BackgroundConsumer health vocabularies (CHVs) have been developed to aid consumer health informatics applications. This purpose is best served if the vocabulary evolves with consumers’ language.ObjectiveOur objective was to create a computer assisted update (CAU) system that works with live corpora to identify new candidate terms for inclusion in the open access and collaborative (OAC) CHV.MethodsThe CAU system consisted of three main parts: a Web crawler and an HTML parser, a candidate term filter that utilizes natural language processing tools including term recognition methods, and a human review interface. In evaluation, the CAU system was applied to the health-related social network website PatientsLikeMe.com. The system’s utility was assessed by comparing the candidate term list it generated to a list of valid terms hand extracted from the text of the crawled webpages.ResultsThe CAU system identified 88,994 unique terms 1- to 7-grams (“n-grams” are n consecutive words within a sentence) in 300 crawled PatientsLikeMe.com webpages. The manual review of the crawled webpages identified 651 valid terms not yet included in the OAC CHV or the Unified Medical Language System (UMLS) Metathesaurus, a collection of vocabularies amalgamated to form an ontology of medical terms, (ie, 1 valid term per 136.7 candidate n-grams). The term filter selected 774 candidate terms, of which 237 were valid terms, that is, 1 valid term among every 3 or 4 candidates reviewed.ConclusionThe CAU system is effective for generating a list of candidate terms for human review during CHV development.

BackgroundEffective implementation of a Primary Care Medical Home model of care (PCMH) requires integration of patients’ contextual information (physical, mental, social and financial status) into an easily retrievable information source for the healthcare team and clinical decision-making.This project explored clinicians’ perceptions about important attributes of contextual information for clinical decision-making, how contextual information is expressed in CPRS clinical documentation as well as how clinicians in a highly computerized environment manage information flow related to these areas.MethodsA qualitative design using Cognitive Task Analyses and a modified Critical Incident Technique were used. The study was conducted in a large VA with a fully implemented EHR located in the western United States. Seventeen providers working in a PCMH model of care in Primary Care, Home Based Care and Geriatrics reported on a recent difficult transition requiring contextual information for decision-making. The transcribed interviews were qualitatively analyzed for thematic development related to contextual information using an iterative process and multiple reviewers with ATLAS@ti software.ResultsSix overarching themes emerged as attributes of contextual information: Informativeness, goal language, temporality, source attribution, retrieval effort, and information quality.ConclusionsThese results indicate that specific attributes are needed to in order for contextual information to fully support clinical decision-making in a Medical Home care delivery environment. Improved EHR designs are needed for ease of contextual information access, displaying linkages across time and settings, and explicit linkages to both clinician and patient goals. Implications relevant to providers’ information needs, team functioning and EHR design are discussed.

BackgroundWe develop medical-specialty specific ontologies that contain the settled science and common term usage. We leverage current practices in information and relationship extraction to streamline the ontology development process. Our system combines different text types with information and relationship extraction techniques in a low overhead modifiable system. Our SEmi-Automated ontology Maintenance (SEAM) system features a natural language processing pipeline for information extraction. Synonym and hierarchical groups are identified using corpus-based semantics and lexico-syntactic patterns. The semantic vectors we use are term frequency by inverse document frequency and context vectors.Clinical documents contain the terms we want in an ontology. They also contain idiosyncratic usage and are unlikely to contain the linguistic constructs associated with synonym and hierarchy identification. By including both clinical and biomedical texts, SEAM can recommend terms from those appearing in both document types. The set of recommended terms is then used to filter the synonyms and hierarchical relationships extracted from the biomedical corpus.We demonstrate the generality of the system across three use cases: ontologies for acute changes in mental status, Medically Unexplained Syndromes, and echocardiogram summary statements.ResultsAcross the three uses cases, we held the number of recommended terms relatively constant by changing SEAM’s parameters. Experts seem to find more than 300 recommended terms to be overwhelming. The approval rate of recommended terms increased as the number and specificity of clinical documents in the corpus increased. It was 60% when there were 199 clinical documents that were not specific to the ontology domain and 90% when there were 2879 documents very specific to the target domain.We found that fewer than 100 recommended synonym groups were also preferred. Approval rates for synonym recommendations remained low varying from 43% to 25% as the number of journal articles increased from 19 to 47. Overall the number of recommended hierarchical relationships was very low although approval was good. It varied between 67% and 31%.ConclusionSEAM produced a concise list of recommended clinical terms, synonyms and hierarchical relationships regardless of medical domain.

This paper reports on a set of studies designed to identify sublanguages in documents for domain-specific processing across institutions. Psychological evidence indicates that humans use context-specific linguistic information when they read. Natural Language Processing (NLP) pipelines are successful within specific domains (i.e., contexts). To limit the number of domain-specific NLP systems, a natural focus would be on sublanguages. Sublanguages are identified by shared lexical and semantic features.[1] Patterson and Hurdle[2] developed a sublanguage identification system that functioned well for 12 clinical specialties at the University of Utah. The current work compares sublanguages across institutions. Using a clinical NLP pipeline augmented by a new document corpus from the University of Pittsburg (UPitt), new documents were assigned to clusters based on the minimum cosine-distance to a Utah cluster centroid. The UPitt documents were divided into a nine-group specialty corpus. Across institutions, five of the specialty groups fell within the expected clusters. We find that clustering encounters difficulty due to documents with mixed sublanguages; naming convention differences across institutions; and document types used across specialties. The findings indicate that clinical specialty sublanguages can be identified across institutions.

BackgroundA Cardiac-centered Frailty Ontology can be an important foundation for using NLP to assess patient frailty. Frailty is an important consideration when making patient treatment decisions, particularly in older adults, those with a cardiac diagnosis, or when major surgery is a consideration. Clinicians often report patient’s frailty in progress notes and other documentation. Frailty is recorded in many different ways in patient records and many different validated frailty-measuring instruments are available, with little consistency across instruments. We specifically explored concepts relevant to decisions regarding cardiac interventions. We based our work on text found in a large corpus of clinical notes from the Department of Veterans Affairs (VA) national Electronic Health Record (EHR) database.ResultsThe full ontology has 156 concepts, with 246 terms. It includes 86 concepts we expect to find in clinical documents, with 12 qualifier values. The remaining 58 concepts represent hierarchical groups (e.g., physical function findings). Our top-level class is clinical finding, which has children clinical history finding, instrument finding, and physical examination finding, reflecting the OGMS definition of clinical finding. Instrument finding is any score found for the existing frailty instruments. Within our ontology, we used SNOMED-CT concepts where possible. Some of the 86 concepts we expect to find in clinical documents are associated with the properties like ability interpretation. The concept ability to walk can either be able, assisted or unable. Each concept-property level pairing gets a different frailty score. Each scored concept received three scores: a frailty score, a relevance to cardiac decisions score, and a likelihood of resolving after the recommended intervention score. The ontology includes the relationship between scores from ten frailty instruments and frailty as assessed using ontology concepts. It also included rules for mapping ontology elements to instrument items for three common frailty assessment instruments. Ontology elements are used in two clinical NLP systems.ConclusionsWe developed and validated a Cardiac-centered Frailty Ontology, which is a machine-interoperable description of frailty that reflects all the areas that clinicians consider when deciding which cardiac intervention will best serve the patient as well as frailty indications generally relevant to medical decisions. The ontology owl file is available on Bioportal at http://bioportal.bioontology.org/ontologies/CCFO.Electronic supplementary materialThe online version of this article (10.1186/s13326-019-0195-3) contains supplementary material, which is available to authorized users.