ACORN SDOH survey: Terminological representation for use with NLP and CDS.

Objective: Social Determinants of Health (SDOH) greatly influence health outcomes. SDOH surveys, such as the Assessing Circumstances & Offering Resources for Needs (ACORN) survey, have been developed to screen for SDOH in Veterans. The purpose of this study is to determine the terminological representation of the ACORN survey, to aid in natural language processing (NLP). Methods: Each ACORN survey question was read to determine its concepts. Next, Solor was searched for each of the concepts and for the appropriate attributes. If no attributes or concepts existed, they were proposed. Then, each question's concepts and attributes were arranged into subject-relation-object triples. Results: Eleven unique attributes and 18 unique concepts were proposed. These results demonstrate a gap in representing SDOH with terminologies. We believe that using these new concepts and relations will improve NLP, and thus, the care provided to Veterans.

COVID-19 vaccination and venous thromboembolism risk in older veterans.

Introduction: It is important for SARS-CoV-2 vaccine providers, vaccine recipients, and those not yet vaccinated to be well informed about vaccine side effects. We sought to estimate the risk of post-vaccination venous thromboembolism (VTE) to meet this need. Methods: We conducted a retrospective cohort study to quantify excess VTE risk associated with SARS-CoV-2 vaccination in US veterans age 45 and older using data from the Department of Veterans Affairs (VA) National Surveillance Tool. The vaccinated cohort received at least one dose of a SARS-CoV-2 vaccine at least 60 days prior to 3/06/22 (N = 855,686). The control group was those not vaccinated (N = 321,676). All patients were COVID-19 tested at least once before vaccination with a negative test. The main outcome was VTE documented by ICD10-CM codes. Results: Vaccinated persons had a VTE rate of 1.3755 (CI: 1.3752-1.3758) per thousand, which was 0.1 percent over the baseline rate of 1.3741 (CI: 1.3738-1.3744) per thousand in the unvaccinated patients, or 1.4 excess cases per 1,000,000. All vaccine types showed a minimal increased rate of VTE (rate of VTE per 1000 was 1.3761 (CI: 1.3754-1.3768) for Janssen; 1.3757 (CI: 1.3754-1.3761) for Pfizer, and for Moderna, the rate was 1.3757 (CI: 1.3748-1.3877)). The tiny differences in rates comparing either Janssen or Pfizer vaccine to Moderna were statistically significant (p < 0.001). Adjusting for age, sex, BMI, 2-year Elixhauser score, and race, the vaccinated group had a minimally higher relative risk of VTE as compared to controls (1.0009927 CI: 1.007673-1.0012181; p < 0.001). Conclusion: The results provide reassurance that there is only a trivial increased risk of VTE with the current US SARS-CoV-2 vaccines used in veterans older than age 45. This risk is significantly less than VTE risk among hospitalized COVID-19 patients. The risk-benefit ratio favors vaccination, given the VTE rate, mortality, and morbidity associated with COVID-19 infection.

Automated Modeling of Clinical Narrative with High Definition Natural Language Processing Using Solor and Analysis Normal Form.

OBJECTIVE: One important concept in informatics is data which meets the principles of Findability, Accessibility, Interoperability and Reusability (FAIR). Standards, such as terminologies (findability), assist with important tasks like interoperability, Natural Language Processing (NLP) (accessibility) and decision support (reusability). One terminology, Solor, integrates SNOMED CT, LOINC and RxNorm. We describe Solor, HL7 Analysis Normal Form (ANF), and their use with the high definition natural language processing (HD-NLP) program. METHODS: We used HD-NLP to process 694 clinical narratives prior modeled by human experts into Solor and ANF. We compared HD-NLP output to the expert gold standard for 20% of the sample. Each clinical statement was judged "correct" if HD-NLP output matched ANF structure and Solor concepts, or "incorrect" if any ANF structure or Solor concepts were missing or incorrect. Judgements were summed to give totals for "correct" and "incorrect". RESULTS: 113 (80.7%) correct, 26 (18.6%) incorrect, and 1 error. Inter-rater reliability was 97.5% with Cohen's kappa of 0.948. CONCLUSION: The HD-NLP software provides useable complex standards-based representations for important clinical statements designed to drive CDS.

[An online dynamic knowledge base in multiple languages on general medicine and primary care]. / Une base de connaissance multilingue et dynamique en ligne pour la médecine générale et les soins primaires.

INTRODUCTION: The International Classification of Primary Care, Second version (ICPC-2) aligned with the 10th Revision of the International Classification of Disease (ICD-10) is a standard for primary care epidemiology compendium. ICPC-2 has been also intended to identify the clinical topics in family medicine. Contextual field-specific knowledge in family medicine and primary care such as health structures, management, categories of patients, research methods, ethical or environmental features are not standardized and reflect, more often, the views of experts. METHODS: A qualitative research method, applied to the analysis of several Family Medicine congresses, has helped identify, in addition to clinical items, a spectrum of contextual concepts addressed by family doctors during their exchanges at the congresses. Assembled in a hierarchical manner, these concepts were given expression, together with ICPC-2, under the name of Q-codes Version 2.5, in the multilingual multi-terminology semantic server of the Department of Information and medical informatics (D2Im) at the University of Rouen, France. The two classifications are edited under the acronym 3 CGP for Core Content classification of General Practice. This free access server allows you to consult the ICPC-2 in 22 languages and the Q-codes in ten languages. RESULTS: The result of the joint use of these two classifications, as descriptors in congress to identify the concepts in texts or index the gray literature for family medicine and primary care is presented here in its various pilot uses. The validity and generalizability of 3CGP appears to be good in the light of the translations already carried out by colleagues around the world and of the applicability of the method in the two sides of the Atlantic. However the reproducibility and the inter-coder variations still remain to be tested for Q-codes. Maintenance remains an issue. CONCLUSION: This method highlights the conceptual extension, the complexity and the dynamics of the role of general practitioner and family doctor as well as of primary care physician.

Development, dissemination, and applications of a new terminological resource, the Q-Code taxonomy for professional aspects of general practice/family medicine.

BACKGROUND: While documentation of clinical aspects of General Practice/Family Medicine (GP/FM) is assured by the International Classification of Primary Care (ICPC), there is no taxonomy for the professional aspects (context and management) of GP/FM. OBJECTIVES: To present the development, dissemination, applications, and resulting face validity of the Q-Codes taxonomy specifically designed to describe contextual features of GP/FM, proposed as an extension to the ICPC. DEVELOPMENT: The Q-Codes taxonomy was developed from Lamberts' seminal idea for indexing contextual content (1987) by a multi-disciplinary team of knowledge engineers, linguists and general practitioners, through a qualitative and iterative analysis of 1702 abstracts from six GP/FM conferences using Atlas.ti software. A total of 182 concepts, called Q-Codes, representing professional aspects of GP/FM were identified and organized in a taxonomy. Dissemination: The taxonomy is published as an online terminological resource, using semantic web techniques and web ontology language (OWL) ( http://www.hetop.eu/Q ). Each Q-Code is identified with a unique resource identifier (URI), and provided with preferred terms, and scope notes in ten languages (Portuguese, Spanish, English, French, Dutch, Korean, Vietnamese, Turkish, Georgian, German) and search filters for MEDLINE and web searches. APPLICATIONS: This taxonomy has already been used to support queries in bibliographic databases (e.g., MEDLINE), to facilitate indexing of grey literature in GP/FM as congress abstracts, master theses, websites and as an educational tool in vocational teaching, Conclusions: The rapidly growing list of practical applications provides face-validity for the usefulness of this freely available new terminological resource.

A Terminology in General Practice/Family Medicine to Represent Non-Clinical Aspects for Various Usages: The Q-Codes.

The hereby proposed terminology called "Q-Codes" can be defined as an extension of the International Classification of Primary Care (ICPC-2). It deals with non-clinical concepts that are relevant in General Practice/Family Medicine (GP/FM). This terminology is a good way to put an emphasis on underestimated topics such as Teaching, Patient issues or Ethics. It aims at indexing GP/FM documents such as congress abstracts and theses to get a more comprehensive view about the GP/FM domain. The 182 identified Q-Codes have been very precisely defined by a college of experts (physicians and terminologists) from twelve countries. The result is available on the Health Terminology/Ontology Portal (http://www.hetop.org/Q) and formatted in OWL-2 for further semantic considerations and will be used to index the 2016 WONCA World congress communications.

Analysis of definitions of general practice, family medicine, and primary health care: a terminological analysis.

BACKGROUND: There are numerous definitions of general practice/family medicine (GP/FM) and primary health care (PHC), but the distinction between the two concepts is unclear. AIM: To conduct a terminological analysis of a set of definitions of GP/FM and of PHC, to clarify the commonalities and differences between these two concepts. DESIGN: Sets of 20 definitions were collected in two 'bags of words' (one for GP/FM and one for PHC terms). A terminological analysis of these two collections was performed to prioritise the terms and analyse their universe of discourse. METHOD: The two collections were extracted with VocabGrabber, configured in two 'term clouds' using Wordle, and further explored for similarities using Tropes. The main terms were analysed using the Aristotelian approach to the categorisation of things. RESULTS: Although continuity of care (characterised by a person-centred approach and shared decision making) is common to both sets, the two sets of definitions differ greatly in content. The main terms specific to GP/FM (community, medicine, responsibility, individual, problem, and needs) are different from those specific to PHC (home, team, promotion, collaborator, engagement, neighbourhood, and medical centre). CONCLUSION: Terminological analysis of the definitions for GP/FM and PHC shows two overlapping but distinct entities, necessitating a different taxonomic approach and different bibliographic search strategies.

Representing second opinion requests from primary care within the Brazilian tele-health program: international classification of primary care, second edition.

Standardization of second opinion question-answer pairs with a classification system can be used to facilitate data sharing and reuse. The Brazilian telehealth program faces the problem of representing biomedical knowledge from the primary care second opinion demands generated by rural health care teams. The objective is to determine if one of the medical classification systems has a superior ability to standardize Portuguese-language second opinion question-answer pairs. Data from 2,638 second opinions from 2010 were randomly reduced to a 264 question-answer pair data set. The semantic meaning of the question-answer pairs was manually assigned to an International Classification of Primary Care, Second edition (ICPC2) code. Eight question-answer pairs did not contain sufficient medical semantic meaning to allow for mapping to an ICPC2 code; 53 question-answer pairs did contain sufficient medical semantic meaning for mapping, however an appropriate ICPC2 code did not exist; and 203 question-answer pairs did contain sufficient medical semantic meaning for mapping to an ICPC2 code. A review of the literature indicates that there is no baseline to compare the 77% success rate against.

Extending SemRep to the Public Health Domain.

We describe the use of a domain-independent methodology to extend a natural language processing (NLP) application, SemRep (Rindflesch, Fiszman, & Libbus, 2005), based on the knowledge sources afforded by the Unified Medical Language System (UMLS®) (Humphreys, Lindberg, Schoolman, & Barnett, 1998) to support the area of health promotion within the public health domain. Public health professionals require good information about successful health promotion policies and programs that might be considered for application within their own communities. Our effort seeks to improve access to relevant information for the public health profession, to help those in the field remain an information-savvy workforce. NLP and semantic techniques hold promise to help public health professionals navigate the growing ocean of information by organizing and structuring this knowledge into a focused public health framework paired with a user-friendly visualization application as a way to summarize results of PubMed searches in this field of knowledge.

Working toward a common goal: a collaborative obstetrics and gynecology practice.

Health care reform in the United States will continue to necessitate creativity in the organization and staffing of health care models. The Department of Obstetrics and Gynecology at Bronx-Lebanon Hospital Center has expanded its staff by placing midwives as primary providers for most routine care and much of the specialty care offered within the department. Midwives and attending physicians work collaboratively in outpatient specialty clinics. Inpatient care is provided by a team of midwives, residents, and attending physicians. This model of care is easily replicated, and has resulted in improvements in clinical practice and increased patient and personnel satisfaction.

Depression after infection with West Nile virus.

Previous reports have noted depression after West Nile virus (WNV) infection. We further measured this outcome and found that 31% of patients reported new-onset depression and 75% of these had Center for Epidemiologic Studies Depression scores indicative of mild-to-severe depression. Physicians should be aware of neuropsychiatric consequences of WNV in patients.