Related Articles

The overarching informatics grand challenge facing society is the creation of knowledge management systems that can acquire, conserve, organize, retrieve, display, and distribute what is known today in a manner that informs and educates, facilitates the discovery and creation of new knowledge, and contributes to the health and welfare of the planet. At one time the private, national, and university libraries of the world collectively constituted the memory of society's intellectual history. In the future, these new digital knowledge management systems will constitute human memory in its entirety. The current model of multiple local collections of duplicated resources will give way to specialized sole-source servers. In this new environment all scholarly scientific knowledge should be public domain knowledge: managed by scientists, organized for the advancement of knowledge, and readily available to all. Over the next decade, the challenge for the field of medical informatics and for the libraries that serve as the continuous memory for the biomedical sciences will be to come together to form a new organization that will lead to the development of postmodern digital knowledge management systems for medicine. These systems will form a portion of the evolving world brain of the 21st century.

The advent of open access to peer reviewed scholarly literature in the biomedical sciences creates the opening to examine scholarship in general, and chemistry in particular, to see where and how novel forms of network technology can accelerate the scientific method. This paper examines broad trends in information access and openness with an eye towards their applications in chemistry.

Summary

Objective

To provide an overview of the expansion in public access to electronic biomedical information over the past two decades, with an emphasis on developments to which the U.S. National Library of Medicine contributed.

Methods

Review of the increasingly broad spectrum of web-accessible genomic data, biomedical literature, consumer health information, clinical trials data, and images.

Results

The amount of publicly available electronic biomedical information has increased dramatically over the past twenty years. Rising expectations regarding access to biomedical information were stimulated by the spread of the Internet, the World Wide Web, advanced searching and linking techniques. These informatics advances simplified and improved access to electronic information and reduced costs, which enabled inter-organizational collaborations to build and maintain large international information resources and also aided outreach and education efforts The demonstrated benefits of free access to electronic biomedical information encouraged the development of public policies that further increase the amount of information available.

Conclusions

Continuing rapid growth of publicly accessible electronic biomedical information presents tremendous opportunities and challenges, including the need to ensure uninterrupted access during disasters or emergencies and to manage digital resources so they remain available for future generations.

Over the past century, the library profession has collaborated with other interested groups to develop a variety of standards for the production, distribution, organization, and description of the published literature. Early successes in standardizing the content and format of bibliographic records gave the library community a firm basis for the creation of information standards for use in automated systems. The current array of relatively mature standards related to the published literature holds more than academic interest for those engaged in medical informatics research and development. In addition to their obvious utility for many applications involving access to the biomedical literature, some of the standards are also applicable to other types of biomedical information. Because bibliographic data share some of the complex characteristics of clinical data, a look at the types of standards that have emerged for the published literature can be helpful in identifying the range of standards to be considered for the clinical environment. An examination of the reasons for success in the development of bibliographic standards may also provide a useful perspective on efforts to develop information standards in other areas of concern to the medical informatics community.

Rapid prototyping is an important element in researching new imaging analysis techniques and developing custom medical applications. In the last ten years, the open source community and the number of open source libraries and freely available frameworks for biomedical research have grown significantly. What they offer are now considered standards in medical image analysis, computer-aided diagnosis, and medical visualization. A cursory review of the peer-reviewed literature in imaging informatics (indeed, in almost any information technology-dependent scientific discipline) indicates the current reliance on open source libraries to accelerate development and validation of processes and techniques. In this survey paper, we review and compare a few of the most successful open source libraries and frameworks for medical application development. Our dual intentions are to provide evidence that these approaches already constitute a vital and essential part of medical image analysis, diagnosis, and visualization and to motivate the reader to use open source libraries and software for rapid prototyping of medical applications and tools.

Rapid prototyping is an important element in researching new imaging analysis techniques and developing custom medical applications. In the last ten years, the open source community and the number of open source libraries and freely available frameworks for biomedical research have grown significantly. What they offer are now considered standards in medical image analysis, computer-aided diagnosis, and medical visualization. A cursory review of the peer-reviewed literature in imaging informatics (indeed, in almost any information technology-dependent scientific discipline) indicates the current reliance on open source libraries to accelerate development and validation of processes and techniques. In this survey paper, we review and compare a few of the most successful open source libraries and frameworks for medical application development. Our dual intentions are to provide evidence that these approaches already constitute a vital and essential part of medical image analysis, diagnosis, and visualization and to motivate the reader to use open source libraries and software for rapid prototyping of medical applications and tools.

Purpose: The paper reviews and analyzes the evolution of the open access (OA) publishing movement and its impact on the traditional scholarly publishing model.

Procedures: A literature survey and analysis of definitions of OA, problems with the current publishing model, historical developments, funding agency responses, stakeholder viewpoints, and implications for scientific libraries and publishing are performed.

Findings: The Internet's transformation of information access has fueled interest in reshaping what many see as a dysfunctional, high-cost system of scholarly publishing. For years, librarians alone advocated for change, until relatively recently when interest in OA and related initiatives spread to the scientific community, governmental groups, funding agencies, publishers, and the general public.

Conclusions: Most stakeholders acknowledge that change in the publishing landscape is inevitable, but heated debate continues over what form this transformation will take. The most frequently discussed remedies for the troubled current system are the “green” road (self-archiving articles published in non-OA journals) and the “gold” road (publishing in OA journals). Both movements will likely intensify, with a multiplicity of models and initiatives coexisting for some time.

Background

Numerous biomedical software applications access databases maintained by the US National Center for Biotechnology Information (NCBI). To ease software automation, NCBI provides a powerful but complex Web-service-based programming interface, eUtils. This paper describes a toolset that simplifies eUtils use through a graphical front-end that can be used by non-programmers to construct data-extraction pipelines. The front-end relies on a code library that provides high-level wrappers around eUtils functions, and which is distributed as open-source, allowing customization and enhancement by individuals with programming skills.

Methods

We initially created an application that queried eUtils to retrieve nephrology-specific biomedical literature citations for a user-definable set of genes. We later augmented the application code to create a general-purpose library that accesses eUtils capability as individual functions that could be combined into user-defined pipelines.

Results

The toolset’s use is illustrated with an application that serves as a front-end to the library and can be used by non-programmers to construct user-defined pipelines. The operation of the library is illustrated for the literature-surveillance application, which serves as a case-study. An overview of the library is also provided.

Conclusions

The library simplifies use of the eUtils service by operating at a higher level, and also transparently addresses robustness issues that would need to be individually implemented otherwise, such as error recovery and prevention of overloading of the eUtils service.

Behavioral momentum theory (Nevin, 1992, Nevin & Grace, 2000) describes the relation between the characteristic level of reinforcement within a context and behavioral resistance to change within that context. This paper will describe the multiple-schedule-disrupter paradigm for basic behavioral momentum research and illustrate it with two representative examples from the literature with non-human subjects. The remainder of the paper will provide a review of translational research in human populations with intellectual and developmental disabilities (IDD) employing the multiple-schedule-disrupter paradigm and closely related variations. The results of this research show that the reinforcer-rate effects predicted by behavioral momentum theory are widely replicated in IDD populations. The intended audience for this paper is the practitioner interested in learning about the current status of translational research in behavioral momentum as a foundation for considering ways in which behavioral momentum theory may be relevant to clinical issues.

The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the EMBL-EBI. Currently, users can access information from more than 62 distinct datasets covering some 400 million entries. The data resources represented in the EB-eye include: nucleotide and protein sequences at both the genomic and proteomic levels, structures ranging from chemicals to macro-molecular complexes, gene-expression experiments, binary level molecular interactions as well as reaction maps and pathway models, functional classifications, biological ontologies, and comprehensive literature libraries covering the biomedical sciences and related intellectual property. The EB-eye can be accessed over the web or programmatically using a SOAP Web Services interface. This allows its search and retrieval capabilities to be exploited in workflows and analytical pipe-lines. The EB-eye is a novel alternative to existing biological search and retrieval engines. In this article we describe in detail how to exploit its powerful capabilities.

Open access to the peer-reviewed primary research literature would greatly facilitate knowledge transfer between the creators and the users of the results of research and scholarship. Criteria are needed to assess the impact of recent initiatives, such as the Budapest Open Access Initiative. For example, how many open-access research journals exist within a given field, and what is the reputation of each one? And, how many openly-accessible institutional e-print archives have been created and how many are actually are being used by researchers and scholars? A simple approach to an assessment of the open-access portion of the medical literature is described, and some preliminary results are summarized. These preliminary results point to the need for incentives to foster the implementation of initiatives such as the Budapest Open Access Initiative. An example of an incentive model is proposed, where an agency or foundation that provides peer-reviewed grants-in-aid to researchers establishes an e-print archive. Only current grantees of the agency would be eligible to post reports about the results of research projects or programs that have been supported by the agency. Some advantages and implications of this particular model are outlined. It is suggested that incentive models of this kind are needed to increase the likelihood that open access to the primary medical research literature will soon reach a "tipping point" and move quickly toward wide acceptance.

The North Carolina Area Health Education Centers Library and Information Services (NC AHEC LIS) Network provides library outreach services to rural health care providers in all nine AHEC regions of North Carolina. Over the last twenty-five years, the AHEC and university-based librarians have collaborated to create a model program for support of community-based clinical education and information access for rural health care providers. Through several collaborative projects, they have supported Internet access for rural health clinics. The NC AHEC Digital Library—under development by NC AHEC, University of North Carolina at Chapel Hill, Duke University, East Carolina University, and Wake Forest University—will further extend access to electronic biomedical information and resources to health professionals in a statewide digital library.

Objective: This paper examines the influence of the digital divide on disparities in health outcomes for vulnerable populations, identifying implications for medical and public libraries.

Method: The paper describes the results of the Digital Divide Pilot Projects demonstration research programs funded by the National Cancer Institute to test new strategies for disseminating relevant health information to underserved and at-risk audiences.

Results: The Digital Divide Pilot Projects field-tested innovative systemic strategies for helping underserved populations access and utilize relevant health information to make informed health-related decisions about seeking appropriate health care and support, resisting avoidable and significant health risks, and promoting their own health.

Implications: The paper builds on the Digital Divide Pilot Projects by identifying implications for developing health communication strategies that libraries can adopt to provide digital health information to vulnerable populations.

Biomedical informatics is a young, highly interdisciplinary field that is evolving quickly. It is important to know which published topics in generalist biomedical informatics journals elicit the most interest from the scientific community, and whether this interest changes over time, so that journals can better serve their readers. It is also important to understand whether free access to biomedical informatics articles impacts their citation rates in a significant way, so authors can make informed decisions about unlock fees, and journal owners and publishers understand the implications of open access. The topics and JAMIA articles from years 2009 and 2010 that have been most cited according to the Web of Science are described. To better understand the effects of free access in article dissemination, the number of citations per month after publication for articles published in 2009 versus 2010 was compared, since there was a significant change in free access to JAMIA articles between those years. Results suggest that there is a positive association between free access and citation rate for JAMIA articles.

Background

Physical activity is an important determinant of health. Walking is the most common physical activity performed by adults and the presence of sidewalks along roads is a determinant of walking. Geographic information systems (GIS) can be used to measure sidewalks; however, GIS sidewalk data are difficult to access. The purpose of this study was to present a new GIS method for measuring the distance and coverage of sidewalks along roadways.

Methods

The new method contains three stages. Stage 1 involves calculating the distance of all road segments within the region of interest (e.g., neighborhood), extracting geospatial information on these road segments, and saving this information as a Google Earth file. This stage was performed in ArcGIS software. Stage 2 involves opening the extracted road segment geospatial data in Google Earth, visually examining road segments to see if they contain sidewalks, and deleting road segments without sidewalks. Stage 3 involves importing the modified road geospatial data into ArcGIS and calculating the length of road segments with sidewalks. The new method was tested in 315 sites across Canada. Each site consisted of a one km radius circular buffer surrounding a school.

Results

A detailed, step-by-step protocol is provided in the paper. The length of road segments with sidewalks in the testing sites ranged from 0.00 to 55.05 km (median 16.20 km). When expressed relative to the length of all road segments, the length of road segments with sidewalks ranged from 0% to 100% (median 53%). By comparison to urban testing sites, rural sites had shorter sidewalk lengths and a smaller proportion of the roads had sidewalk coverage.

Conclusion

This study provides a new GIS protocol that researchers can use to measure the distance and coverage of sidewalks along roadways.

The medical libraries of Vietnam maintain high profiles within their institutions and are recognized by health care professionals and administrators as an important part of the health care system. Despite the multitude of problems in providing even a minimal level of medical library services, librarians, clinicians, and researchers nevertheless are determined that enhanced services be made available. Currently, services can be described as basic and unsophisticated, yet viable and surprisingly well organized. The lack of hard western currency required to buy materials and the lack of library technology will be major obstacles to improving information services. Vietnam, like many developing nations, is about to enter a period of technological upheaval, which ultimately will result in a transition from the traditional library limited by walls to a national resource that will rely increasingly on electronic access to international knowledge networks. Technology such as CD-ROM, Integrated Services Digital Network (ISDN), and satellite telecommunication networks such as Internet can provide the technical backbone to provide access to remote and widely distributed electronic databases to support the information needs of the health care community. Over the long term, access to such databases likely will be cost-effective, in contrast to the assuredly astronomical cost of building a comparable domestic print collection. The advent of new, low-cost electronic technologies probably will revolutionize health care information services in developing nations. However, for the immediate future, the medical libraries of Vietnam will require ongoing sustained support from the international community, so that minimal levels of resources will be available to support the information needs of the health care community. It is remarkable, and a credit to the determination of Vietnam's librarians that, in a country with a legacy of war, economic deprivation, and international isolation, they have somehow managed to provide a sound basic level of information services for health care professionals.

In 1990, the Republican Scientific-Medical Library (RSML) of the Ministry of Health of Armenia in collaboration with the Fund for Armenian Relief created a vision of a national library network supported by information technology. This vision incorporated four goals: (1) to develop a national resource collection of biomedical literature accessible to all health professionals, (2) to develop a national network for access to bibliographic information, (3) to develop a systematic mechanism for sharing resources, and (4) to develop a national network of health sciences libraries. During the last decade, the RSML has achieved significant progress toward all four goals and has realized its vision of becoming a fully functional national library. The RSML now provides access to the literature of the health sciences including access to the Armenian medical literature, provides education and training to health professionals and health sciences librarians, and manages a national network of libraries of the major health care institutions in Armenia. The RSML is now able to provide rapid access to the biomedical literature and train health professionals and health sciences librarians in Armenia in information system use. This paper describes the evolution of the RSML and how it was accomplished.

Background

Recent years have seen an increased amount of natural language processing (NLP) work on full text biomedical journal publications. Much of this work is done with Open Access journal articles. Such work assumes that Open Access articles are representative of biomedical publications in general and that methods developed for analysis of Open Access full text publications will generalize to the biomedical literature as a whole. If this assumption is wrong, the cost to the community will be large, including not just wasted resources, but also flawed science. This paper examines that assumption.

Results

We collected two sets of documents, one consisting only of Open Access publications and the other consisting only of traditional journal publications. We examined them for differences in surface linguistic structures that have obvious consequences for the ease or difficulty of natural language processing and for differences in semantic content as reflected in lexical items. Regarding surface linguistic structures, we examined the incidence of conjunctions, negation, passives, and pronominal anaphora, and found that the two collections did not differ. We also examined the distribution of sentence lengths and found that both collections were characterized by the same mode. Regarding lexical items, we found that the Kullback-Leibler divergence between the two collections was low, and was lower than the divergence between either collection and a reference corpus. Where small differences did exist, log likelihood analysis showed that they were primarily in the area of formatting and in specific named entities.

Conclusion

We did not find structural or semantic differences between the Open Access and traditional journal collections.

Background

This paper examines how the adoption of a subject-specific library service has changed the way in which its users interact with a digital library. The LitMiner text-analysis application was developed to enable biologists to explore gene relationships in the published literature. The application features a suite of interfaces that enable users to search PubMed as well as local databases, to view document abstracts, to filter terms, to select gene name aliases, and to visualize the co-occurrences of genes in the literature. At each of these stages, LitMiner offers the functionality of a digital library. Documents that are accessible online are identified by an icon. Users can also order documents from their institution's library collection from within the application. In so doing, LitMiner aims to integrate digital library services into the research process of its users.

Methods

Case study

Results

This integration of digital library services into the research process of biologists results in increased access to the published literature.

Conclusion

In order to make better use of their collections, digital libraries should customize their services to suit the research needs of their patrons.

To extend our understanding of flowering time control in eudicots, we screened for mutants in the model legume Medicago truncatula (Medicago). We identified an early flowering mutant, spring1, in a T-DNA mutant screen, but spring1 was not tagged and was deemed a somaclonal mutant. We backcrossed the mutant to wild type R108. The F1 plants and the majority of F2 plants were early flowering like spring1, strongly indicating that spring1 conferred monogenic, dominant early flowering. We hypothesized that the spring1 phenotype resulted from over expression of an activator of flowering. Previously, a major QTL for flowering time in different Medicago accessions was located to an interval on chromosome 7 with six candidate flowering- time activators, including a CONSTANS gene, MtCO, and three FLOWERING LOCUS T (FT) genes. Hence we embarked upon linkage mapping using 29 markers from the MtCO/FT region on chromosome 7 on two populations developed by crossing spring1 with Jester. Spring1 mapped to an interval of ∼0.5 Mb on chromosome 7 that excluded MtCO, but contained 78 genes, including the three FT genes. Of these FT genes, only FTa1 was up-regulated in spring1 plants. We then investigated global gene expression in spring1 and R108 by microarray analysis. Overall, they had highly similar gene expression and apart from FTa1, no genes in the mapping interval were differentially expressed. Two MADS transcription factor genes, FRUITFULLb (FULb) and SUPPRESSOR OF OVER EXPRESSION OF CONSTANS1a (SOC1a), that were up-regulated in spring1, were also up-regulated in transgenic Medicago over-expressing FTa1. This suggested that their differential expression in spring1 resulted from the increased abundance of FTa1. A 6255 bp genomic FTa1 fragment, including the complete 5′ region, was sequenced, but no changes were observed indicating that the spring1 mutation is not a DNA sequence difference in the FTa1 promoter or introns.

Some forms of scholarly productivity, such as peer-reviewed publications, are easily recognized and incorporated into processes involving evaluation, retention, and promotion of faculty. A method for initiating peer review of unpublished scholarly activity may serve to permit recognition of such work in faculty evaluation. This article shares an instrument for the peer review of unpublished scholarship, such as scholarship of integration or teaching. A nonquantitative rubric for the evaluation of scholarly activity was developed, based on previously proposed standards from the Carnegie Foundation for the Advancement of Teaching. Such a process for forms of scholarly productivity other than publication provides potential for intellectual growth and development for both reviewers and reviewed faculty

This article reviews the extraordinary growth in the scientific literature that has resulted from increased federal expenditures in the past decade or two. The article further notes that the impact of the knowledge explosion has impinged on the Health Sciences Library as well as on the individual scientist who needs access to the information. A strong plea is made for the librarian to assume a more active role in: doing internal research with respect to how best to use the library as a tool in the dissemination of new information; educating newcomers to the field of library science with respect to the management of scientific information; and converting the library from a passive to an active instrument in disseminating the scholarly record to and among those who require access to it. Medical center administrators are reminded that if the librarian succeeds in these ventures then he will fulfill all of the research, teaching, and service requirements ordinarily made of other academic departments and, in turn, should be rewarded with departmental status for the library.

Unrestricted, open access to scholarly scientific literature provides an opportunity for chemistry educators to go beyond the textbook, introducing students to the real work of scientists. Despite the best efforts of textbook authors to provide information about recent research results, textbooks are not a substitute for learning to use the primary literature. Chemical educators can use open access articles to develop research-related skills, to foster curiosity, and to cultivate the next generation of scientists. It is becoming increasingly important for chemical educators to teach undergraduates how online journals are changing the nature of chemical research. Some institutions can not afford online subscription costs, and open access journals can be an important resource to provide practical experience. Open access publications eliminate the barriers to the central work of scientists providing chemistry educators (whether at well-endowed or economically limited colleges) with the key resources for enhancing student learning through current, relevant research.

Background

Chronic diseases affect millions of children worldwide leading to substantial disease burden to the children and their families as well as escalating health care costs. The increasing trend in the prevalence of complex pediatric chronic diseases requires innovative and optimal delivery of care. Biomedical informatics applications play an important role in improving health outcomes while being cost-effective. However, their utility in pediatric chronic diseases has not been studied in a comprehensive and systematic way. The objective of this study was to conduct a systematic review of the effects of biomedical informatics applications in pediatric chronic diseases.

Methods

A comprehensive literature search was conducted using MEDLINE, the Cochrane Library and EMBASE databases from inception of each database to September 2008. We included studies of any methodological type and any language that applied biomedical informatics to chronic conditions in children and adolescents 18 years of age or younger. Two independent reviewers carried out study selection and data extraction. Quality assessment was performed using a study design evaluation instrument to appraise the strength of the studies and their methodological adequacy. Because of heterogeneity in the conditions and outcomes we studied, a formal meta-analysis was not performed.

Results

Based on our search strategy, 655 titles and abstracts were reviewed. From this set we identified 27 relevant articles that met our inclusion criteria. The results from these studies indicated that biomedical informatics applications have favourable clinical and patient outcomes including, but not limited to, reduced number of emergency room visits, improved knowledge on disease management, and enhanced satisfaction. Seventy percent of reviewed papers were published after year 2000, 89% of users were patients and 11% were either providers or caregivers. The majority (96%) of the selected studies reported improved outcomes.

Conclusion

Published studies suggested positive impacts of informatics predominantly in pediatric asthma. As electronic tools become more widely adopted, there will be opportunities to improve patient care in a wide range of chronic illnesses through informatics solutions.

Objective: The research analyzes usage of a major biomedical library's pre-1993 print journal collection.

Methodology: In July 2003, in preparation for a renovation and expansion project, the Biomedical Library at the University of California, San Diego, moved all of its pre-1993 journal volumes off-site, with the exception of twenty-two heavily used titles. Patrons wishing to consult one of these stored volumes could request that it be delivered to the library for their use. In the spring of 2006, an analysis was made of these requests.

Results: By July of 2006, 79,827 journal volumes published in 1992 or earlier had been requested from storage. The number of requests received declined with age of publication. The usage distribution exhibited a “long tail”: 50% of the 79,827 requests were for journal volumes published before 1986. The availability of electronic access dramatically reduced the chance that corresponding print journal volumes would be requested.

Conclusions: The older biomedical print journal literature appears to be of continued value to the biomedical research community. When electronic access was provided to the older literature, demand for older print volumes declined dramatically.