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. Author manuscript; available in PMC: 2019 Jul 4.
Published in final edited form as: Genet Med. 2018 Dec 5;21(7):1585–1593. doi: 10.1038/s41436-018-0381-1

Fig. 2. ClinPhen sentence analysis process.

Fig. 2

ClinPhen splits the clinical notes into sentences, and those sentences into subsentences. It then finds phenotypes whose synonyms appear in the subsentences. A high-precision, high-sensitivity, rule-based natural language processing system decides which phenotypes correspond to true mentions and which are false positives. Because the third sentence contains the flag word “father,” for instance, it is assumed that this sentence does not refer to the patient, and any phenotype synonyms found in the sentence will not be associated with the patient. ClinPhen sorts the identified phenotypes first by how many times they appeared in the set of notes (descending), then by the index of the first subsentence in which they were found (ascending), and then by Human Phenotype Ontology (HPO) ID (ascending).