HPO to SNOMED mapping - the objectives
The objectives was to produce a mapping with a fully logically defined product so that if a direct map to a SNOMED concept was not available, an expression was constructed using Compositional Grammar and post-coordination.
Mapping - the resources
Post coordination resources
Enclosed are two spreadsheets of the mapping of HPO (Human Phenotype Ontology) to SNOMED. The first is a list of the complete mappings of 17960 HPO terms, including direct maps and expressions, the second contains just the expressions. These expressions have been authored using the following resources and validated against the April 2024 Release of SNOMED International;
- Machine Readable Concept Model
- https://browser.ihtsdotools.org/mrcm/?branch=MAIN%2F2020-07-31
- Postco-ordination demonstrator - expression validation (classification)
- Ihtsdo.github.io/ii-postcoordination/
- Postcoordination Implementation Demo (ihtsdo.github.io)
- Practical Guide to Post-coordination
- https://snomed.org/postcoordination
- SNOMED International browser
HPO to SNOMED Cross Mapping - the results
Based on the HPO release of August 2024, and the SNOMED International release of April 2024, the mapping results are given below.
Note that 86% of the HPO terms are mappable either directly or involving an expression, so that the missing 13% could potentially be reduced with new SNOMED content.
The expressions have been validated using the Post-coordination Demonstrator resource. (Postcoordination Implementation Demo (ihtsdo.github.io))
| Group | Number (%) |
|---|---|
| One to one map | 7184 (41%) |
| One to many | 81 (0.5%) |
| Map with expression | 7833 (45%) |
| Map to parent | 2338 (13.4%) |
| Clarification | 22 (0.1%) |
| Out of scope | 685 (3.9) |
| Total | 18,370 |
Examples of post-coordination
HPO concept | SNOMED post-coordinated expression | ||
1 | HP:0001525 Severe failure to thrive | 54840006 |Failure to thrive (disorder)|: {246112005 |Severity (attribute)|=24484000 |Severe (severity modifier) (qualifier value)|} | approx (45%) |
2 | HP:0004363 Abnormal circulating calcium concentration. | 1217344005 |Finding of blood substance level (finding)|: {363713009 |Has interpretation (attribute)| =394844007 |Outside reference range (qualifier value)|, 363714003 |Interprets (attribute)| =312472004 |Blood calcium measurement (procedure)|} | approx 30% |
3 | HP:6000554 Positive bloodstream plasmodium falciparum nucleic acid pathogen test. | 434156008 |Infectious agent in bloodstream (finding)|: {363713009 |Has interpretation (attribute)| = 10828004 |Positive (qualifier value)|, 363714003 |Interprets (attribute)| = (398545005 |Nucleic acid assay (procedure)|: 246093002 |Component (attribute)| =708396002 |Deoxyribonucleic acid of Plasmodium falciparum (substance)|, 370129005 |Measurement method (attribute)|=444077007 |Analysis using reverse transcriptase polymerase chain reaction technique (procedure)|)} | 637 (8%) |