Joyce A Mitchell

University of Utah | UOU · Department of Biomedical Informatics

Use of electronic medical records (EMR) and residual clinical biospecimens have become important for the conduct of biomedical research. Currently, human subjects' protection regulations permit much of this research to be conducted without individual informed consent, posing a risk to biomedical research from public objection. We sought to understa...

The multi-institutional PHIS+ clinical database is currently being developed to support pediatric comparative effectiveness research, and will include information extracted from clinical narratives. We are currently developing a pneumonia information extraction application for this purpose, aiming at the rapid adaptation of existing recent informat...

Federation and integration of data from disparate data sources requires semantic interoperability by mapping local coding schemas to standard terminologies. Absence of local coding schemas for some data and the use of free text entries has made mapping to standards a time and resource consuming endeavor. We are currently developing an automated fra...

The University of Utah Health Sciences (UUHSC) and Intermountain Healthcare (IH) support high value clinical and translational research programs. The Utah Biohealth Initiative will facilitate next generation research by leveraging the combined resources of both institutions through an infrastructure which links biospecimens and electronic health re...

How can health sciences librarians and biomedical informaticians offer relevant support to Clinical and Translational Science Award (CTSA) personnel? The Spencer S. Eccles Health Sciences Library and the associate vice president for information technology for the health sciences office at the University of Utah conducted a needs assessment. Faculty...

Objectives: To explore medical student perspectives regarding the importance of biomedical informatics learning objectives to career development, and the amount of emphasis that should be placed on content associated with these objectives in the curriculum. Methods A Web-based survey was e-mailed to 405 students enrolled at the University of Utah,...

In the last 50 years, computational applications have been developed to aid clinicians and researchers alike in the broad field of Biomedicine. Adopted early in the evolution of the field, the term medical informatics has been applied to the various sub-disciplines of computer applications and methods of organizing and using information principles...

Microbiology study results are necessary for conducting many comparative effectiveness research studies. Unlike core laboratory test results, microbiology results have a complex structure. Federating and integrating microbiology data from six disparate electronic medical record systems is challenging and requires a team of varied skills. The PHIS+...

Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous informatio...

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also off...

Accurate interpretation of gene testing is a key component in customizing patient therapy. Where confirming evidence for a gene variant is lacking, computational prediction may be employed. A standardized framework, however, does not yet exist for quantitative evaluation of disease association for uncertain or novel gene variants in an objective ma...

Additional figures. Figures S1 and S2: test results from representative algorithms such as Scolioscore and FibroTest. Figure S3: analysis of variance explained as determined using principal components. (A) Scree plot of descending eigenvalues displaying the five principal components corresponding to the combined predictor algorithms. (B) Percent va...

Additional tables. Table S1: five predictor results for benign RET gene variants. Table S2: five predictor results for pathogenic RET gene variants. Table S3: five predictor results for uncertain RET gene variants. Table S4: descriptive statistics, correlation of predictors and significance for RET gene variants with known disease association. Tabl...

The rapid advance of gene sequencing technologies has produced an unprecedented rate of discovery of genome variation in humans. A growing number of authoritative clinical repositories archive gene variants and disease phenotypes, yet there are currently many more gene variants that lack clear annotation or disease association. To date, there has b...

Clinical research, being patient-oriented, is based predominantly on clinical data— symptoms reported by patients, observations of patients made by healthcare providers, radiological images, and various metrics, including laboratory measurements that reflect physiological functions. Recently, however, a new type of data—genes and their products—has...

Integrating clinical data with administrative data across disparate electronic medical record systems will help improve the internal and external validity of comparative effectiveness research. The Pediatric Health Information System (PHIS) currently collects administrative information from 43 pediatric hospital members of the Child Health Corporat...

In the last 50 years, computational applications have been developed to aid clinicians and researchers alike in the broad field of Biomedicine. Adopted early in the evolution of the field, the term medical informatics has been applied to the various sub-disciplines of computer applications and methods of organizing and using information principles...

To reflect on the history, status, and future trends of decision support in health and biomedical informatics. To highlight the new challenges posed by the complexity and diversity of genomic and clinical domains. To examine the emerging paradigms for supporting cost-effective, personalized decision making. A group of international experts in healt...

List of abbreviations. List of different standard and local abbreviations, used in the manuscript.

Retrospective research requires longitudinal data, and repositories derived from electronic health records (EHR) can be sources of such data. With Health Information Technology for Economic and Clinical Health (HITECH) Act meaningful use provisions, many institutions are expected to adopt EHRs, but may be left with large amounts of financial and hi...

To compare colonoscopy screening/surveillance rates by level of risk for colorectal cancer based on age, personal history of adenomatous polyps or colorectal cancer, or family history of colorectal cancer. Participants were aged 30-90 years, were seen within 5 years at Intermountain Healthcare, and had family history in the Utah Population Database...

Although reported gene variants in the RET oncogene have been directly associated with multiple endocrine neoplasia type 2 and hereditary medullary thyroid carcinoma, other mutations are classified as variants of uncertain significance (VUS) until the associated clinical phenotype is made clear. Currently, some 46 non-synonymous VUS entries exist i...

Using a large, retrospective cohort from the Utah Population Database, we assess how well family history predicts who will acquire colorectal cancer during a 20-year period. Individuals were selected between ages 35 and 80 with no prior record of colorectal cancer diagnosis, as of the year 1985. Numbers of colorectal cancer-affected relatives and d...

The objectives of this study were to assess the reactions of adult patients and parents of children with metabolic conditions to receipt of an "information prescription" (IP) to visit Genetics Home Reference (GHR), a National Institutes of Health/National Library of Medicine online resource, and evaluate the perceived utility of information found o...

Nanomedicine and nanoinformatics are novel disciplines facing substantial challenges. Since nanomedicine involves complex and massive data analysis and management, a new discipline named nanoinformatics is now emerging to provide the vision and the informatics methods and tools needed for such purposes. Methods from biomedi-cal informatics may prov...

The American College of Medical Informatics is an honorary society established to recognize those who have made sustained contributions to the field. Its highest award, for lifetime achievement and contributions to the discipline of medical informatics, is the Morris F Collen Award. Dr Collen's own efforts as a pioneer in the field stand out as the...

The Federated Utah Research and Translational Health e-Repository (FURTHeR) is a Utah statewide informatics platform for the new Center for Clinical and Translational Science at the University of Utah. We have been working on one of FURTHeR's key components, a federated query engine for heterogeneous resources, that we believe has the potential to...

Genetic testing is becoming increasingly important to medical practice. Integrating genetics and genomics data into electronic medical records is crucial in translating genetic discoveries into improved patient care. Information technology, especially Clinical Decision Support Systems, holds great potential to help clinical professionals take full...

To evaluate the i2b2 Hive as a tool to query, visualize, and extract clinical data, we selected a use case from the i2b2 airways diseases driving biology project: asthma exacerbations prediction. We analyzed the cohort selection and the extraction of the clinical data used by this asthma exacerbations prediction study. The structured data included...

'Description of the data requests presented in tables 1 &2'. 'Additional file 1' contains descriptions of the data requests as they were entered in the data-request tool, and the numbering is consistent with that used in tables 1 &2 in the manuscript.

Selecting patient cohorts is a critical, iterative, and often time-consuming aspect of studies involving human subjects; informatics tools for helping streamline the process have been identified as important infrastructure components for enabling clinical and translational research. We describe the evaluation of a free and open source cohort select...

We investigated the suitability of representing discrete genetic test results in the electronic health record (EHR) as individual single nucleotide polymorphisms (SNPs) and as alleles, using the CYP2C9 gene and its polymorphic states, as part of a pilot study. The purpose of our investigation was to determine the appropriate level of data abstracti...

Over the last decades Nanotechnology has promised to advance science and technology in many areas. Within medicine, Nanomedicine promises to deliver new methods for diagnosis, prognosis and therapy. As the amount of available information is rapidly growing, new Biomedical Informatics approaches have to be developed to satisfy the increasing demand...

The IOM report, Preventing Medication Errors, emphasizes the overall lack of knowledge of the incidence of adverse drug events (ADE). Operating rooms, emergency departments and intensive care units are known to have a higher incidence of ADE. Labor and delivery (L&D) is an emergency care unit that could have an increased risk of ADE, where reported...

Infobuttons are decision support tools that provide links within electronic medical record systems to relevant content in online information resources. The aim of infobuttons is to help clinicians promptly meet their information needs. The objective of this study was to determine whether infobutton links that direct to specific content topics ("top...

The University of Utah has initiated the design and implementation of an innovative data and knowledge management informatics platform for the new Center for Clinical and Translational Science. The main component of the platform is described, along with preliminary project objectives and current status.

Biomedical Informatics as a whole faces a difficult epistemological task, since there is no foundation to explain the complexities of modeling clinical medicine and the many relationships between genotype, phenotype, and environment. This paper discusses current efforts to investigate such relationships, intended to lead to better diagnostic and th...

Clinical gene sequencing is growing in importance and cost-effectiveness. In the past two years, the number of genes associated with disease has grown by roughly 25%. Knowledge of genetic variations will soon guide drug selection and dosages, predict risks from toxin exposures, and inform nutritional needs. Despite the significance of sequencing, m...

Advances in newborn screening (NBS) have led to earlier detection of heritable conditions. Little is known about the natural history of these conditions or the long-term benefits of NBS. This study will examine the user and data requirements necessary to develop a long-term follow-up registry for these patients. The system will subsequently be anal...

The standard method for comparing gene products (proteins or RNA) is to compare their DNA or amino acid sequences. Additional information about some gene products may come from multiple sources, including the set of Gene Ontology (GO) annotations and the set of journal abstracts related to each gene product. Gene product similarity measures can be...

One of the most important objects in bioinformatics is a gene product (protein or RNA). For many gene products, functional information is summarized in a set of Gene Ontology (GO) annotations. For these genes, it is reasonable to include similarity measures based on the terms found in the GO or other taxonomy. In this paper, we introduce several no...

This paper focuses on the first two years of operation of Genetics Home Reference (GHR), a Web-based resource <http://www.ghr.nlm.nih.gov> for the general public that helps to explain the health implications of findings from the Human Genome Project. Key challenges of Web-based consumer health communication encountered in the growth and maintenance...

As the knowledge about the genetic factors associated with clinical conditions increases, access to information that can help practicing clinicians better understand these factors becomes essential for optimal care and communication with patients. We describe the implementation of 'infobuttons' from the problem list module of an electronic health r...

An emphasis on patient safety and an administrative mandate to have information systems in place in most health care agencies in the USA by 2014 has put pressure on nursing informatics programs to increase the number of graduates. At the same time a need for change in health professions education was emphasized at an educational summit sponsored by...

The surge of information generated by the Human Genome Project has left many health professionals and their patients struggling to understand the role of genetics in health and disease. To aid the lay public and health professionals, the US National Library of Medicine developed an online resource called 'Genetics Home Reference' (GHR), located at...

The human genome project and its related research bring the promise of a revolution in our knowledge of the function of genes and their interactions with environmental factors across multiple species. However, there is a huge amount of information related to these genes that is located in multiple knowledge sources available on the Internet, with m...

Recent years have seen an explosive growth in the amount of biological data available for analysis. The large volume of data collected makes it necessary to automatically classify and sort such data on a very large scale. Typically, investigators use computational sequence analysis tools to assign functions to newly found gene products. The problem...

The article, “Telegenetics in Maine: Successful clinical and educational service delivery model” published in this issue of Genetics in Medicine¹ demonstrates the continuation of a 30-year trend to make genetics services available to remote populations through outreach efforts from clinical genetics units located at tertiary care genetics centers.2...

The paper addresses the problem of constructing a functional summarization of groups of gene products that are found by clustering a database of such products annotated by the Gene Ontology. Our method builds the "most representative term" (MRT) for each cluster in three increasingly sensitive ways. Initially, we perform crisp hierarchical clusteri...

In an earlier paper we developed an algorithm based on Linear combinations of Order Statistics (LOS) operators that constructs dissimilarity measures on pairs of gene products described by sets of terms from the Gene Ontology. Examples using a data set named GPD194 12·10·03 showed that LOS measures produced relational data with more (visually appar...

We present BITOLA, an interactive literature-based biomedical discovery support system. The goal of this system is to discover new, potentially meaningful relations between a given starting concept of interest and other concepts, by mining the bibliographic database MEDLINE. To make the system more suitable for disease candidate gene discovery and...

This study describes the system architecture and user acceptance of a suite of programs that deliver information about newly updated library resources to clinicians' personal digital assistants (PDAs). Participants received headlines delivered to their PDAs alerting them to new books, National Guideline Clearinghouse guidelines, Cochrane Reviews, a...

The authors have developed the Genetics Home Reference, a consumer resource that addresses the health implications of the Human Genome Project. The research results made possible by the Human Genome Project are being made available increasingly in scientific databases on the Internet, but, because of the often highly technical nature of these datab...

As telemedicine alters the process of health care and introduces new technology, the extent to which it introduces new errors or allows for the occurrence of familiar errors needs to be examined. TELEMEDICINE'S IMPACT ON PATIENT SAFETY FEATURES OF TRADITIONAL CARE: The accuracy of diagnostic decisions reached via telemedicine can be directly affect...

One of the most important objects in bioinformatics is a gene product (a protein or an RNA). Besides the gene sequence and expression values found following a microarray experiment, for many gene products, additional functional information comes from the set of gene ontology (GO) annotations and the set of journal abstracts related to the gene prod...

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-Colum...

Clinical decisions based on a meta-analysis that is based on an ineffective retrieval strategy may have serious negative consequences for patients. The study objective was to investigate the extent to which meta-analyses report proof of their retrieval strategies' effectiveness. The authors examined a random sample (n = 100) of articles in the 1996...

The Genetics Home Reference (GHR) is a new information resource developed to be part of the National Library of Medicine's (NLM's) consumer health initiatives. The GHR's guiding principle is to make the health implications of the Human Genome Project accessible to the public. The GHR accomplishes this by providing a bridge between the NLM's consume...

The Human Genome Project (HGP) and e-Health are two fundamental changes that will alter the way we approach human health and life. These two scientific and societal forces will inevitably impact each other. This paper not only explores the ways that the HGP will change health care but also investigates the ways that e-Health systems will be influen...

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-Colum...

We collected data on patient satisfaction with the use of teledermatology services. During a 27-month study, a single dermatologist saw a total of 321 patients via telemedicine. The patients completed 483 surveys, although not all questions were answered on all surveys. There was a high level of satisfaction among patients using teledermatology: 88...

We present an initial analysis of the National Library of Medicine's (NLM) Gene Indexing initiative. Gene Indexing occurs at the time of indexing for all 4600 journals and over 500,000 articles added to PubMed/MEDLINE each year. Gene Indexing links articles about the basic biology of a gene or protein within eight model organisms to a specific reco...

One of the goals of biomedical scientists in this exciting era of molecular biology is the discovery of novel genes and their relationship to the molecular basis of disease. Part of this information connecting the geno-type to the phenotype is already known and available through hubs such as LocusLink. Although Locus-Link is a valuable resource tha...

Microarrays allow researchers to gather data about the expression patterns of thousands of genes simultaneously. Statistical analysis can reveal which genes show statistically significant results. Making biological sense of those results requires the retrieval of functional information about the genes thus identified, typically a manual gene-by-gen...

The Genetics Home Reference (GHR) is a new information resource developed to be part of the National Library of Medicine's (NLM's) consumer health initiatives. The GHR's guiding principle is to make the health implications of the Human Genome Project accessible to the public. The GHR accomplishes this by providing a bridge between the NLM's consume...

Physicians need better access to information when making patient care decisions. Hospitals should allow electronic data transfers to physician PDAs to improve patient care, and physicians must institute measures to secure the confidentiality of patient information on their PDAs. By explicitly excluding copies from their designated record set, hospi...

We present an interactive literature based biomedical discovery support system (BITOLA). The goal of the system is to discover new, potentially meaningful relations between a given starting concept of interest and other concepts, by mining the bibliographic database Medline. To make the system more suitable for disease candidate gene discovery and...

While several sources of biomedical knowledge are available, these resources are often highly specialized and usually not suitable for a lay audience. This paper evaluates whether concepts needed for molecular biology and genetic diseases are present in WordNet, the electronic lexical database. Terms for four broad categories of concepts (phenotype...

As part of an investigation of connecting health professionals and the lay public to both disease and genomic information, we assessed the availability and nature of the data from the Human Genome Project relating to human genetic diseases. We focused on a set of single gene diseases selected from main topics in MEDLINEplus, the NLM's principal res...

Objectives: As part of an investigation of connecting health professionals and the lay public to both disease and genomic information, we assessed the availability and nature of the data from the Human Genome Project relating to human genetic diseases. Methods: We focused on a set of single gene diseases selected from main topics in MEDLINEplus, th...

Autonomous agents for topic driven retrieval of information from the Web are currently a very active area of research. The ability to conduct real time searches for information is important for many users including biomedical scientists, health care professionals and the general public. We present preliminary research on different retrieval agents...

Objectives: Terminology and knowledge resources are essential components of interoperability among disparate systems. This paper evaluates whether names and relationships needed in biomedical informatics are present in the UMLS. Terms for five broad categories of concepts were extracted from LocusLink and mapped to the UMLS Metathesausus. Relations...

As part of an investigation of connecting health professionals and the lay public to both the disease and genomic information, we assessed the availability and nature of the data from the Human Genome Project relating to human genetic diseases. We focused on a set of single gene diseases selected from main topics in MEDLINEplus. We used publicly av...

Access to emergency treatment in rural areas can often mean the difference between life and death. Telemedicine technologies have the potential of providing earlier diagnosis and intervention, of saving lives and of avoiding unnecessary transfers from rural hospital emergency departments to urban hospitals. This study examined the hypothetical impa...