Table 2.
Comparisons of Manual Extraction and Two NLP Tools in Terms of the Total and Correct HPO Concepts Recognized from Clinical Notes
| Phenotype Extraction Methods |
Expert Manual Extraction |
NLP |
||
|---|---|---|---|---|
| Heuristic Chart Review | Single Genetics Note | MetaMap | MedLEE | |
| Total no. of HPO concepts selected | 223 | 309 | 493 | 543 |
| Mean no. of concepts per individual | 8.0 | 11.0 | 17.6 | 19.4 |
| Median no. of concepts per individual | 8 | 12 | 17.5 | 19.0 |
| Semantically correctly matched concepts | – | – | 199 (64%) | 222 (72%) |
| Mean no. of correctly matched concepts per individual note | – | – | 7.1 | 7.9 |
The following abbreviations are used: HPO, Human Phenotype Ontology; and NLP, natural language processing.