Combining expert knowledge and knowledge automatically acquired from electronic data sources for continued ontology evaluation and improvement

Development and Optimization of Clinical Informatics Infrastructure to Support Bioinformatics at an Oncology Center

Translational bioinformatics for therapeutic discovery requires the infrastructure of clinical informatics. In this chapter, we describe the clinical informatics components needed for successful implementation of translational research at a cancer center. This chapter is meant to be an introduction to those clinical informatics concepts that are needed for translational research. For a detailed account of clinical informatics, the authors will guide the reader to comprehensive resources. We provide examples of workflows from Moffitt Cancer Center led by Drs. Perkins and Markowitz. This perspective represents an interesting collaboration as Dr. Perkins is the Chief Medical Information Officer and Dr. Markowitz is a translational researcher in Melanoma with an active informatics component to his laboratory to study the mechanisms of resistance to checkpoint blockade and an active member of the clinical informatics team.

Comprehensive analysis of rule formalisms to represent clinical guidelines: Selection criteria and case study on antibiotic clinical guidelines

BACKGROUND

The over-use of antibiotics in clinical domains is causing an alarming increase in bacterial resistance, thus endangering their effectiveness as regards the treatment of highly recurring severe infectious diseases. Whilst Clinical Guidelines (CGs) focus on the correct prescription of antibiotics in a narrative form, Clinical Decision Support Systems (CDSS) operationalize the knowledge contained in CGs in the form of rules at the point of care. Despite the efforts made to computerize CGs, there is still a gap between CGs and the myriad of rule technologies (based on different logic formalisms) that are available to implement CDSSs in real clinical settings.

OBJECTIVE

To helpCDSS designers to determine the most suitable rule-based technology (medical-oriented rules, production rules and semantic web rules) with which to model knowledge from CGs for the prescription of antibiotics. We propose a framework of criteria for this purpose that is extensible to more generic CGs.

MATERIALS AND METHODS

Our proposal is based on the identification of core technical requirements extracted from both literature and the analysis of CGs for antibiotics, establishing three dimensions for analysis: language expressivity, interoperability and industrial aspects. We present a case study regarding the John Hopkins Hospital (JHH) Antibiotic Guidelines for Urinary Tract Infection (UTI), a highly recurring hospital acquired infection. We have adopted our framework of criteria in order to analyse and implement these CGs using various rule technologies: HL7 Arden Syntax, general-purpose Production Rules System (Drools), HL7 standard Rule Interchange Format (RIF), Semantic Web Rule Language (SWRL) and SParql Inference Notation (SPIN) rule extensions (implementing our own ontology for UTI).

RESULTS

We have identified the main criteria required to attain a maintainable and cost-affordable computable knowledge representation for CGs. We have represented the JHH UTI CGs knowledge in a total of 12 Arden Syntax MLMs, 81 Drools rules and 154 ontology classes, properties and individuals. Our experiments confirm the relevance of the proposed set of criteria and show the level of compliance of the different rule technologies with the JHH UTI CGs knowledge representation.

CONCLUSIONS

The proposed framework of criteria may help clinical institutions to select the most suitable rule technology for the representation of CGs in general, and for the antibiotic prescription domain in particular, depicting the main aspects that lead to Computer Interpretable Guidelines (CIGs), such as Logic expressivity (Open/Closed World Assumption, Negation-As-Failure), Temporal Reasoning and Interoperability with existing HIS and clinical workflow. Future work will focus on providing clinicians with suggestions regarding new potential steps for CGs, considering process mining approaches and CGs Process Workflows, the use of HL7 FHIR for HIS interoperability and the representation of Knowledge-as- a-Service (KaaS).

PARS, a system combining semantic technologies with multiple criteria decision aiding for supporting antibiotic prescriptions

OBJECTIVE

Motivated by the well documented worldwide spread of adverse drug events, as well as the increased danger of antibiotic resistance (caused mainly by inappropriate prescribing and overuse), we propose a novel recommendation system for antibiotic prescription (PARS).

METHOD

Our approach is based on the combination of semantic technologies with MCDA (Multiple Criteria Decision Aiding) that allowed us to build a two level decision support model. Given a specific domain, the approach assesses the adequacy of an alternative/action (prescription of antibiotic) for a specific subject (patient) with an issue (bacterial infection) in a given context (medical). The goal of the first level of the decision support model is to select the set of alternatives which have the potential to be suitable. Then the second level sorts the alternatives into categories according to their adequacy using an MCDA sorting method (MR-Sort with Veto) and a structured set of description logic queries.

RESULTS

We applied this approach in the domain of antibiotic prescriptions, working closely with the EpiCura Hospital Center (BE). Its performance was compared to the EpiCura recommendation guidelines which are currently in use. The results showed that the proposed system is more consistent in its recommendations when compared with the static EpiCura guidelines. Moreover, with PARS the antibiotic prescribing workflow becomes more flexible. PARS allows the user (physician) to update incrementally and dynamically a patient's profile with more information, or to input knowledge modifications that accommodate the decision context (like the introduction of new side effects and antibiotics, the development of germs that are resistant, etc). At the end of our evaluation, we detail a number of limitations of the current version of PARS and discuss future perspectives.

Development and Validation of a Functional Behavioural Assessment Ontology to Support Behavioural Health Interventions

Background

In the cognitive-behavioral approach, Functional Behavioural Assessment is one of the most effective methods to identify the variables that determine a problem behavior. In this context, the use of modern technologies can encourage the collection and sharing of behavioral patterns, effective intervention strategies, and statistical evidence about antecedents and consequences of clusters of problem behaviors, encouraging the designing of function-based interventions.

Objective

The paper describes the development and validation process used to design a specific Functional Behavioural Assessment Ontology (FBA-Ontology). The FBA-Ontology is a semantic representation of the variables that intervene in a behavioral observation process, facilitating the systematic collection of behavioral data, the consequential planning of treatment strategies and, indirectly, the scientific advancement in this field of study.

Methods

The ontology has been developed deducing concepts and relationships of the ontology from a gold standard and then performing a machine-based validation and a human-based assessment to validate the Functional Behavioural Assessment Ontology. These validation and verification processes were aimed to verify how much the ontology is conceptually well founded and semantically and syntactically correct.

Results

The Pellet reasoner checked the logical consistency and the integrity of classes and properties defined in the ontology, not detecting any violation of constraints in the ontology definition. To assess whether the ontology definition is coherent with the knowledge domain, human evaluation of the ontology was performed asking 84 people to fill in a questionnaire composed by 13 questions assessing concepts, relations between concepts, and concepts’ attributes. The response rate for the survey was 29/84 (34.52%). The domain experts confirmed that the concepts, the attributes, and the relationships between concepts defined in the FBA-Ontology are valid and well represent the Functional Behavioural Assessment process.

Conclusions

The new ontology developed could be a useful tool to design new evidence-based systems in the Behavioral Interventions practices, encouraging the link with other Linked Open Data datasets and repositories to provide users with new models of eHealth focused on the management of problem behaviors. Therefore, new research is needed to develop and implement innovative strategies to improve the poor reproducibility and translatability of basic research findings in the field of behavioral assessment.

A two-staged approach to developing and evaluating an ontology for delivering personalized education to diabetic patients

Ontologies are often used in biomedical and health domains to provide a concise and consistent means of attributing meaning to medical terminology. While they are novices in terms of ontology engineering, the evaluation of an ontology by domain specialists provides an opportunity to enhance its objectivity, accuracy, and coverage of the domain itself. This paper provides an evaluation of the viability of using ontology engineering novices to evaluate and enrich an ontology that can be used for personalized diabetic patient education. We describe a methodology for engaging healthcare and information technology specialists with a range of ontology engineering tasks. We used 87.8% of the data collected to validate the accuracy of our ontological model. The contributions also enabled a 16% increase in the class size and an 18% increase in object properties. Furthermore, we propose that ontology engineering novices can make valuable contributions to ontology development. Application-specific evaluation of the ontology using a semantic-web-based architecture is also discussed.

A Knowledge-Constrained Access Control Model for Protecting Patient Privacy in Hospital Information Systems

Current access control mechanisms of the hospital information system can hardly identify the real access intention of system users. A relaxed access control increases the risk of compromise of patient privacy. To reduce unnecessary access of patient information by hospital staff, this paper proposes a knowledge-constrained role-based access control (KC-RBAC) model in which a variety of medical domain knowledge is considered in access control. Based on the proposed Purpose Tree and knowledge-involved algorithms, the model can dynamically define the boundary of access to the patient information according to the context, which helps to protect patient privacy by controlling access. Compared with the role-based access control model, KC-RBAC can effectively protect patient information according to the results of the experiments.

Clinical Decision Support: a 25 Year Retrospective and a 25 Year Vision

OBJECTIVE

The objective of this review is to summarize the state of the art of clinical decision support (CDS) circa 1990, review progress in the 25 year interval from that time, and provide a vision of what CDS might look like 25 years hence, or circa 2040.

METHOD

Informal review of the medical literature with iterative review and discussion among the authors to arrive at six axes (data, knowledge, inference, architecture and technology, implementation and integration, and users) to frame the review and discussion of selected barriers and facilitators to the effective use of CDS.

RESULT

In each of the six axes, significant progress has been made. Key advances in structuring and encoding standardized data with an increased availability of data, development of knowledge bases for CDS, and improvement of capabilities to share knowledge artifacts, explosion of methods analyzing and inferring from clinical data, evolution of information technologies and architectures to facilitate the broad application of CDS, improvement of methods to implement CDS and integrate CDS into the clinical workflow, and increasing sophistication of the end-user, all have played a role in improving the effective use of CDS in healthcare delivery.

CONCLUSION

CDS has evolved dramatically over the past 25 years and will likely evolve just as dramatically or more so over the next 25 years. Increasingly, the clinical encounter between a clinician and a patient will be supported by a wide variety of cognitive aides to support diagnosis, treatment, care-coordination, surveillance and prevention, and health maintenance or wellness.

Bacterial clinical infectious diseases ontology (BCIDO) dataset

This article describes the Bacterial Infectious Diseases Ontology (BCIDO) dataset related to research published in http:dx.doi.org/ 10.1016/j.jbi.2015.07.014 [1], and contains the Protégé OWL files required to run BCIDO in the Protégé environment. BCIDO contains 1719 classes and 39 object properties.