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Biomedical subjects

Peter Tarczy-Hornoch

Publications and source records attributed to Peter Tarczy-Hornoch.

11 recordsLinked to original sources
PubMed2006

A qualitative study of the implementation of a bioinformatics tool in a biological research laboratory.

OBJECTIVE: To explore how the implementation of a comprehensive new bioinformatics analysis system would affect workflow, collaboration and information management in a small genetic research lab. DESIGN: This was a longitudinal qualitative study of seven individuals involved in genomic and proteomic research. The study data were gathered using the illuminative/responsive approach of immersion in the environment. Additional qualitative data were gathered using informal semi-structured interviews, participant observation in lab meetings, and direct observation of lab researchers engaged in specific tasks. MEASUREMENTS: Interview, observation and field note data were coded and analyzed based on three analysis perspectives. A subset of the data was independently evaluated by an external researcher to enhance the trustworthiness of results. RESULTS: Three reoccurring themes were observed in the study. (1) Satisfaction and acceptance of software tools tended to be role and goal specific. (2) The system was seen primarily as a measurement system rather than a "total laboratory analysis system". (3) Lab meetings deemphasized the system, preferring more traditional data analysis techniques. These themes support the observations that the system was not used to its full potential in the lab. CONCLUSION: Themes identified in this study suggest that sophisticated genetic researchers face similar problems of technology implementation as do professionals in other fields. We recommend that leadership support and on-going training and evolution of academic curricula can improve chances of bioinformatics analysis systems becoming used more effectively.

Computational Biology↗
PubMed2006

On the persistence of supplementary resources in biomedical publications.

BACKGROUND: Providing for long-term and consistent public access to scientific data is a growing concern in biomedical research. One aspect of this problem can be demonstrated by evaluating the persistence of supplementary data associated with published biomedical papers. METHODS: We manually evaluated 655 supplementary data links extracted from PubMed abstracts published 1998-2005 (Method 1) as well as a further focused subset of 162 full-text manuscripts published within three representative high-impact biomedical journals between September and December 2004 (Method 2). RESULTS: For Method 1 we found that since 2001, only 71 - 92% of supplementary data were still accessible via the links provided, with 93% of these inaccessible links occurring where supplementary data was not stored with the publishing journal. Of the manuscripts evaluated in Method 2, we found that only 83% of these links were available approximately a year after publication, with 55% of these inaccessible links were at locations outside the journal of publication. CONCLUSION: We conclude that if supplemental data is required to support the publication, journals policies must take-on the responsibility to accept and store such data or require that it be maintained with a credible independent institution or under the terms of a strategic data storage plan specified by the authors. We further recommend that publishers provide automated systems to ensure that supplementary links remain persistent, and that granting bodies such as the NIH develop policies and funding mechanisms to maintain long-term persistent access to these data.

Abstracting and Indexing↗
PubMed2006

Data integration and genomic medicine.

Genomic medicine aims to revolutionize health care by applying our growing understanding of the molecular basis of disease. Research in this arena is data intensive, which means data sets are large and highly heterogeneous. To create knowledge from data, researchers must integrate these large and diverse data sets. This presents daunting informatic challenges such as representation of data that is suitable for computational inference (knowledge representation), and linking heterogeneous data sets (data integration). Fortunately, many of these challenges can be classified as data integration problems, and technologies exist in the area of data integration that may be applied to these challenges. In this paper, we discuss the opportunities of genomic medicine as well as identify the informatics challenges in this domain. We also review concepts and methodologies in the field of data integration. These data integration concepts and methodologies are then aligned with informatics challenges in genomic medicine and presented as potential solutions. We conclude this paper with challenges still not addressed in genomic medicine and gaps that remain in data integration research to facilitate genomic medicine.

Biomedical Research↗
PubMed2006

The University of Washington Health Sciences Library BioCommons: an evolving Northwest biomedical research information support infrastructure.

SETTING: The University of Washington Health Sciences Libraries and Information Center BioCommons serves the bioinformatics needs of researchers at the university and in the vibrant for-profit and not-for-profit biomedical research sector in the Washington area and region. PROGRAM COMPONENTS: The BioCommons comprises services addressing internal University of Washington, not-for-profit, for-profit, and regional and global clientele. The BioCommons is maintained and administered by the BioResearcher Liaison Team. The BioCommons architecture provides a highly flexible structure for adapting to rapidly changing resources and needs. EVALUATION MECHANISMS: BioCommons uses Web-based pre- and post-course evaluations and periodic user surveys to assess service effectiveness. Recent surveys indicate substantial usage of BioCommons services and a high level of effectiveness and user satisfaction. NEXT STEPS/FUTURE DIRECTIONS: BioCommons is developing novel collaborative Web resources to distribute bioinformatics tools and is experimenting with Web-based competency training in bioinformation resource use.

Academic Medical Centers↗
PubMed2004

Incorporating ideas from computer-supported cooperative work.

Many information systems have failed when deployed into complex health-care settings. We believe that one cause of these failures is the difficulty in systematically accounting for the collaborative and exception-filled nature of medical work. In this methodological review paper, we highlight research from the field of computer-supported cooperative work (CSCW) that could help biomedical informaticists recognize and design around the kinds of challenges that lead to unanticipated breakdowns and eventual abandonment of their systems. The field of CSCW studies how people collaborate with each other and the role that technology plays in this collaboration for a wide variety of organizational settings. Thus, biomedical informaticists could benefit from the lessons learned by CSCW researchers. In this paper, we provide a focused review of CSCW methods and ideas-we review aspects of the field that could be applied to improve the design and deployment of medical information systems. To make our discussion concrete, we use electronic medical record systems as an example medical information system, and present three specific principles from CSCW: accounting for incentive structures, understanding workflow, and incorporating awareness.

Artificial Intelligence↗
PubMed2004

The effect of point-of-care personal digital assistant use on resident documentation discrepancies.

BACKGROUND: We recently found documentation discrepancies in 60% of resident daily-progress notes with respect to patient weight, medications, or vascular lines. To what extent information systems can decrease such discrepancies is unknown. OBJECTIVE: To determine whether a point-of-care personal digital assistant (PDA)-based patient record and charting system could reduce the number of resident progress-note documentation discrepancies in a neonatal intensive care unit (NICU). DESIGN/METHODS: We conducted a before-and-after trial in an academic NICU. Our intervention was a PDA-based patient record and charting system used by all NICU resident physicians over the study period. We analyzed all resident daily-progress notes from 40 randomly selected days over 4 months in both the baseline and intervention periods. Using predefined reference standards, we determined the accuracy of recorded information for patient weights, medications, and vascular lines. Logistic and Poisson regression were used in analyses to control for potential confounding factors. RESULTS: A total of 339 progress notes in the baseline period and 432 progress notes in the intervention period were reviewed. When controlling for covariates in the regression, there were significantly fewer documentation discrepancies of patient weights in notes written by using the PDA system (14.4%-4.4% of notes; odds ratio [OR]: 0.29; 95% confidence interval [CI]: 0.15-0.56). When using the PDA system, there were no significant changes in the numbers of notes with documentation discrepancies of medications (27.7%-17.1% of notes; OR: 0.63; 95% CI: 0.35-1.13) or vascular lines (33.6%-36.1% of notes; OR: 1.11; 95% CI: 0.66-1.87). CONCLUSIONS: The use of our PDA-based point-of-care patient record and charting system showed a modest benefit in reducing the number of documentation discrepancies in resident daily-progress notes. Further study of PDAs in information systems is warranted before they are widely adopted.

Computers, Handheld↗
PubMed2004

The BioMediator system as a data integration tool to answer diverse biologic queries.

We present the BioMediator (www.biomediator.org) system and the process of executing queries on it. The system was designed as a tool for posing queries across semantically and syntactically heterogeneous data particularly in the biological arena. We use examples from researchers at the University of Washington, and the University of Missouri-Columbia, to discuss the BioMediator system architecture, query execution, modifications to the system to support the queries, and summarize our findings and our future directions. Finally, we discuss the system's flexibility and generalized approach and give examples of how the system can be extended for a variety of objectives.

Computational Biology↗
PubMed2003

Resident documentation discrepancies in a neonatal intensive care unit.

CONTEXT: Medical errors are common and potentially dangerous. Little is known about the role of documentation errors. OBJECTIVE: To determine the proportion of resident physician progress notes that contained discrepancies, and to identify predictors of such discrepancies. DESIGN/METHODS: We conducted a retrospective cross-sectional chart review of resident physician progress notes over 40 random days in a 4-month period in a neonatal intensive care unit. Using predetermined criteria, we compared resident documentation of patient weights, medications, and vascular lines to other sources of information and recorded the numbers of documentation discrepancies. RESULTS: There were discrepancies in 209 (61.7%) notes with respect to weight, vascular lines, or medications. Discrepancies occurred in the documentation of medications in 103 (27.7%) progress notes, of vascular lines in 119 (33.9%) progress notes, and of weights in 45 (13.3%) progress notes. Notes both omitted information regarding medications (18.2%) and vascular lines (13.9%) and documented inaccurate information regarding medications (18.6%) and vascular lines (30.1%). Patients with more medications or vascular lines, and with longer lengths of stay, were significantly more likely to have higher rates of documentation errors. CONCLUSIONS: Daily progress notes written by resident physicians in the neonatal intensive care unit often contain inaccurate, or omit pertinent, information. Alternative means or methods of documentation are warranted.

Birth Weight↗
PubMed2002

GeneTests-GeneClinics: genetic testing information for a growing audience.

The development and usage of two companion NIH-funded genetic testing information databases, GeneTests (www.genetests.org) and GeneClinics (www.geneclinics.org), now merged into one web site, reflect the steadily increasing use of genetic testing and the expanding audience for genetic testing information. Established in 1993 as Helix, a genetics laboratory directory of approximately 110 listings, GeneTests has grown into a database of over 900 tests for inherited diseases, a directory of over 500 international laboratories, a directory of over 1,000 U.S. and international genetics clinics, and a resource for educational/teaching materials and reports of summary genetic test data. GeneClinics, founded in 1997 as an expert-authored, peer-reviewed, disease-specific knowledge base relating genetic testing to patient care, has grown steadily, now containing over 130 expert-authored, peer-reviewed full-text entries relating genetic testing information to diagnosis, management, and genetic counseling of specific inherited diseases. In spring 2001 the two databases were merged and in October 2001 the two web sites were merged for the purpose of seamless navigation into the GeneTests-GeneClinics site (www.genetests.org or www.geneclinics.org); the GeneClinics knowledge base was renamed "GeneReviews" to avoid confusion with the U.S. and international clinic directories. As genetic testing has moved steadily out of research venues and into routine medical practice, the user audience for these databases has become international and expansive and includes healthcare providers, patients, educators, policy makers, and the media. The use of these combined resources has grown to approximately 3,200 visits/day.

Databases, Genetic↗
PubMed2002

The implementation of a Personal Digital Assistant (PDA) based patient record and charting system: lessons learned.

Personal Digital Assistants (PDAs) offer many potential advantages to clinicians. A number of systems have begun to appear for all types of PDAs that allow for the recording and tracking of patient information. PDAs allow information to be both entered and accessed at the point of care. They also allow information entered away from a central repository to be added or "synced" with data through the use of a wireless or wired connection. Few systems, however, have been designed to work in the client/server environment. Even fewer have been designed as point of care additions to already existing enterprise systems. This paper describes the issues encountered in deploying such a system for use in the University of Washington Neonatal Intensive Care Unit (NICU). The lessons learned could be applied to other institutions that will seek to add handheld technology to information systems in the future.

Computers, Handheld↗