Deploying a national clinical text processing infrastructure.

OBJECTIVES: Clinical text processing offers a promising avenue for improving multiple aspects of healthcare, though operational deployment remains a substantial challenge. This case report details the implementation of a national clinical text processing infrastructure within the Department of Veterans Affairs (VA). METHODS: Two foundational use cases, cancer case management and suicide and overdose prevention, illustrate how text processing can be practically implemented at scale for diverse clinical applications using shared services. RESULTS: Insights from these use cases underline both commonalities and differences, providing a replicable model for future text processing applications. CONCLUSIONS: This project enables more efficient initiation, testing, and future deployment of text processing models, streamlining the integration of these use cases into healthcare operations. This project implementation is in a large integrated health delivery system in the United States, but we expect the lessons learned to be relevant to any health system, including smaller local and regional health systems in the United States.

Development of a 3-Step theory of suicide ontology to facilitate 3ST factor extraction from clinical progress notes.

OBJECTIVE: Suicide risk prediction algorithms at the Veterans Health Administration (VHA) do not include predictors based on the 3-Step Theory of suicide (3ST), which builds on hopelessness, psychological pain, connectedness, and capacity for suicide. These four factors are not available from structured fields in VHA electronic health records, but they are found in unstructured clinical text. An ontology and controlled vocabulary that maps psychosocial and behavioral terms to these factors does not exist. The objectives of this study were 1) to develop an ontology with a controlled vocabulary of terms that map onto classes that represent the 3ST factors as identified within electronic clinical progress notes, and 2) to determine the accuracy of automated extractions based on terms in the controlled vocabulary. METHODS: A team of four annotators did linguistic annotation of 30,000 clinical progress notes from 231 Veterans in VHA electronic health records who attempted suicide or who died by suicide for terms relating to the 3ST factors. Annotation involved manually assigning a label to words or phrases that indicated presence or absence of the factor (polarity). These words and phrases were entered into a controlled vocabulary that was then used by our computational system to tag 14 million clinical progress notes from Veterans who attempted or died by suicide after 2013. Tagged text was extracted and machine-labelled for presence or absence of the 3ST factors. Accuracy of these machine-labels was determined for 1000 randomly selected extractions for each factor against a ground truth created by our annotators. RESULTS: Linguistic annotation identified 8486 terms that related to 33 subclasses across the four factors and polarities. Precision of machine-labeled extractions ranged from 0.73 to 1.00 for most factor-polarity combinations, whereas recall was somewhat lower 0.65-0.91. CONCLUSION: The ontology that was developed consists of classes that represent each of the four 3ST factors, subclasses, relationships, and terms that map onto those classes which are stored in a controlled vocabulary (https://bioportal.bioontology.org/ontologies/THREE-ST). The use case that we present shows how scores based on clinical notes tagged for terms in the controlled vocabulary capture meaningful change in the 3ST factors during weeks preceding a suicidal event.