Dataset Information

An Ontology to Improve Transparency in Case Definition and Increase Case Finding of Infectious Intestinal Disease: Database Study in English General Practice.

ABSTRACT:

Background

Infectious intestinal disease (IID) has considerable health impact; there are 2 billion cases worldwide resulting in 1 million deaths and 78.7 million disability-adjusted life years lost. Reported IID incidence rates vary and this is partly because terms such as "diarrheal disease" and "acute infectious gastroenteritis" are used interchangeably. Ontologies provide a method of transparently comparing case definitions and disease incidence rates.

Objective

This study sought to show how differences in case definition in part account for variation in incidence estimates for IID and how an ontological approach provides greater transparency to IID case finding.

Methods

We compared three IID case definitions: (1) Royal College of General Practitioners Research and Surveillance Centre (RCGP RSC) definition based on mapping to the Ninth International Classification of Disease (ICD-9), (2) newer ICD-10 definition, and (3) ontological case definition. We calculated incidence rates and examined the contribution of four supporting concepts related to IID: symptoms, investigations, process of care (eg, notification to public health authorities), and therapies. We created a formal ontology using ontology Web language.

Results

The ontological approach identified 5712 more cases of IID than the ICD-10 definition and 4482 more than the RCGP RSC definition from an initial cohort of 1,120,490. Weekly incidence using the ontological definition was 17.93/100,000 (95% CI 15.63-20.41), whereas for the ICD-10 definition the rate was 8.13/100,000 (95% CI 6.70-9.87), and for the RSC definition the rate was 10.24/100,000 (95% CI 8.55-12.12). Codes from the four supporting concepts were generally consistent across our three IID case definitions: 37.38% (3905/10,448) (95% CI 36.16-38.5) for the ontological definition, 38.33% (2287/5966) (95% CI 36.79-39.93) for the RSC definition, and 40.82% (1933/4736) (95% CI 39.03-42.66) for the ICD-10 definition. The proportion of laboratory results associated with a positive test result was 19.68% (546/2775).

Conclusions

The standard RCGP RSC definition of IID, and its mapping to ICD-10, underestimates disease incidence. The ontological approach identified a larger proportion of new IID cases; the ontology divides contributory elements and enables transparency and comparison of rates. Results illustrate how improved diagnostic coding of IID combined with an ontological approach to case definition would provide a clearer picture of IID in the community, better inform GPs and public health services about circulating disease, and empower them to respond. We need to improve the Pathology Bounded Code List (PBCL) currently used by laboratories to electronically report results. Given advances in stool microbiology testing with a move to nonculture, PCR-based methods, the way microbiology results are reported and coded via PBCL needs to be reviewed and modernized.

SUBMITTER: de Lusignan S

PROVIDER: S-EPMC5639210 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Publications

An Ontology to Improve Transparency in Case Definition and Increase Case Finding of Infectious Intestinal Disease: Database Study in English General Practice.

de Lusignan Simon S Shinneman Stacy S Yonova Ivelina I van Vlymen Jeremy J Elliot Alex J AJ Bolton Frederick F Smith Gillian E GE O'Brien Sarah S

JMIR medical informatics 20170928 3

<h4>Background</h4>Infectious intestinal disease (IID) has considerable health impact; there are 2 billion cases worldwide resulting in 1 million deaths and 78.7 million disability-adjusted life years lost. Reported IID incidence rates vary and this is partly because terms such as "diarrheal disease" and "acute infectious gastroenteritis" are used interchangeably. Ontologies provide a method of transparently comparing case definitions and disease incidence rates.<h4>Objective</h4>This study soug ...[more]

PMID: 28958989

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Project description:ObjectivesThe importance of 'whole person' or 'holistic' care is widely recognised, particularly with an increasing prevalence of chronic multimorbidity internationally. This approach to care is a defining feature of general practice. However, its precise meaning remains ambiguous. We aimed to determine how the term 'whole person' care is understood by general practitioners (GPs), and whether it is synonymous with '[w]holistic' and 'biopsychosocial' care.DesignSystematic literature review.MethodsMEDLINE, PubMed, EMBASE, CINAHL, PsycINFO, Web of Science, Proquest Dissertations and Theses, Science.gov (Health and Medicine database), Google Scholar and included studies' reference lists were searched with an unlimited date range. Systematic or literature reviews, original research, theoretical articles or books/book chapters; specific to general practice; relevant to the research question; and published in English were included. Included literature was critically appraised, and data were extracted and analysed using thematic synthesis.ResultsFifty publications were included from 4297 non-duplicate records retrieved. Six themes were identified: a multidimensional, integrated approach; the importance of the therapeutic relationship; acknowledging doctors' humanity; recognising patients' individual personhood; viewing health as more than absence of disease; and employing a range of treatment modalities. Whole person, biopsychosocial and holistic terminology were often used interchangeably, but were not synonymous.ConclusionsWhole person, holistic and biopsychosocial terminology are primarily characterised by a multidimensional approach to care and incorporate additional elements described above. Whole person care probably represents the closest representation of the basis for general practice. Health systems aiming to provide whole person care need to address the challenge of integrating the care of other health professionals, and maintaining the patient-doctor relationship central to the themes identified. Further research is required to clarify the representativeness of the findings, and the relative importance GPs' assign to each theme.Prospero registration numberCRD42017058824.

Project description:BACKGROUND: Caused by intracellular Gram-negative bacteria Brucella spp., brucellosis is the most common bacterial zoonotic disease. Extensive studies in brucellosis have yielded a large number of publications and data covering various topics ranging from basic Brucella genetic study to vaccine clinical trials. To support data interoperability and reasoning, a community-based brucellosis-specific biomedical ontology is needed. RESULTS: The Brucellosis Ontology (IDOBRU: http://sourceforge.net/projects/idobru), a biomedical ontology in the brucellosis domain, is an extension ontology of the core Infectious Disease Ontology (IDO-core) and follows OBO Foundry principles. Currently IDOBRU contains 1503 ontology terms, which includes 739 Brucella-specific terms, 414 IDO-core terms, and 350 terms imported from 10 existing ontologies. IDOBRU has been used to model different aspects of brucellosis, including host infection, zoonotic disease transmission, symptoms, virulence factors and pathogenesis, diagnosis, intentional release, vaccine prevention, and treatment. Case studies are typically used in our IDOBRU modeling. For example, diurnal temperature variation in Brucella patients, a Brucella-specific PCR method, and a WHO-recommended brucellosis treatment were selected as use cases to model brucellosis symptom, diagnosis, and treatment, respectively. Developed using OWL, IDOBRU supports OWL-based ontological reasoning. For example, by performing a Description Logic (DL) query in the OWL editor Protégé 4 or a SPARQL query in an IDOBRU SPARQL server, a check of Brucella virulence factors showed that eight of them are known protective antigens based on the biological knowledge captured within the ontology. CONCLUSIONS: IDOBRU is the first reported bacterial infectious disease ontology developed to represent different disease aspects in a formal logical format. It serves as a brucellosis knowledgebase and supports brucellosis data integration and automated reasoning.

Dataset Information

An Ontology to Improve Transparency in Case Definition and Increase Case Finding of Infectious Intestinal Disease: Database Study in English General Practice.

Background

Objective

Methods

Results

Conclusions

Publications

An Ontology to Improve Transparency in Case Definition and Increase Case Finding of Infectious Intestinal Disease: Database Study in English General Practice.

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