Finding potentially new multimorbidity patterns of psychiatric and somatic diseases: exploring the use of literature-based discovery in primary care research

Development of a prognostic prediction model to estimate the risk of multiple chronic diseases: constructing a copula-based model using Canadian primary care electronic medical record data

Introduction

The ability to estimate risk of multimorbidity will provide valuable information to patients and primary care practitioners in their preventative efforts. Current methods for prognostic prediction modelling are insufficient for the estimation of risk for multiple outcomes, as they do not properly capture the dependence that exists between outcomes.

Objectives

We developed a multivariate prognostic prediction model for the 5-year risk of diabetes, hypertension, and osteoarthritis that quantifies and accounts for the dependence between each disease using a copula-based model.

Methods

We used data from the Canadian Primary Care Sentinel Surveillance Network (CPCSSN) from 2009 onwards, a collection of electronic medical records submitted by participating primary care practitioners across Canada. We identified patients 18 years and older without all three outcome diseases and observed any incident diabetes, osteoarthritis, or hypertension within 5-years, resulting in a large retrospective cohort for model development and internal validation (n=425,228). First, we quantified the dependence between outcomes using unadjusted and adjusted Ø coefficients. We then estimated a copula-based model to quantify the non-linear dependence between outcomes that can be used to derive risk estimates for each outcome, accounting for the observed dependence. Copula-based models are defined by univariate models for each outcome and a dependence function, specified by the parameter θ. Logistic regression was used for the univariate models and the Frank copula was selected as the dependence function.

Results

All outcome pairs demonstrated statistically significant dependence that was reduced after adjusting for covariates. The copula-based model yielded statistically significant θ parameters in agreement with the adjusted and unadjusted Ø coefficients. Our copula-based model can effectively be used to estimate trivariate probabilities.

Discussion

Quantitative estimates of multimorbidity risk inform discussions between patients and their primary care practitioners around prevention in an effort to reduce the incidence of multimorbidity.

Rediscovering Don Swanson: the Past, Present and Future of Literature-Based Discovery

The late Don R. Swanson was well appreciated during his lifetime as Dean of the Graduate Library School at University of Chicago, as winner of the American Society for Information Science Award of Merit for 2000, and as author of many seminal articles. In this informal essay, I will give my personal perspective on Don's contributions to science, and outline some current and future directions in literature-based discovery that are rooted in concepts that he developed.

Enriching plausible new hypothesis generation in PubMed

Background

Most of earlier studies in the field of literature-based discovery have adopted Swanson's ABC model that links pieces of knowledge entailed in disjoint literatures. However, the issue concerning their practicability remains to be solved since most of them did not deal with the context surrounding the discovered associations and usually not accompanied with clinical confirmation. In this study, we aim to propose a method that expands and elaborates the existing hypothesis by advanced text mining techniques for capturing contexts. We extend ABC model to allow for multiple B terms with various biological types.

Results

We were able to concretize a specific, metabolite-related hypothesis with abundant contextual information by using the proposed method. Starting from explaining the relationship between lactosylceramide and arterial stiffness, the hypothesis was extended to suggest a potential pathway consisting of lactosylceramide, nitric oxide, malondialdehyde, and arterial stiffness. The experiment by domain experts showed that it is clinically valid.

Conclusions

The proposed method is designed to provide plausible candidates of the concretized hypothesis, which are based on extracted heterogeneous entities and detailed relation information, along with a reliable ranking criterion. Statistical tests collaboratively conducted with biomedical experts provide the validity and practical usefulness of the method unlike previous studies. Applying the proposed method to other cases, it would be helpful for biologists to support the existing hypothesis and easily expect the logical process within it.

Detecting the association of health problems in consumer-level medical text

Consumers usually do not know the complicated links between related health problems. This fact may cause troubles when they wish to seek complete information regarding such problems. This study detects the associations among health problems by extending the meaning of health terms with methods based on the latent Dirichlet allocation (LDA) probability topic model, the Medical Subject Headings (MeSH) thesaurus structure and the Wikipedia concept mapping. The terms represented health problems are selected from and extended by the consumer-level medical text. The vocabulary is different between the consumer-level and the professional-level medical text. Thus, the findings can be easily understood by the general public and be suitable to consumer-oriented applications. The methods were evaluated in two ways: (1) correlation analysis with expert rating to show the overall performance and (2) P@ N to reflect the ability of detecting strong associations. The LDA topic-model-based method outperforms the other two types. The judgment incongruence between the best method and the expert ratings has been examined, and the evidence shows that the automatic method sometimes detects real associations beyond those identified by human experts.

The potential relationship discovery model based on result fusion for biomedical medicine research

With the amount of biomedical data growing explosively, medical scientists use many datasets in research for new medicine. However, the amount of biomedical data is growing too fast to abstract hidden information. At the same time, with the development of data storage diversification, scientists prefer to have data fusion based on heterogeneous data sources as opposed to a single data source, and ultimately to achieve knowledge and discovery across heterogeneous databases. Our study focuses on extending the application of latent semantic analysis methodologies into the area of biomedical research. Our purpose is to develop a model for discovering potential relationships between medicines and diseases based on biomedical latent semantic analysis. This model could be used in constructing link maps for biomedical entities, and provide a theoretical basis and practical support for biomedical scientists in their study of the disease–medicine relationship. In detail, we discuss the study of the integration of the latent semantic analysis model and data fusion methodologies. Our result fusion solution combines scientific literature repositories and a biomedical database based on context and the ABC model, and is supervised by a semi-supervised learning algorithm and data fusion algorithms. The expectation is that fused data could represent multilevel potential relationships between biological entities and related emotional relationship expression. The model is validated by experience and proven to be feasible and effective.

Networks of neuroinjury semantic predications to identify biomarkers for mild traumatic brain injury

Objective

Mild traumatic brain injury (mTBI) has high prevalence in the military, among athletes, and in the general population worldwide (largely due to falls). Consequences can include a range of neuropsychological disorders. Unfortunately, such neural injury often goes undiagnosed due to the difficulty in identifying symptoms, so the discovery of an effective biomarker would greatly assist diagnosis; however, no single biomarker has been identified. We identify several body substances as potential components of a panel of biomarkers to support the diagnosis of mild traumatic brain injury.

Methods

Our approach to diagnostic biomarker discovery combines ideas and techniques from systems medicine, natural language processing, and graph theory. We create a molecular interaction network that represents neural injury and is composed of relationships automatically extracted from the literature. We retrieve citations related to neurological injury and extract relationships (semantic predications) that contain potential biomarkers. After linking all relationships together to create a network representing neural injury, we filter the network by relationship frequency and concept connectivity to reduce the set to a manageable size of higher interest substances.

Results

99,437 relevant citations yielded 26,441 unique relations. 18,085 of these contained a potential biomarker as subject or object with a total of 6246 unique concepts. After filtering by graph metrics, the set was reduced to 1021 relationships with 49 unique concepts, including 17 potential biomarkers.

Conclusion

We created a network of relationships containing substances derived from 99,437 citations and filtered using graph metrics to provide a set of 17 potential biomarkers. We discuss the interaction of several of these (glutamate, glucose, and lactate) as the basis for more effective diagnosis than is currently possible. This method provides an opportunity to focus the effort of wet bench research on those substances with the highest potential as biomarkers for mTBI.

Applying MetaMap to Medline for identifying novel associations in a large clinical dataset: a feasibility analysis

OBJECTIVE

We describe experiments designed to determine the feasibility of distinguishing known from novel associations based on a clinical dataset comprised of International Classification of Disease, V.9 (ICD-9) codes from 1.6 million patients by comparing them to associations of ICD-9 codes derived from 20.5 million Medline citations processed using MetaMap. Associations appearing only in the clinical dataset, but not in Medline citations, are potentially novel.

METHODS

Pairwise associations of ICD-9 codes were independently identified in both the clinical and Medline datasets, which were then compared to quantify their degree of overlap. We also performed a manual review of a subset of the associations to validate how well MetaMap performed in identifying diagnoses mentioned in Medline citations that formed the basis of the Medline associations.

RESULTS

The overlap of associations based on ICD-9 codes in the clinical and Medline datasets was low: only 6.6% of the 3.1 million associations found in the clinical dataset were also present in the Medline dataset. Further, a manual review of a subset of the associations that appeared in both datasets revealed that co-occurring diagnoses from Medline citations do not always represent clinically meaningful associations.

DISCUSSION

Identifying novel associations derived from large clinical datasets remains challenging. Medline as a sole data source for existing knowledge may not be adequate to filter out widely known associations.

CONCLUSIONS

In this study, novel associations were not readily identified. Further improvements in accuracy and relevance for tools such as MetaMap are needed to realize their expected utility.