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. 2018 Jun 28;103(1):58–73. doi: 10.1016/j.ajhg.2018.05.010

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.