find a suitable code in an existing terminology, you will need to know what terminology to search, and you will need a tool that would facilitate your search.

DICOM has a preference for using SNOMED-CT codes. If you find a code in SNOMED-CT that would fill an important gap, but is not in the standard, you can propose inclusion of that new code into the standard. While looking for codes in SNOMED-CT, note the following guideline from the standard (PS3.16, Section 8.1.1):

8.1.1 Use of SNOMED Anatomic Concepts

In general, DICOM uses the anatomic concepts with the term "structure", rather than with the term "entire". This is an important distinction in SNOMED. "Entire" is a child concept to "structure", has a more restricted meaning, and typically is used in conjunction with treatments (e.g., "excision of entire right kidney"). It is used in distinction to other sibling children of the parent concept that may identify parts of the parent anatomic feature. Since imaging typically targets both the anatomic feature and the area around it, or sometimes just part of the anatomic feature, DICOM usually uses "structure" concepts that are more inclusive than the "entire" concepts.

However, keep in mind that:

  1. the process of contributing something into the DICOM standard is lengthy and can take a year before you see your change in the standard text;

  2. you will need to learn the procedures of contributing changes to the standard;

  3. although the SNOMED-CT codes included in the standard are exempt from the licensing constraints of SNOMED-CT, the ontology defined by SNOMED-CT is NOT covered by the exemption. Therefore, you will still need a secondary ontology if you are concerned about the license, and want to do reasoning on your data.

If a certain term is not found in SNOMED, it might be possible to add it. If you would like to request adding a new term in the context of DICOM, you can contact DICOM secretariat at http://www.dicomstandard.org/contact/secretariat/, and they would then pass your request to the person responsible for the interactions with SNOMED. Also, each country has its SNOMED national member contact: http://www.snomed.org/our-customers/members, in case you want to make a non-DICOM related request.

Using existing terminologies other than SNOMED

Therefore, it can be more practical to find a suitable term in an ontology other than SNOMED-CT.

In this regard, David Clunie, the long-time Editor of the DICOM standard, gave the following guidance on what terminologies to consider when a gap in the standard is identified:

[...] we (DICOM) use FMA then NeuroNames as a fallback when there are no appropriate SNOMED codes (yet), and have contacts with each of the appropriate groups to extend the schemes as necessary. We have not used RadLex for anatomy, since it is all/mostly(?) in FMA anyway (and if I recall correctly, was derived from it, since the original RadLex protagonists had no interest in reinventing that wheel).

If you need to automate anatomical code mapping, consider using the UMLS as a tool ... frequently both SNOMED and FMA terms map to a common UMLS code which helps a lot.

You can also use the FMAIDs included in the RadLex ontology (http://purl.bioontology.org/ontology/RADLEX) to map from RadLex back to FMA (or the reverse, since I think the FMA OWL file also includes the RadLex RIDs), then to UMLS and on to SNOMED, and indeed then undo the pre-coordinated laterality (if necessary) using the SNOMED hierarchy.

To search existing terminologies, you can consider using the following tools that search across different ontologies:

With both of these search engines you have an option of the advanced search to restrict the terms to a specific ontology.

There are also some search tools that provide searches for the individual ontologies (such as FMA), but in some instances their search capabilities are not flexible enough, and as such we recommend BioPortal and OLS. Unfortunately, neither BioPortal nor OLS include Neuronames, so you will need to use the specialized search tool for that ontology: http://braininfo.rprc.washington.edu/.

Here is an illustrative example of searching for a term "anterior cingulate gyrus", which is not included in DICOM (note that you can use AnatomicRegionModifier to encode laterality of the structure).

  1. Using BioPortal, go to the Advanced search, put the search term in the search box, and specify FMA in the "Ontologies" selector:

The search is successful, leading to this entry, which includes the FMA ID 61916. Coding scheme designator for FMA is FMA, so the you can use the following code to describe the item:

(61916, FMA, "Anterior cingulate gyrus")

  1. Using OLS, you can select the specific ontology, and search specifically in FMA for the same term, which will result in the same code:

Note that OLS is (as of writing this) using a "slimmed down version of FMA", but for common purposes perhaps this should still be sufficient.

References

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