Preparing healthcare delivery organizations for managing computable knowledge

IntroductionThe growth of data science has led to an explosion in new knowledge alongside various approaches to representing and sharing biomedical knowledge in computable form. These changes have not been matched by an understanding of what healthcare delivery organizations need to do to adapt and continuously deploy computable knowledge. It is therefore important to begin to conceptualize such changes in order to facilitate routine and systematic application of knowledge that improves the health of individuals and populations.MethodsAn AHRQâ funded conference convened a group of experts from a range of fields to analyze the current state of knowledge management in healthcare delivery organizations and describe how it needs to evolve to enable computable knowledge management. Presentations and discussions were recorded and analyzed by the author team to identify foundational concepts and new domains of healthcare delivery organization knowledge management capabilities.ResultsThree foundational concepts include 1) the current state of knowledge management in healthcare delivery organizations relies on an outdated biomedical library model, and only a small number of organizations have developed enterpriseâ scale knowledge management approaches that â pushâ knowledge in computable form to frontline decisions, 2) the concept of Learning Health Systems creates an imperative for scalable computable knowledge management approaches, and 3) the ability to represent data science discoveries in computable form that is FAIR (findable, accessible, interoperable, reusable) is fundamental to spread knowledge at scale. For healthcare delivery organizations to engage with computable knowledge management at scale, they will need new organizational capabilities across three domains: policies and processes, technology, and people. Examples of specific capabilities were developed.ConclusionsHealthcare delivery organizations need to substantially scale up and retool their knowledge management approaches in order to benefit from computable biomedical knowledge.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149202/1/lrh210070.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149202/2/lrh210070_am.pd

The Knowledge Grid: A Platform to Increase the Interoperability of Computable Knowledge and Produce Advice for Health

Here we demonstrate how more highly interoperable computable knowledge enables systems to generate large quantities of evidence-based advice for health. We first provide a thorough analysis of advice. Then, because advice derives from knowledge, we turn our focus to computable, i.e., machine-interpretable, forms for knowledge. We consider how computable knowledge plays dual roles as a resource conveying content and as an advice enabler. In this latter role, computable knowledge is combined with data about a decision situation to generate advice targeted at the pending decision. We distinguish between two types of automated services. When a computer system provides computable knowledge, we say that it provides a knowledge service. When computer system combines computable knowledge with instance data to provide advice that is specific to an unmade decision we say that it provides an advice-giving service. The work here aims to increase the interoperability of computable knowledge to bring about better knowledge services and advice-giving services for health. The primary motivation for this research is the problem of missing or inadequate advice about health topics. The global demand for well-informed health advice far exceeds the global supply. In part to overcome this scarcity, the design and development of Learning Health Systems is being pursued at various levels of scale: local, regional, state, national, and international. Learning Health Systems fuse capabilities to generate new computable biomedical knowledge with other capabilities to rapidly and widely use computable biomedical knowledge to inform health practices and behaviors with advice. To support Learning Health Systems, we believe that knowledge services and advice-giving services have to be more highly interoperable. I use examples of knowledge services and advice-giving services which exclusively support medication use. This is because I am a pharmacist and pharmacy is the biomedical domain that I know. The examples here address the serious problems of medication adherence and prescribing safety. Two empirical studies are shared that demonstrate the potential to address these problems and make improvements by using advice. But primarily we use these examples to demonstrate general and critical differences between stand-alone, unique approaches to handling computable biomedical knowledge, which make it useful for one system, and common, more highly interoperable approaches, which can make it useful for many heterogeneous systems. Three aspects of computable knowledge interoperability are addressed: modularity, identity, and updateability. We demonstrate that instances of computable knowledge, and related instances of knowledge services and advice-giving services, can be modularized. We also demonstrate the utility of uniquely identifying modular instances of computable knowledge. Finally, we build on the computing concept of pipelining to demonstrate how computable knowledge modules can automatically be updated and rapidly deployed. Our work is supported by a fledgling technical knowledge infrastructure platform called the Knowledge Grid. It includes formally specified compound digital objects called Knowledge Objects, a conventional digital Library that serves as a Knowledge Object repository, and an Activator that provides an application programming interface (API) for computable knowledge. The Library component provides knowledge services. The Activator component provides both knowledge services and advice-giving services. In conclusion, by increasing the interoperability of computable biomedical knowledge using the Knowledge Grid, we demonstrate new capabilities to generate well-informed health advice at a scale. These new capabilities may ultimately support Learning Health Systems and boost health for large populations of people who would otherwise not receive well-informed health advice.PHDInformationUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/146073/1/ajflynn_1.pd

The Global academic research organization network: Data sharing to cure diseases and enable learning health systems.

Introduction:Global data sharing is essential. This is the premise of the Academic Research Organization (ARO) Council, which was initiated in Japan in 2013 and has since been expanding throughout Asia and into Europe and the United States. The volume of data is growing exponentially, providing not only challenges but also the clear opportunity to understand and treat diseases in ways not previously considered. Harnessing the knowledge within the data in a successful way can provide researchers and clinicians with new ideas for therapies while avoiding repeats of failed experiments. This knowledge transfer from research into clinical care is at the heart of a learning health system. Methods:The ARO Council wishes to form a worldwide complementary system for the benefit of all patients and investigators, catalyzing more efficient and innovative medical research processes. Thus, they have organized Global ARO Network Workshops to bring interested parties together, focusing on the aspects necessary to make such a global effort successful. One such workshop was held in Austin, Texas, in November 2017. Representatives from Japan, Taiwan, Singapore, Europe, and the United States reported on their efforts to encourage data sharing and to use research to inform care through learning health systems. Results:This experience report summarizes presentations and discussions at the Global ARO Network Workshop held in November 2017 in Austin, TX, with representatives from Japan, Korea, Singapore, Taiwan, Europe, and the United States. Themes and recommendations to progress their efforts are explored. Standardization and harmonization are at the heart of these discussions to enable data sharing. In addition, the transformation of clinical research processes through disruptive innovation, while ensuring integrity and ethics, will be key to achieving the ARO Council goal to overcome diseases such that people not only live longer but also are healthier and happier as they age. Conclusions:The achievement of global learning health systems will require further exploration, consensus-building, funding aligned with incentives for data sharing, standardization, harmonization, and actions that support global interests for the benefit of patients

Doctor of Philosophy

dissertationClinical research plays a vital role in producing knowledge valuable for understanding human disease and improving healthcare quality. Human subject protection is an obligation essential to the clinical research endeavor, much of which is governed by federal regulations and rules. Institutional Review Boards (IRBs) are responsible for overseeing human subject research to protect individuals from harm and to preserve their rights. Researchers are required to submit and maintain an IRB application, which is an important component in the clinical research process that can significantly affect the timeliness and ethical quality of the study. As clinical research has expanded in both volume and scope over recent years, IRBs are facing increasing challenges in providing efficient and effective oversight. The Clinical Research Informatics (CRI) domain has made significant efforts to support various aspects of clinical research through developing information systems and standards. However, information technology use by IRBs has not received much attention from the CRI community. This dissertation project analyzed over 100 IRB application systems currently used at major academic institutions in the United States. The varieties of system types and lack of standardized application forms across institutions are discussed in detail. The need for building an IRB domain analysis model is identified. . iv In this dissertation, I developed an IRB domain analysis model with a special focus on promoting interoperability among CRI systems to streamline the clinical research workflow. The model was evaluated by a comparison with five real-world IRB application systems. Finally, a prototype implementation of the model was demonstrated by the integration of an electronic IRB system with a health data query system. This dissertation project fills a gap in the research of information technology use for the IRB oversight domain. Adoption of the IRB domain analysis model has potential to enhance efficient and high-quality ethics oversight and to streamline the clinical research workflow

Automated Injection of Curated Knowledge Into Real-Time Clinical Systems: CDS Architecture for the 21st Century

abstract: Clinical Decision Support (CDS) is primarily associated with alerts, reminders, order entry, rule-based invocation, diagnostic aids, and on-demand information retrieval. While valuable, these foci have been in production use for decades, and do not provide a broader, interoperable means of plugging structured clinical knowledge into live electronic health record (EHR) ecosystems for purposes of orchestrating the user experiences of patients and clinicians. To date, the gap between knowledge representation and user-facing EHR integration has been considered an “implementation concern” requiring unscalable manual human efforts and governance coordination. Drafting a questionnaire engineered to meet the specifications of the HL7 CDS Knowledge Artifact specification, for example, carries no reasonable expectation that it may be imported and deployed into a live system without significant burdens. Dramatic reduction of the time and effort gap in the research and application cycle could be revolutionary. Doing so, however, requires both a floor-to-ceiling precoordination of functional boundaries in the knowledge management lifecycle, as well as formalization of the human processes by which this occurs. This research introduces ARTAKA: Architecture for Real-Time Application of Knowledge Artifacts, as a concrete floor-to-ceiling technological blueprint for both provider heath IT (HIT) and vendor organizations to incrementally introduce value into existing systems dynamically. This is made possible by service-ization of curated knowledge artifacts, then injected into a highly scalable backend infrastructure by automated orchestration through public marketplaces. Supplementary examples of client app integration are also provided. Compilation of knowledge into platform-specific form has been left flexible, in so far as implementations comply with ARTAKA’s Context Event Service (CES) communication and Health Services Platform (HSP) Marketplace service packaging standards. Towards the goal of interoperable human processes, ARTAKA’s treatment of knowledge artifacts as a specialized form of software allows knowledge engineers to operate as a type of software engineering practice. Thus, nearly a century of software development processes, tools, policies, and lessons offer immediate benefit: in some cases, with remarkable parity. Analyses of experimentation is provided with guidelines in how choice aspects of software development life cycles (SDLCs) apply to knowledge artifact development in an ARTAKA environment. Portions of this culminating document have been further initiated with Standards Developing Organizations (SDOs) intended to ultimately produce normative standards, as have active relationships with other bodies.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications

The Micropublications semantic model for scientific claims, evidence, argumentation and annotation in biomedical publications, is a metadata model of scientific argumentation, designed to support several key requirements for exchange and value-addition of semantic metadata across the biomedical publications ecosystem. Micropublications allow formalizing the argument structure of scientific publications so that (a) their internal structure is semantically clear and computable; (b) citation networks can be easily constructed across large corpora; (c) statements can be formalized in multiple useful abstraction models; (d) statements in one work may cite statements in another, individually; (e) support, similarity and challenge of assertions can be modelled across corpora; (f) scientific assertions, particularly in review articles, may be transitively closed to supporting evidence and methods. The model supports natural language statements; data; methods and materials specifications; discussion and commentary; as well as challenge and disagreement. A detailed analysis of nine use cases is provided, along with an implementation in OWL 2 and SWRL, with several example instantiations in RDF.Comment: Version 4. Minor revision

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.

Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch\u27s APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch\u27s data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch\u27s analytic tools by developing a customized plugin for OpenAI\u27s ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app