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Background Electronic Health Records (EHRs) have the potential to improve many aspects of care and their use has increased in the last decade. Because of this, acceptance and adoption of EHRs is less of a concern than adaptation to use. To understand this issue more deeply, we conducted a qualitative study of physician perspectives on EHR use to identify factors that facilitate adaptation. Methods We conducted semi-structured interviews with 9 physicians across a range of inpatient disciplines at a large Academic Medical Center. Interviews were conducted by phone, lasting approximately 30 min, and were transcribed verbatim for analysis. We utilized inductive and deductive methods in our analysis. Results We identified 4 major themes related to EHR adaptation: impact of EHR changes on physicians, how physicians managed these changes, factors that facilitated adaptation to using the EHR and adapting to using the EHR in the patient encounter. Within these themes, physicians felt that a positive mindset toward change, providing upgrade training that was tailored to their role, and the opportunity to learn from colleagues were important facilitators of adaptation. Conclusions As EHR use moves beyond implementation, physicians continue to be required to adapt to the technology and to its frequent changes. Our study provides actionable findings that allow healthcare systems to focus on factors that facilitate the adaptation process for physicians.

Objectives: To develop and apply formal ontology creation methods to the domain of antimicrobial prescribing and to formally evaluate the resulting ontology through intrinsic and extrinsic evaluation studies. Methods: We extended existing ontology development methods to create the ontology and implemented the ontology using Protege-OWL. Correctness of the ontology was assessed using a set of ontology design principles and domain expert review via the laddering technique. We created three artifacts to support the extrinsic evaluation (set of prescribing rules, alerts and an ontology-driven alert module, and a patient database) and evaluated the usefulness of the ontology for performing knowledge management tasks to maintain the ontology and for generating alerts to guide antibiotic prescribing. Results: The ontology includes 199 classes, 10 properties, and 1636 description logic restrictions. Twenty-three Semantic Web Rule Language rules were written to generate three prescribing alerts: (1) antibiotic-microorganism mismatch alert; (2) medication-allergy alert; and (3) non-recommended empiric antibiotic therapy alert. The evaluation studies confirmed the correctness of the ontology, usefulness of the ontology for representing and maintaining antimicrobial treatment knowledge rules, and usefulness of the ontology for generating alerts to provide feedback to clinicians during antibiotic prescribing. Conclusions: This study contributes to the understanding of ontology development and evaluation methods and addresses one knowledge gap related to using ontologies as a clinical decision support system component-a need for formal ontology evaluation methods to measure their quality from the perspective of their intrinsic characteristics and their usefulness for specific tasks.

Background Molecular experiments using multiplex strategies such as cDNA microarrays or proteomic approaches generate large datasets requiring biological interpretation. Text based data mining tools have recently been developed to query large biological datasets of this type of data. PubMatrix is a web-based tool that allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term co-occurrence. Results For example, a simple term selection procedure allows automatic pair-wise comparisons of approximately 1–100 search terms versus approximately 1–10 modifier terms, resulting in up to 1,000 pair wise comparisons. The matrix table of pair-wise comparisons can then be surveyed, queried individually, and archived. Lists of keywords can include any terms currently capable of being searched in PubMed. In the context of cDNA microarray studies, this may be used for the annotation of gene lists from clusters of genes that are expressed coordinately. An associated PubMatrix public archive provides previous searches using common useful lists of keyword terms. Conclusions In this way, lists of terms, such as gene names, or functional assignments can be assigned genetic, biological, or clinical relevance in a rapid flexible systematic fashion. http://pubmatrix.grc.nia.nih.gov/