Biomedical subjects

Mor Peleg

Publications and source records attributed to Mor Peleg.

12 recordsLinked to original sources

PubMed2005

Interpreting procedures from descriptive guidelines.

Errors in clinical practice guidelines may translate into errors in real-world clinical practice. The best way to eliminate these errors is to understand how they are generated, thus enabling the future development of methods to catch errors made in creating the guideline before publication. We examined the process by which a medical expert from the American College of Physicians (ACP) created clinical algorithms from narrative guidelines, as a case study. We studied this process by looking at intermediate versions produced during the algorithm creation. We identified and analyzed errors that were generated at each stage, categorized them using Knuth's classification scheme, and studied patterns of errors that were made over the set of algorithm versions that were created. We then assessed possible explanations for the sources of these errors and provided recommendations for reducing the number of errors, based on cognitive theory and on experience drawn from software engineering methodologies.

Artificial Intelligence↗

PubMed2004

Using Petri Net tools to study properties and dynamics of biological systems.

Petri Nets (PNs) and their extensions are promising methods for modeling and simulating biological systems. We surveyed PN formalisms and tools and compared them based on their mathematical capabilities as well as by their appropriateness to represent typical biological processes. We measured the ability of these tools to model specific features of biological systems and answer a set of biological questions that we defined. We found that different tools are required to provide all capabilities that we assessed. We created software to translate a generic PN model into most of the formalisms and tools discussed. We have also made available three models and suggest that a library of such models would catalyze progress in qualitative modeling via PNs. Development and wide adoption of common formats would enable researchers to share models and use different tools to analyze them without the need to convert to proprietary formats.

Algorithms↗

PubMed2004

GLIF3: a representation format for sharable computer-interpretable clinical practice guidelines.

The Guideline Interchange Format (GLIF) is a model for representation of sharable computer-interpretable guidelines. The current version of GLIF (GLIF3) is a substantial update and enhancement of the model since the previous version (GLIF2). GLIF3 enables encoding of a guideline at three levels: a conceptual flowchart, a computable specification that can be verified for logical consistency and completeness, and an implementable specification that is intended to be incorporated into particular institutional information systems. The representation has been tested on a wide variety of guidelines that are typical of the range of guidelines in clinical use. It builds upon GLIF2 by adding several constructs that enable interpretation of encoded guidelines in computer-based decision-support systems. GLIF3 leverages standards being developed in Health Level 7 in order to allow integration of guidelines with clinical information systems. The GLIF3 specification consists of an extensible object-oriented model and a structured syntax based on the resource description framework (RDF). Empirical validation of the ability to generate appropriate recommendations using GLIF3 has been tested by executing encoded guidelines against actual patient data. GLIF3 is accordingly ready for broader experimentation and prototype use by organizations that wish to evaluate its ability to capture the logic of clinical guidelines, to implement them in clinical systems, and thereby to provide integrated decision support to assist clinicians.

Artificial Intelligence↗

PubMed2004

Design and implementation of the GLIF3 guideline execution engine.

We have developed the GLIF3 Guideline Execution Engine (GLEE) as a tool for executing guidelines encoded in the GLIF3 format. In addition to serving as an interface to the GLIF3 guideline representation model to support the specified functions, GLEE provides defined interfaces to electronic medical records (EMRs) and other clinical applications to facilitate its integration with the clinical information system at a local institution. The execution model of GLEE takes the "system suggests, user controls" approach. A tracing system is used to record an individual patient's state when a guideline is applied to that patient. GLEE can also support an event-driven execution model once it is linked to the clinical event monitor in a local environment. Evaluation has shown that GLEE can be used effectively for proper execution of guidelines encoded in the GLIF3 format. When using it to execute each guideline in the evaluation, GLEE's performance duplicated that of the reference systems implementing the same guideline but taking different approaches. The execution flexibility and generality provided by GLEE, and its integration with a local environment, need to be further evaluated in clinical settings. Integration of GLEE with a specific event-monitoring and order-entry environment is the next step of our work to demonstrate its use for clinical decision support. Potential uses of GLEE also include quality assurance, guideline development, and medical education.

Database Management Systems↗

PubMed2004

Modeling and analyzing biomedical processes using workflow/Petri Net models and tools.

Computer simulation enables system developers to execute a model of an actual or theoretical system on a computer and analyze the execution output. We have been exploring the use of Petri Net (PN) tools to study the behavior of systems that are represented using three kinds of biomedical models: a biological workflow model used to represent biological processes, and two different computer-interpretable models of health care processes that are derived from clinical guidelines. We developed and implemented software that maps the three models into a single underlying process model (workflow), which is then converted into PNs in formats that are readable by several PN simulation and analysis tools. These analysis tools enabled us to simulate and study the behavior of two biomedical systems: a Malaria parasite invading a host cell, and patients undergoing management of chronic cough.

Algorithms↗

PubMed2003

The InterMed approach to sharable computer-interpretable guidelines: a review.

InterMed is a collaboration among research groups from Stanford, Harvard, and Columbia Universities. The primary goal of InterMed has been to develop a sharable language that could serve as a standard for modeling computer-interpretable guidelines (CIGs). This language, called GuideLine Interchange Format (GLIF), has been developed in a collaborative manner and in an open process that has welcomed input from the larger community. The goals and experiences of the InterMed project and lessons that the authors have learned may contribute to the work of other researchers who are developing medical knowledge-based tools. The lessons described include (1) a work process for multi-institutional research and development that considers different viewpoints, (2) an evolutionary lifecycle process for developing medical knowledge representation formats, (3) the role of cognitive methodology to evaluate and assist in the evolutionary development process, (4) development of an architecture and (5) design principles for sharable medical knowledge representation formats, and (6) a process for standardization of a CIG modeling language.

Computer Systems↗

PubMed2003

Approaches for guideline versioning using GLIF.

Computer-interpretable clinical guidelines (CIGs) aim to eliminate clinician errors, reduce practice variation, and promote best medical practices by delivering patient-specific advice during patient encounters. Clinical guidelines are being regularly updated and revised to handle expanding clinical knowledge. When revising CIGs, much effort can be saved by specifying changes among versions instead of encoding revised guidelines from scratch. A representation of differences between versions could focus the process of re-implementing CIGs in a clinical environment and help users understand and embrace changes. Guideline versioning has not been adequately dealt with by existing CIG formalisms. We present three approaches for CIG versioning. Focusing on one approach, we developed a versioning tool based on version 3 of the GuideLine Interchange Format (GLIF3), and used it to represent two guideline versions for management of community-acquired pneumonia (CAP) and the changes between them.

Algorithms↗

PubMed2003

GESDOR - a generic execution model for sharing of computer-interpretable clinical practice guidelines.

We developed the Guideline Execution by Semantic Decomposition of Representation (GESDOR) model to share guidelines encoded in different formats at the execution level. For this purpose, we extracted a set of generalized guideline execution tasks from the existing guideline representation models. We then created the mappings between specific guideline representation models and the set of the common guideline execution tasks. Finally, we developed a generic task-scheduling model to harmonize the existing approaches to guideline task scheduling. The evaluation has shown that the GESDOR model can be used for the effective execution of guidelines encoded in different formats, and thus realizes guideline sharing at the execution level.

Decision Making, Computer-Assisted↗

PubMed2002

Representation primitives, process models and patient data in computer-interpretable clinical practice guidelines: a literature review of guideline representation models.

Representation of clinical practice guidelines in a computer-interpretable format is a critical issue for guideline development, implementation, and evaluation. We studied 11 types of guideline representation models that can be used to encode guidelines in computer-interpretable formats. We have consistently found in all reviewed models that primitives for representation of actions and decisions are necessary components of a guideline representation model. Patient states and execution states are important concepts that closely relate to each other. Scheduling constraints on representation primitives can be modeled as sequences, concurrences, alternatives, and loops in a guideline's application process. Nesting of guidelines provides multiple views to a guideline with different granularities. Integration of guidelines with electronic medical records can be facilitated by the introduction of a formal model for patient data. Data collection, decision, patient state, and intervention constitute four basic types of primitives in a guideline's logic flow. Decisions clarify our understanding on a patient's clinical state, while interventions lead to the change from one patient state to another.

Artificial Intelligence↗

PubMed2002

Modelling biological processes using workflow and Petri Net models.

MOTIVATION: Biological processes can be considered at many levels of detail, ranging from atomic mechanism to general processes such as cell division, cell adhesion or cell invasion. The experimental study of protein function and gene regulation typically provides information at many levels. The representation of hierarchical process knowledge in biology is therefore a major challenge for bioinformatics. To represent high-level processes in the context of their component functions, we have developed a graphical knowledge model for biological processes that supports methods for qualitative reasoning. RESULTS: We assessed eleven diverse models that were developed in the fields of software engineering, business, and biology, to evaluate their suitability for representing and simulating biological processes. Based on this assessment, we combined the best aspects of two models: Workflow/Petri Net and a biological concept model. The Workflow model can represent nesting and ordering of processes, the structural components that participate in the processes, and the roles that they play. It also maps to Petri Nets, which allow verification of formal properties and qualitative simulation. The biological concept model, TAMBIS, provides a framework for describing biological entities that can be mapped to the workflow model. We tested our model by representing malaria parasites invading host erythrocytes, and composed queries, in five general classes, to discover relationships among processes and structural components. We used reachability analysis to answer queries about the dynamic aspects of the model. AVAILABILITY: The model is available at http://smi.stanford.edu/projects/helix/pubs/process-model/.

Animals↗

PubMed2002

Support for guideline development through error classification and constraint checking.

Clinical guidelines aim to eliminate clinician errors, reduce practice variation, and promote best medical practices. Computer-interpretable guidelines (CIGs) can deliver patient-specific advice during clinical encounters, which makes them more likely to affect clinician behavior than narrative guidelines. To reduce the number of errors that are introduced while developing narrative guidelines and CIGs, we studied the process used by the ACP-ASIM to develop clinical algorithms from narrative guidelines. We analyzed how changes progressed between subsequent versions of an algorithm and between a narrative guideline and its derived clinical algorithm. We recommend procedures that could limit the number of errors produced when generating clinical algorithms. In addition, we developed a tool for authoring CIGs in GLIF3 format and validating their syntax, data type matches, cardinality constraints, and structural integrity constraints. We used this tool to author guidelines and to check them for errors.

Algorithms↗

PubMedDate not supplied

Comparing computer-interpretable guideline models: a case-study approach.

OBJECTIVES: Many groups are developing computer-interpretable clinical guidelines (CIGs) for use during clinical encounters. CIGs use "Task-Network Models" for representation but differ in their approaches to addressing particular modeling challenges. We have studied similarities and differences between CIGs in order to identify issues that must be resolved before a consensus on a set of common components can be developed. DESIGN: We compared six models: Asbru, EON, GLIF, GUIDE, PRODIGY, and PROforma. Collaborators from groups that created these models represented, in their own formalisms, portions of two guidelines: American College of Chest Physicians cough guidelines [correction] and the Sixth Report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure. MEASUREMENTS: We compared the models according to eight components that capture the structure of CIGs. The components enable modelers to encode guidelines as plans that organize decision and action tasks in networks. They also enable the encoded guidelines to be linked with patient data-a key requirement for enabling patient-specific decision support. RESULTS: We found consensus on many components, including plan organization, expression language, conceptual medical record model, medical concept model, and data abstractions. Differences were most apparent in underlying decision models, goal representation, use of scenarios, and structured medical actions. CONCLUSION: We identified guideline components that the CIG community could adopt as standards. Some of the participants are pursuing standardization of these components under the auspices of HL7.

Decision Support Systems, Clinical↗