Personalized medicine

pre-printWith the completion of the Human Genome Project in 2003, the world's attention has focused on converting this vast storehouse of information into innovative health care solutions. The ultimate promise, assuming we know everyone's genotype, is to ensure that every person has optimum health throughout his/her life. This promise has many parts, including optimum nutrition, clean air and water supplies, up-to-date immunizations and regular health screenings. The part of the promise to be fulfilled by knowledge and information stemming from genomics, proteomics and other "omics" is yet unfolding, but the first cautious steps are being taken and are called "Personalized Medicine". Personalized Medicine implies that optimum health goes beyond the basics of clean air and water and takes advantage of the "omics" knowledge to allow the person and his/her clinicians to make therapeutic and lifestyle choices which take the "omics" into account

The Missouri planning grant for the education and training of health sciences librarians

pre-printThe planning grant at the School of Library and Informational Science (SLIS) at the University of Missouri has two aims: (a) developing a model curriculum for health sciences librarianship at the master's level and (b) developing materials that can be delivered by alternative instructional methods. To accomplish the first aim, the faculty will investigate the possibility of offering courses in other disciplines, such as health care administration, educational technology, adult education, and medical sociology. In addition, the SLIS faculty will investigate the development of new kinds of placement for the students' practicum experience. To reach the second aim, the SLIS faculty will investigate alternative means of delivering both graduate and continuing education. Three instructional modalities will be evaluated. Some material will be delivered via satellite broadcast, some material will be made available via the World Wide Web and some will be presented in an intensive seminar. The outcome of the planning grant will be two distinct plans. The first will be a plan for the curriculum in health sciences librarianship at the master's level. The second will be a plan for offering instruction through alternative methods, both for graduate education and for continuing education

Beyond relevance--characteristics of key papers for clinicians: an exploratory study in an academic setting

pre-printObjective: The purpose of this study was to determine what factors beyond relevance influence a clinician's decision to choose to read one journal article over another in satisfying an information need. Design: Seventeen health care providers were interviewed and then surveyed regarding the characteristics of key articles (those they would not want to miss). On a Likert scale, the clinicians graded forty-two characteristics for importance in the decision process. Relevance was assumed and not at issue. Setting: The study took place in an academic health sciences center. Subjects: The subjects were seventeen clinicians, all with patient care responsibilities. There were four internists, four surgeons, three family practitioners, three pediatricians, two psychiatrists, and one clinical psychologist. Results: Factors beyond relevance that most often influenced the decision process pertained to methodological rigor, authors and their institutional affiliations, document types, and population studied. Conclusions: Among the clinicians surveyed, factors beyond topicality influenced judgments as to what constitutes an important article. The emphasis respondents gave to certain attributes is echoed in other published work and highlights the need for more intensive investigation of these non-subject indicators as search parameters. Improved searching capabilities might well lead to a significant reduction in the clinician's information overload

Nanoinformatics: a new area of research in nanomedicine

pre-printAbstract: 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 information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and -omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings

Assessing clinical researchers information needs to create responsive portals and tools: my research assistant (MyRA) at the University of Utah: a case study

pre-printQuestion: How can health sciences librarians and biomedical informaticians offer relevant support to Clinical and Translational Science Award (CTSA) personnel? Setting: 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. Methods: Faculty and staff from these two units, with the services of a consultant and other CTSA partners, employed a survey, focus groups, interviews, and committee discussions. An information portal was created to meet identified needs. Results: A directive white paper was created. The process employed to plan a virtual and physical collaborative, collegial space for clinical researchers at the university and its three inter-institutional CTSA partners is described. Conclusion: The university's model can assist other librarians and informaticians with how to become part of a CTSA-focused infrastructure for clinical and translational research and serve researchers in general

Fuzzy measures on the Gene Ontology for gene product similarity

pre-printOne 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 novel measures for computing the similarity of two gene products annotated with GO terms. The fuzzy measure similarity (FMS) has the advantage that it takes into consideration the context of both complete sets of annotation terms when computing the similarity between two gene products. When the two gene products are not annotated by common taxonomy terms, we propose a method that avoids a zero similarity result. To account for the variations in the annotation reliability, we propose a similarity measure based on the Choquet integral. These similarity measures provide extra tools for the biologist in search of functional information for gene products. The initial testing on a group of 194 sequences representing three proteins families shows a higher correlation of the FMS and Choquet similarities to the BLAST sequence similarities than the traditional similarity measures such as pairwise average or pairwise maximum

Challenges and strategies of the Genetics Home Reference

pre-printObjective: This paper focuses on the first two years of operation of Genetics Home Reference (GHR), a Web-based resource for the general public that helps to explain the health implications of findings from the Human Genome Project. Methods and Findings: Key challenges of Web-based consumer health communication encountered in the growth and maintenance of GHR are discussed: prioritizing topics for GHR, streamlining the development process while keeping genetic information accurate, and designing a system that helps consumers navigate complex genetic relationships. Various strategies are used to address these challenges. Tying content development to topics of national priority and addressing topics requested by users makes the site increasingly important for both consumers and health professionals. Informatics methods are essential for quality control, particularly for genetic information that changes frequently. Indexing and hierarchical browsing features help to facilitate navigation. Conclusions: GHR is a credible, dynamic Website that uses lay language to explain the effects of genetic variation on human health. Informatics strategies are key to effective management of a large and expanding body of genetics information. Feedback from formal and informal sources indicates increasing usage and favorable acceptance of GHR

Evaluating the informatics for integrating biology and the bedside system for clinical research

pre-printBackground: 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 selection tool from the Informatics for Integrating Biology and the Bedside (i2b2) group: the i2b2 hive. Methods: Our evaluation included the usability and functionality of the i2b2 hive using several real world examples of research data requests received electronically at the University of Utah Health Sciences Center between 2006 - 2008. The hive server component and the visual query tool application were evaluated for their suitability as a cohort selection tool on the basis of the types of data elements requested, as well as the effort required to fulfill each research data request using the i2b2 hive alone. Results: We found the i2b2 hive to be suitable for obtaining estimates of cohort sizes and generating research cohorts based on simple inclusion/exclusion criteria, which consisted of about 44% of the clinical research data requests sampled at our institution. Data requests that relied on post-coordinated clinical concepts, aggregate values of clinical findings, or temporal conditions in their inclusion/exclusion criteria could not be fulfilled using the i2b2 hive alone, and required one or more intermediate data steps in the form of pre-or post-processing, modifications to the hive metadata, etc. Conclusion: The i2b2 hive was found to be a useful cohort-selection tool for fulfilling common types of requests for research data, and especially in the estimation of initial cohort sizes. For another institution that might want to use the i2b2 hive for clinical research, we recommend that the institution would need to have structured, coded clinical data and metadata available that can be transformed to fit the logical data models of the i2b2 hive, strategies for extracting relevant clinical data from source systems, and the ability to perform substantial pre- and post-processing of these data

The creation and early implementation of a high speed fiber optic network for a university health sciences center

pre-printIn late 1989 the University of Missouri Health Sciences Center began the process of creating an extensive fiber optic network throughout its facilities, with the intent to provide networked computer access to anyone in the Center desiring such access, regardless of geographic location or organizational affiliation. A committee representing all disciplines within the Center produced and, in conjunction with independent consultants, approved a comprehensive design for the network. Installation of network backbone components commenced in the second half of 1990 and was completed in early 1991. As the network entered its initial phases of operation, the first realities of this important new resource began to manifest themselves as enhanced functional capacity in the Health Sciences Center. This paper describes the development of the network, with emphasis on its design criteria, installation, early operation, and management. Also included are discussions on its organizational impact and its evolving significance as a medical community resource

Computational Feature of Selection and Classification of RET Phenotypic Severity

pre-printAlthough many reported mutations in the RET oncogene have been directly associated with hereditary thyroid carcinoma, other mutations are labelled as uncertain gene variants because they have not been clearly associated with a clinical phenotype. The process of determining the severity of a mutation is costly and time consuming. Informatics tools and methods may aid to bridge this genotype-phenotype gap. Towards this goal, machine-learning classification algorithms were evaluated for their ability to distinguish benign and pathogenic RET gene variants as characterized by differences in values of physicochemical properties of the residue present in the wild type and the one in the mutated sequence. Representative algorithms were chosen from different categories of machine learning classification techniques, including rules, bayes, and regression, nearest neighbour, support vector machines and trees. Machine-learning models were then compared to well-established techniques used for mutation severity prediction. Machine-learning classification can be used to accurately predict RET mutation status using primary sequence information only. Existing algorithms that are based on sequence homology (ortholog conservation) or protein structural data are not necessarily superior