I have previously posted about Understanding Health Ontologies and Standards. In this post I’ll focus on SNOMED-CT (Systematized Nomenclature of Medicine Clinical Terms). SNOMED-CT is the most comprehensive vocabulary to express clinical terms – it spans languages, specialties and geographic borders.
- Terms or synonyms relating to a clinical concept
- Links between different concepts
To give you a taste here is an example of Blood pressure reading represented using SNOMED-CT from the linked paper (“Towards semantic interoperability in healthcare: ontology mapping from SNOMED-CT to HL7 version 3”, Amanda Ryan):
In addition to having a model to represent concepts and linkages the biggest draw of SNOMED CT is a staggering number of coded qualifiers (which belong to one concept or other). According to IHTSO there are about 311,000 actively used SNOMED CT concepts.
You can register for SNOMED CT here. Its free for companies and individuals in United States, however your registration is processed by NLM and it might take over 3 days to receive a confirmation and access.
Once you are through with registration and have an account, start by downloading the core subset of SNOMED CT concepts here, this list consists of about 5000 most frequently used terms by institutions across US. Its a good set to get familiar with, it consists of the following concept area:
- Clinical finding : 4,550 codes in total
- Procedure : 414 codes in total
- Situation with explicit context : 132 codes in total
- Event : 38 codes in total
- Body structure : 46 codes in total
- Social context : 2 codes in total
We can use BCP to copy the files from SNOMED CT Core in to our local database, and do more interesting queries & data analysis like find distribution on these terms, co-relate problems vs. findings and of course work on the larger SNOMED CT database to find synonyms etc.; but I’ll keep that for another day. Here very quickly I’ll show how one can use a web-based browser, Snowflake, http://snomed.dataline.co.uk/ (requires registration) to lookup a SNOMED code and see what else it relates to. We can see that in line 3 above SNOMED CT concept 10085004 is marked as Metatarsalgia (finding), however using the Snowflake browser we can see in that in addition to being a finding this concept is a problem as well.
This was just tip of the ice-berg, please leave comments for future posts / areas to consider in the Ontology domain.
Further reading / relevant links:
- LexGrid: Wiki
In this series: