Samson W Tu

Samson W Tu
Stanford University | SU · Department of Medicine

MS

About

232
Publications
43,935
Reads
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10,104
Citations
Introduction
Samson W Tu is a Senior Research Scientist Emeritus affiliated with the Center for Biomedical Informatics, Stanford University. He also works as an independent consultant on medical informatics.
Additional affiliations
April 1985 - present
Stanford University
Position
  • Senior Researcher
January 1915 - present
Stanford University
Position
  • Engineer

Publications

Publications (232)
Article
Multimorbidity, the coexistence of two or more health conditions, has become more prevalent as mortality rates in many countries have declined and their populations have aged. Multimorbidity presents significant difficulties for Clinical Decision Support Systems (CDSS), particularly in cases where recommendations from relevant clinical guidelines o...
Conference Paper
Full-text available
An overarching WHO-FIC Content Model will allow uniform modeling of classifications in the WHO Family of International Classifications (WHO-FIC). It will facilitate the development of a unified Foundation to generate variants of ICD, ICF, and ICHI as linearizations and will promote their joint use. We describe a conceptualization and formalization...
Article
Full-text available
Patients with chronic multimorbidity are becoming more common as life expectancy increases, making it necessary for physicians to develop complex management plans. We are looking at the patient management process as a goal-attainment problem. Hence, our aim is to develop a goal-oriented methodology for providing decision support for managing patien...
Article
The Publisher regrets that this article is an accidental duplication of an article that has already been published, https://doi.org/10.1016/j.jbi.2020.103587. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal
Article
Full-text available
An overarching WHO-FIC Content Model will allow uniform modeling of classifications in the WHO Family of International Classifications (WHO-FIC) and promote their joint use. We provide an initial conceptualization of such a model.
Chapter
Goal-based reasoning may be used to support clinical decision making for multimorbidity patients; medical knowledge originating in different computer-interpretable guidelines (CIGs) and from medical ontologies may be matched at the goal level. This matching may be based on CIG metaproperty specifications referring to standard medical ontologies (e....
Article
Full-text available
Computer-interpretable guidelines (CIGs) are based on clinical practice guidelines, which typically address a single morbidity. However, most of the aging population suffers from multiple morbidities. Currently, there is no demonstrated effective mechanism that integrates recommendations from multiple CIGs. We are developing a goal-based method tha...
Article
Software testing of knowledge-based clinical decision support systems is challenging, labor intensive, and expensive; yet, testing is necessary since clinical applications have heightened consequences. Thoughtful test case selection improves testing coverage while minimizing testing burden. ATHENA-CDS is a knowledge-based system that provides guide...
Conference Paper
Full-text available
Computer-interpretable guidelines (CIGs) are based on clinical practice guidelines, which typically address a single morbidity. However, most of the aging population suffers from multiple morbidities. Currently, there is no demonstrated effective mechanism that integrates recommendations from multiple CIGs. We are developing a goal-based method tha...
Article
Full-text available
Clinicians and clinical decision-support systems often follow pharmacotherapy recommendations for patients based on clinical practice guidelines (CPGs). In multimorbid patients, these recommendations can potentially have clinically significant drug–drug interactions (DDIs). In this study, we describe and validate a method for programmatically detec...
Article
Full-text available
Through close analysis of two pairs of systems that implement the automated evaluation of performance measures (PMs) and guideline-based clinical decision support (CDS), we contrast differences in their knowledge encoding and necessary changes to a CDS system that provides management recommendations for patients failing performance measures. We tra...
Article
Full-text available
As utilization of clinical decision support (CDS) increases, it is important to continue the development and refinement of methods to accurately translate the intention of clinical practice guidelines (CPG) into a computable form. In this study, we validate and extend the 13 steps that Shiffman et al.5 identified for translating CPG knowledge for u...
Article
Clinical decision support (CDS) systems with complex logic are being developed. Ensuring the quality of CDS is imperative, but there is no consensus on testing standards. We tested ATHENA-HTN CDS after encoding updated hypertension guidelines into the system. A logic flow and a complexity analysis of the encoding were performed to guide testing. 10...
Article
Decision support tools increasingly integrate clinical knowledge such as medication indications and contraindications with electronic health record (EHR) data to support clinical care and patient safety. The availability of this encoded information and patient data provides an opportunity to develop measures of clinical decision complexity that may...
Article
Biomedical ontologies are a critical component in biomedical research and practice. As an ontology evolves, its structure and content change in response to additions, deletions and updates. When editing a biomedical ontology, small local updates may affect large portions of the ontology, leading to unintended and potentially erroneous changes. Such...
Article
Full-text available
To date, the scientific process for generating, interpreting, and applying knowledge has received less informatics attention than operational processes for conducting clinical studies. The activities of these scientific processes - the science of clinical research - are centered on the study protocol, which is the abstract representation of the sci...
Conference Paper
Purpose: Our aim was to develop methods for automating performance measurement for heart failure (HF) management using electronic health record data to provide prompt results for quality managers and HF clinicians without labor-intensive chart abstraction. Method: HF experts identified high priority evidence-based measures from American College o...
Data
In a previous paper, we presented a proposed expansion of the National Guideline Clearing-house (NGC) classification1. We performed a preliminary evaluation of the classification based on 100 guidelines randomly selected from the NGC collection. We found that 89 of the 100 guidelines could be assigned to a single guideline category. To test inter-o...
Article
Full-text available
An abstraction network is an auxiliary network of nodes and links that provides a compact, high-level view of an ontology. Such a view lends support to ontology orientation, comprehension, and quality-assurance efforts. A methodology is presented for deriving a kind of abstraction network, called a partial-area taxonomy, for the Ontology of Clinica...
Article
Full-text available
Human studies are one of the most valuable sources of knowledge in biomedical research, but data about their design and results are currently widely dispersed in siloed systems. Federation of these data is needed to facilitate large-scale data analysis to realize the goals of evidence-based medicine. The Human Studies Database project has developed...
Conference Paper
Background: Clinical Decision Support (CDS) systems that provide health professionals with evidence-based care recommendations have the potential to improve patient-centeredness of care by individualizing recommendations for each patient; however, it is important to know whether health professionals find them useful and usable. We implemented ATHEN...
Conference Paper
Purpose: Patients with complex chronic disease are often managed with a team approach; yet, clinical decision support (CDS) for teams is limited. We are developing a CDS system for primary care patient panel management with detailed patient-specific recommendations based on clinical practice guidelines. The CDS system will be delivered through an e...
Article
Full-text available
Effective clinical text processing requires accurate extraction and representation of temporal expressions. Multiple temporal information extraction models were developed but a similar need for extracting temporal expressions in eligibility criteria (e.g., for eligibility determination) remains. We identified the temporal knowledge representation r...
Conference Paper
We report on work in progress on the development of SWEETInfo (Semantic Web-Enabled Exploration of Temporal Information), a tool for querying and visualizing time-oriented clinical data. SWEETInfo is based on an open-source Web-based infrastructure that allows clinical investigators to import data and to perform operations on their temporal dimensi...
Conference Paper
Full-text available
We developed an ontology that allows representation and reasoning with effects of clinical actions. The ontology can support three important use-cases: (1) summarization and explanation of observed clinical states, (2) enhancing patient safety using safety rules, and (3) assessing guideline compliance. In this paper we focus on explanation of obser...
Article
Formalizing eligibility criteria in a computer-interpretable language would facilitate eligibility determination for study subjects and the identification of studies on similar patient populations. Because such formalization is extremely labor intensive, we transform the problem from one of fully capturing the semantics of criteria directly in a fo...
Conference Paper
Full-text available
A growing number of biomedical researchers must analyze complex patterns in time-course or longitudinal data. Researchers commonly use Excel, SAS or custom programs to query for relevant patterns in their data. However, these approaches typically entail low-level method development. Analyses are tailored to a specific data set and research question...
Article
We describe SWEETInfo (Semantic Web-Enabled Exploration of Temporal Information), a highly-interactive web-based system for querying and visualizing time-oriented data. SWEETInfo was developed as an open-source Web-based infrastructure and combines Semantic Web technologies, such as OWL and SWRL, with standard Web development software, such as the...
Chapter
Full-text available
We analyzed the graphical representations that are used by various guideline-modeling methods to express process information embodied in clinical guidelines and protocols. From this analysis, we distilled four modeling formalisms and the processes they typically model: (1) flowcharts for capturing problem-solving processes, (2) disease-state maps t...
Article
Full-text available
We present DataMaster, a Protégé plug-in that supports the importing of schema structure and data from relational databases into Protégé. The plug-in supports both OWL and frames-based ontologies and can be used with any relational database with JDBC/ODBC drivers.
Article
Full-text available
Standards-based, computable knowledge representations for eligibility criteria are increasingly needed to provide computer-based decision support for automated research participant screening, clinical evidence application, and clinical research knowledge management. We surveyed the literature and identified five aspects of eligibility criteria know...
Data
Pain Assessment tool. Picture of the pain assessment tool clinicians can interact with and write to the medical record.
Data
Conversion calculator tool. Picture of a conversion calculator tool to support clinicians calculating dose equivalents when converting from one opioid drug to another.
Data
Note in medical record from pain assessment tool. This is a picture of a note written to the electronic medical record when clinicians complete the pain assessment tool.
Article
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Opioid prescribing for chronic pain is common and controversial, but recommended clinical practices are followed inconsistently in many clinical settings. Strategies for increasing adherence to clinical practice guideline recommendations are needed to increase effectiveness and reduce negative consequences of opioid prescribing in chronic pain pati...
Article
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Formal, computer-interpretable representations of eligibility criteria would allow computers to better support key clinical research and care use cases such as eligibility determination. To inform the development of such formal representations for eligibility criteria, we conducted this study to characterize and quantify the complexity present in 1...
Article
Full-text available
Human studies, encompassing interventional and observational studies, are the most important source of evidence for advancing our understanding of health, disease, and treatment options. To promote discovery, the design and results of these studies should be made machine-readable for large-scale data mining, synthesis, and re-analysis. The Human St...
Article
Full-text available
An integrated data repository (IDR) containing aggregations of clinical, biomedical, economic, administrative, and public health data is a key component of an overall translational research infrastructure. But most available data repositories are designed using standard data warehouse architecture that employs arbitrary data encoding standards, mak...
Article
To develop and evaluate a clinical decision support system (CDSS) named Assessment and Treatment in Healthcare: Evidenced-Based Automation (ATHENA)-Opioid Therapy, which encourages safe and effective use of opioid therapy for chronic, noncancer pain. CDSS development and iterative evaluation using the analysis, design, development, implementation,...
Article
Full-text available
Worldwide developments concerning infectious diseases and bioterrorism are driving forces for improving aberrancy detection in public health surveillance. The performance of an aberrancy detection algorithm can be measured in terms of sensitivity, specificity and timeliness. However, these metrics are probabilistically dependent variables and there...
Article
Full-text available
Measuring quality in clinical care is a time-consuming manual task. The vast amounts of clinical data collected through electronic medical records (EMRs) create an opportunity to develop tools that automatically assess quality indicators; however, the diversity of EMR implementations limits the ability to implement general, reusable methods. We eva...
Article
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Problem solving methods (PSMs) are software components that represent and encode reusable algorithms. They can be combined with representations of domain knowledge to produce intelligent application systems. A goal of research on PSMs is to provide principled methods and tools for composing and reusing algorithms in knowledge-based systems. The ult...
Conference Paper
Full-text available
Autism spectrum disorder is an inherently complex phenomenon requiring large studies of many different types to further understanding of its causes. The National Database for Autism Research (NDAR) is being constructed to aid in this effort by providing a means for researchers to share and integrate data. An autism ontology drafted by a group at St...
Article
Transforming narrative guidelines into a computer-interpretable formalism is still a bottleneck in the development of decision-support systems. Our goal was to support this step by providing computer-interpretable templates for representing guideline knowledge using clinical abstractions that are appropriate for particular guideline sub-domains. We...
Conference Paper
Background: An autism ontology should document all terms relevant to the disorder; all relationships between these terms and with terms in other fields; and various assumptions and constraints used in the definition of autism endophenotypes. A data integration system could then assign unique identifiers to the ontological terms such that the same s...
Conference Paper
Background: The multiple ways that autism investigators define clinical phenotypes can lead to challenges in understanding what research findings are being established, communicated, and shared. Objectives: As part of the development of the National Database of Autism Research (NDAR) (http://ndar.nih.gov/), which will maintain and share data gath...
Article
Full-text available
Human studies are the most important source of evidence for advancing our understanding of health and disease. Yet there is no standard method for investigators to query for studies that are relevant to their scientific hypothesis. Querying data and meta-data across clinical trials and observational studies is difficult because of the lack of seman...
Conference Paper
Full-text available
Multi-agent systems have proven to be a powerful technology for building distributed applications. However, the process of designing, configuring and deploying agent-based applications is still primarily a manual one. There is a need for mechanisms and tools to help automate the many development steps required when building these applications. Usin...
Conference Paper
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Ontologies are becoming so large in their coverage that no single per- son or a small group of people can develop them effectively and ontology de- velopment becomes a community-based enterprise. In this paper, we discuss re- quirements for supporting collaborative ontology development and present Col- laborative Prot´ ege—a tool that supports many...
Article
Statistical aberrancy-detection algorithms play a central role in automated public health systems, analyzing large volumes of clinical and administrative data in real-time with the goal of detecting disease outbreaks rapidly and accurately. Not all algorithms perform equally well in terms of sensitivity, specificity, and timeliness in detecting dis...
Chapter
Full-text available
The purpose of this paper is to describe potential improvements in patient safety resulting from design decisions in the development of a computerized decision support system (DSS) for managing opioid therapy for chronic noncancer pain. ATHENA-DSS is an automated decision support system developed in a collaboration between Stanford University and t...
Article
Full-text available
The Open Biomedical Ontologies (OBO) Foundry is a coordinated community-wide effort to develop ontologies that support the annotation and integration of scientific data. In work supported by the National Database of Autism Research (NDAR), we are developing an ontology of autism that extends the ontologies available in the OBO Foundry. We undertook...
Article
Full-text available
Public health surveillance is critical for accurate and timely outbreak detection and effective epidemic control. A wide range of statistical algorithms is used for surveillance, and important differences have been noted in the ability of these algorithms to detect outbreaks. The evidence about the relative performance of these algorithms, however,...
Conference Paper
Full-text available
Data integration is central in Web application development because these applications typically deal with a variety of information formats. Ontology-driven applications face the additional challenge of integrating these multiple formats with the information stored in ontologies. A number of mappings are required to reconcile the variety of formats...
Conference Paper
Full-text available
The SWRLTab is a development environment for working with SWRL rules in Protégé-OWL. It supports the editing and execution of SWRL rules. It also provides mechanisms to allow interoperation with a variety of rule engines and the incorporation of user-defined libraries of methods that can be used in rules. Several built-in libraries are provided, in...
Conference Paper
Full-text available
Software applications that work with biomedical data have significant knowledge-management requirements. Formal knowledge models and knowledge-based methods can be very useful in meeting these requirements. However, most biomedical data are stored in relational databases, a practice that will continue for the foreseeable future. Using these data in...
Conference Paper
Full-text available
A computer-interpretable guideline knowledge base can be a very large network whose information content is difficult for developers and clinicians to comprehend and review. We created a method to annotate a guideline model and use the annotations to export the guideline knowledge base in an XML format that can be transformed into a readable documen...
Article
Full-text available
The SAGE (Standards-Based Active Guideline Environment) project was formed to create a methodology and infrastructure required to demonstrate integration of decision-support technology for guideline-based care in commercial clinical information systems. This paper describes the development and innovative features of the SAGE Guideline Model and rep...
Conference Paper
Full-text available
For the foreseeable future, most data will continue to be stored in relational databases. To work with these data in ontology-based applications, tools and techniques that bridge the two models are required. Mapping all relational data to ontology instances is often not practical so dynamic data access approaches are typically employed, though thes...
Article
Full-text available
Interoperable support of electronic health records and clinical decision support technology are central to the vision of sustainable information infrastructure. Efforts to implement interoperable clinical guidelines for immunization practice have been sparse. We used the SAGE knowledge workbench to develop a knowledge base to provide immunization d...
Conference Paper
Full-text available
The practice of evidence-based medicine requires the integration of individual clinical expertise with the best available external clinical evidence from systematic research and the patient's unique values and circumstances. This paper addresses the problem of making explicit the knowledge on individual clinical expertise which is implicit in the h...
Conference Paper
Many clinical practice guidelines use flowcharts to aid the description of recommendations specified in the guidelines. Similarly a number of computer-interpretable guideline formalisms use graphical task networks to organize knowledge formalized in these models. However, the precise meaning encoded in these graphical structures is often unclear. I...
Article
Full-text available
Within CTMS A studies, which randomized placebo-controlled trials testing “glitazones ” analyzed liver expression profiles? Across all HIV RCTs in CTMSs A&B, what were overall rates of reported adverse events in Study Site A compared to Study Site B? Across all trials and the B-CFR Registry, how many Stage III breast CA patients have tissue samples...