Faculty Bibliography

Transdisciplinary research accelerates scientific progress. Despite the value of social network analysis to characterize interdepartmental collaboration, institutions have been slow to adopt the approach. We use the approach to characterize collaboration among obesity researchers at our institution, identifying cores of researchers engaged in frequent collaborations. Providing an objective view of research across an institution, social network analysis is a baseline for efforts to facilitate transdisciplinary collaboration.

This work has the objective to implement a search strategy model for high precision retrieval of documents in reply to a clinical query. To achieve this goal we designed a series of search filters on a staged configuration that allow documents to be retrieved from the most precise to the less specific. We found that for most questions the most relevant articles are retrieved at early stages of the search.

In the interest of designing an automated high-level, longitudinal clinical summary of a patient record, we analyze traditional ways in which medical problems pertaining to the patient are summarized in the electronic health record. The patient problem list has become a commonly used proxy for a summary of patient history and automated methods have been proposed to generate it. However, little research has been conducted on how to structure the problem list in a manner most effective for supporting clinical care. This study analyzes the structure and content of the Past Medical History (PMH) sections of a large corpus of clinical notes, as a proxy for problem lists. Findings show that when listing patients history, physicians convey several semantic types of information, not only problems. Furthermore, they often group related concepts in a single line of the PMH. In contrast, traditional problem lists allow only a simple enumeration of coded terms. Content analysis goes on to reiterate the value of more complex representations as well as provide valuable data and guidelines for automated generation of a clinical summary.

In this paper we examine frequently performed clinical research activities with the objective of identifying aspects of workflow that could be amenable to informatics-based re-engineering. This paper is part of a series of studies under the NIH Roadmap initiative, which examines workflow of clinical research in community practices. We describe three common work activities, detailing the main actors involved, the tools used and the challenges faced. These activities illustrate inefficiencies in the clinical research workflow which include: a) lack of supporting tools to perform routine work activities, b) redundancy, low reuse of data and poor interoperability between systems and c) the fragmented and distributed nature of the workflow. We identify opportunities for re-engineering at both a micro (activity) and macro level (organization).

Colon cancer screening rates in women are low. Whether screening for breast and cervical cancer is associated with colon cancer screening behavior is unknown but could provide linkage opportunities. To identify the extent to which both breast and cervical cancer screening increases uptake of colon cancer screening among women in New York City. Women at least 50 years old completed questionnaires for the New York Cancer Project. Analyses compared rates of endoscopic colon cancer screening with adherence to screening recommendations for breast and cervical cancer. Of the 3,386 women, 87.8% adhered to breast and cervical cancer screening guidelines, yet only 42.1% had received endoscopic colon cancer screening. Most women with colon cancer screening (95%) also reported past mammogram and Pap-smear. In multivariable analysis, women who adhered to the other two procedures were more likely to have had colon cancer screening than women with no prior history (OR = 4.4; CI = 2.36, 8.20), after accounting for age, race/ethnicity, insurance status, family history of cancer and income. Significant predictors of endoscopic colon cancer screening included: age over 65 years (OR = 1.63; CI = 1.23, 2.15) with 50-65 years old as the reference, any health insurance (OR = 2.18; CI = 1.52, 3.13) and a family history of cancer (OR = 1.38; CI = 1.17, 1.61). Colorectal cancer screening remains low, even among women who undergo other cancer screening tests. Opportunities to link cancer screening tests to encourage colon cancer screening merit closer attention.

Several training programs in biomedical informatics in the United States are attempting to integrate biological and clinical informatics. However, significant differences in the cultures underlying these two disciplines pose barriers to a uniform educational solution. This paper recounts the experience at Columbia University in adapting a graduate program with an initial focus on clinical informatics to train bioinformaticians. The analysis begins by considering the development of the medical and biological informatics cultures over a 17-year period. Then we review how two separate curricula evolved to serve the needs of each group. Interviews with bioinformatics students and faculty indicated some dissatisfaction with the curriculum that developed within clinical informatics. Their comments are considered in the light of an analysis of the relationship between the application domains of biomedical informatics as a discipline. In response, a new curriculum was developed in which bioinformatics and clinical informatics are regarded as subdivisions of the same subject. A key feature of this curriculum is a new course, Theory and Methods in Biomedical Informatics, which presents informatics principles in their general form, and illustrates their application with examples drawn from across the biomedical spectrum. The paper concludes with suggestions for integrating informatics training programs at other institutions.

The use of conceptual knowledge collections or structures within the biomedical domain is pervasive, spanning a variety of applications including controlled terminologies, semantic networks, ontologies, and database schemas. A number of theoretical constructs and practical methods or techniques support the development and evaluation of conceptual knowledge collections. This review will provide an overview of the current state of knowledge concerning conceptual knowledge acquisition, drawing from multiple contributing academic disciplines such as biomedicine, computer science, cognitive science, education, linguistics, semiotics, and psychology. In addition, multiple taxonomic approaches to the description and selection of conceptual knowledge acquisition and evaluation techniques will be proposed in order to partially address the apparent fragmentation of the current literature concerning this domain.

OBJECTIVE:To characterize global structural features of large-scale biomedical terminologies using currently emerging statistical approaches. DESIGN/METHODS:Given rapid growth of terminologies, this research was designed to address scalability. We selected 16 terminologies covering a variety of domains from the UMLS Metathesaurus, a collection of terminological systems. Each was modeled as a network in which nodes were atomic concepts and links were relationships asserted by the source vocabulary. For comparison against each terminology we created three random networks of equivalent size and density. MEASUREMENTS/METHODS:Average node degree, node degree distribution, clustering coefficient, average path length. RESULTS:Eight of 16 terminologies exhibited the small-world characteristics of a short average path length and strong local clustering. An overlapping subset of nine exhibited a power law distribution in node degrees, indicative of a scale-free architecture. We attribute these features to specific design constraints. Constraints on node connectivity, common in more synthetic classification systems, localize the effects of changes and deletions. In contrast, small-world and scale-free features, common in comprehensive medical terminologies, promote flexible navigation and less restrictive organic-like growth. CONCLUSION/CONCLUSIONS:While thought of as synthetic, grid-like structures, some controlled terminologies are structurally indistinguishable from natural language networks. This paradoxical result suggests that terminology structure is shaped not only by formal logic-based semantics, but by rules analogous to those that govern social networks and biological systems. Graph theoretic modeling shows early promise as a framework for describing terminology structure. Deeper understanding of these techniques may inform the development of scalable terminologies and ontologies.

One of the goals of the NIH Roadmap Initiative is to re-engineer the national clinical research enterprise, with an emphasis on information technology solutions. Understanding end-users' workflow is critical to developing technology systems that are grounded in the context of the users' environment and are designed to fulfill their needs. Community practices are becoming the prevailing setting for conducting clinical research. Few studies have assessed clinical research workflow in such settings. We have conducted a series of investigations to model the workflow and have previously reported on some basic aspects of it, like the lack of information systems to support the workflow. In this paper we describe finer details of the workflow, using results of observational studies. These findings highlight the needs and inefficiencies that suggest the kind of information system that must be developed to enhance collaboration, communication and improve efficiency. This preliminary investigation also opens ground for more extensive studies to further elucidate the workflow.

Signout is an unofficial clinical document used traditionally to facilitate patient handoff. Qualitative studies have suggested its importance in clinical care. We used a novel technique to quantify the use of signout by analyzing clinical information system logfiles. Viewing and editing events were collected for 1,677 unique patients admitted to our internal medicine service. We found the average patient's signout on a given day is viewed frequently (>6x) and edited frequently (>2x) with multiple unique viewers (>3) and editors (>1). We also found that signouts are used throughout a 24-hour period, not just at the time of handoff. Finally, we showed that they are viewed months and even years after their creation. Signout is therefore a highly utilized, collaborative, clinical document used for more than patient handoff. Our findings also suggest that clinical information systems may benefit from the introduction of collaborative tools such as subscription, versioning, and author-attribution utilities.