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1.  E-Learning as New Method of Medical Education 
Acta Informatica Medica  2008;16(2):102-117.
Distance learning refers to use of technologies based on health care delivered on distance and covers areas such as electronic health, tele-health (e-health), telematics, telemedicine, tele-education, etc. For the need of e-health, telemedicine, tele-education and distance learning there are various technologies and communication systems from standard telephone lines to the system of transmission digitalized signals with modem, optical fiber, satellite links, wireless technologies, etc. Tele-education represents health education on distance, using Information Communication Technologies (ICT), as well as continuous education of a health system beneficiaries and use of electronic libraries, data bases or electronic data with data bases of knowledge. Distance learning (E-learning) as a part of tele-education has gained popularity in the past decade; however, its use is highly variable among medical schools and appears to be more common in basic medical science courses than in clinical education. Distance learning does not preclude traditional learning processes; frequently it is used in conjunction with in-person classroom or professional training procedures and practices. Tele-education has mostly been used in biomedical education as a blended learning method, which combines tele-education technology with traditional instructor-led training, where, for example, a lecture or demonstration is supplemented by an online tutorial. Distance learning is used for self-education, tests, services and for examinations in medicine i.e. in terms of self-education and individual examination services. The possibility of working in the exercise mode with image files and questions is an attractive way of self education. Automated tracking and reporting of learners’ activities lessen faculty administrative burden. Moreover, e-learning can be designed to include outcomes assessment to determine whether learning has occurred. This review article evaluates the current status and level of tele-education development in Bosnia and Herzegovina outlining its components, faculty development needs for implementation and the possibility of its integration as official learning standard in biomedical curricula in Bosnia and Herzegovina. Tele-education refers to the use of information and communication technologies (ICT) to enhance knowledge and performance. Tele-education in biomedical education is widely accepted in the medical education community where it is mostly integrated into biomedical curricula forming part of a blended learning strategy. There are many biomedical digital repositories of e-learning materials worldwide, some peer reviewed, where instructors or developers can submit materials for widespread use. First pilot project with the aim to introduce tele-education in biomedical curricula in Bosnia and Herzegovina was initiated by Department for Medical Informatics at Medical Faculty in Sarajevo in 2002 and has been developing since. Faculty member’s skills in creating tele-education differ from those needed for traditional teaching and faculty rewards must recognize this difference and reward the effort. Tele-education and use of computers will have an impact of future medical practice in a life long learning. Bologna process, which started last years in European countries, provide us to promote and introduce modern educational methods of education at biomedical faculties in Bosnia and Herzegovina. Cathedra of Medical informatics and Cathedra of Family medicine at Medical Faculty of University of Sarajevo started to use Web based education as common way of teaching of medical students. Satisfaction with this method of education within the students is good, but not yet suitable for most of medical disciplines at biomedical faculties in Bosnia and Herzegovina.
PMCID: PMC3789161  PMID: 24109154
Medical education; Distance learning; Bosnia and Herzegovina
2.  The Internet: will this highway serve the digital library? 
The future of the biomedical enterprise and the biomedical libraries that serve it is tied closely to digital information. The changing nature of this type of information will create new pressures on libraries, particularly in health care organizations. Libraries must learn to deal with these pressures. Currently, libraries depend on the Internet primarily for connections to resources and other libraries; thus enhancements to the Internet will impact the libraries of the present and future significantly. This paper provides an overview of the technical capabilities that will be available in the near to midterm, what libraries will be able to do with those capabilities, and how libraries can position themselves to take advantage of the impending changes.
PMCID: PMC225969  PMID: 7841914
3.  Rising Expectations: Access to Biomedical Information 
Yearbook of medical informatics  2008;3(1):165-172.
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.
Review of the increasingly broad spectrum of web-accessible genomic data, biomedical literature, consumer health information, clinical trials data, and images.
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.
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.
PMCID: PMC2441483  PMID: 18587496
Access to information; genetic databases; digital libraries; consumer health information; clinical trials
4.  The Profiles in Science Digital Library: Behind the Scenes 
This demonstration shows the Profiles in Science® digital library. Profiles in Science contains digitized selections from the personal manuscript collections of prominent biomedical researchers, medical practitioners, and those fostering science and health. The Profiles in Science Web site1 is the delivery mechanism for content derived from the digital library system. The system is designed according to our basic principles for digital library development [1]. The digital library includes the rules and software used for digitizing items, creating and editing database records and performing quality control as well as serving the digital content to the public. Among the types of data managed by the digital library are detailed item-level, collection-level and cross-collection metadata, digitized photographs, papers, audio clips, movies, born-digital electronic files, optical character recognized (OCR) text, and annotations (see Figure 1). The digital library also tracks the status of each item, including digitization quality, sensitivity of content, and copyright. Only items satisfying all required criteria are released to the public through the World Wide Web. External factors have influenced all aspects of the digital library's infrastructure.
PMCID: PMC3609548  PMID: 23543833
H.3.7 [Information Storage and Retrieval]: Digital Libraries –; Collection; Dissemination; Systems issues; Design; Legal Aspects; Digital Library; Information System; Digitized Manuscripts; Adaptability
5.  Improving Software Sustainability: Lessons Learned from Profiles in Science 
The Profiles in Science® digital library features digitized surrogates of historical items selected from the archival collections of the U.S. National Library of Medicine as well as collaborating institutions. In addition, it contains a database of descriptive, technical and administrative metadata. It also contains various software components that allow creation of the metadata, management of the digital items, and access to the items and metadata through the Profiles in Science Web site [1]. The choices made building the digital library were designed to maximize the sustainability and long-term survival of all of the components of the digital library [2]. For example, selecting standard and open digital file formats rather than proprietary formats increases the sustainability of the digital files [3]. Correspondingly, using non-proprietary software may improve the sustainability of the software--either through in-house expertise or through the open source community.
Limiting our digital library software exclusively to open source software or to software developed in-house has not been feasible. For example, we have used proprietary operating systems, scanning software, a search engine, and office productivity software. We did this when either lack of essential capabilities or the cost-benefit trade-off favored using proprietary software. We also did so knowing that in the future we would need to replace or upgrade some of our proprietary software, analogous to migrating from an obsolete digital file format to a new format as the technological landscape changes. Since our digital library’s start in 1998, all of its software has been upgraded or replaced, but the digitized items have not yet required migration to other formats.
Technological changes that compelled us to replace proprietary software included the cost of product licensing, product support, incompatibility with other software, prohibited use due to evolving security policies, and product abandonment. Sometimes these changes happen on short notice, so we continually monitor our library’s software for signs of endangerment. We have attempted to replace proprietary software with suitable in-house or open source software. When the replacement involves a standalone piece of software with a nearly equivalent version, such as replacing a commercial HTTP server with an open source HTTP server, the replacement is straightforward. Recently we replaced software that functioned not only as our search engine but also as the backbone of the architecture of our Web site. In this paper, we describe the lessons learned and the pros and cons of replacing this software with open source software.
PMCID: PMC4176707  PMID: 25267934
6.  Picture This... Developing Standards for Electronic Images at the National Library of Medicine 
New computer technologies have made it feasible to represent, store, and communicate high resolution biomedical images via electronic means. Traditional two dimensional medical images such as those on printed pages have been supplemented by three dimensional images which can be rendered, rotated, and “dissected” from any point of view. The library of the future will provide electronic access not only to words and numbers, but to pictures, sounds, and other nontextual information. There currently exist few widely-accepted standards for the representation and communication of complex images, yet such standards will be critical to the feasibility and usefulness of digital image collections in the life sciences. The National Library of Medicine is embarked on a project to develop a complete digital volumetric representation of an adult human male and female. This “Visible Human Project” will address the issue of standards for computer representation of biological structure.
PMCID: PMC2245484
7.  Things to come: postmodern digital knowledge management and medical informatics. 
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.
PMCID: PMC116240  PMID: 7743318
8.  Comparison of Iranian National Medical Library with digital libraries of selected countries 
The important role of information and communication technologies and their influence on methods of storing, retrieving information in digital libraries, has not only changed the meanings behind classic library activates but has also created great changes in their services. However, it seems that not all digital libraries provide their users with similar services and only some of them are successful in fulfilling their role in digital environment. The Iranian National Medical library is among those that appear to come short compared to other digital libraries around the world. By knowing the different services provided by digital libraries worldwide, one can evaluate the services provided by Iranian National Medical library. The goal of this study is a comparison between Iranian National Medical library and digital libraries of selected countries.
Materials and Methods:
This is an applied study and uses descriptive – survey method. The statistical population is the digital libraries around the world which were actively providing library services between October and December 2011 and were selected by using the key word “Digital Library” in Google search engine. The data-gathering tool was direct access to the websites of these digital libraries. The statistical study is descriptive and Excel software was used for data analysis and plotting of the charts.
The findings showed that among the 33 digital libraries investigated worldwide, most of them provided Browse (87.87%), Search (84.84%), and Electronic information retrieval (57.57%) services. The “Help” in public services (48/48%) and “Interlibrary Loan” in traditional services (27/27%) had the highest frequency. The Iranian National Medical library provides more digital services compared to other libraries but has less classic and public services and has less than half of possible public services. Other than Iranian National Medical library, among the 33 libraries investigated, the leaders in providing different services are Library of University of California in classic services, Count Way Library of Medicine in digital services, and Library of Finland in public services.
Results and Discussion:
The results of this study show that among the digital libraries investigated, most provided similar public, digital, and classic services and The Iranian National Medical library has been somewhat successful in providing these services compared to other digital libraries. One can also conclude that the difference in services is at least in part due to difference in environments, information needs, and users.
Iranian National Medical Library has been somewhat successful in providing library services in digital environment and needs to identify the services which are valuable to its users by identifying the users’ needs and special characteristics of its environment
PMCID: PMC4275611  PMID: 25540782
Digital library; Iranian National Medical Library; services
9.  PhysiomeSpace: digital library service for biomedical data 
Every research laboratory has a wealth of biomedical data locked up, which, if shared with other experts, could dramatically improve biomedical and healthcare research. With the PhysiomeSpace service, it is now possible with a few clicks to share with selected users biomedical data in an easy, controlled and safe way. The digital library service is managed using a client–server approach. The client application is used to import, fuse and enrich the data information according to the PhysiomeSpace resource ontology and upload/download the data to the library. The server services are hosted on the Biomed Town community portal, where through a web interface, the user can complete the metadata curation and share and/or publish the data resources. A search service capitalizes on the domain ontology and on the enrichment of metadata for each resource, providing a powerful discovery environment. Once the users have found the data resources they are interested in, they can add them to their basket, following a metaphor popular in e-commerce web sites. When all the necessary resources have been selected, the user can download the basket contents into the client application. The digital library service is now in beta and open to the biomedical research community.
PMCID: PMC3263791  PMID: 20478910
physiome; virtual physiological human; living human project; digital library; data sharing
10.  Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web 
PLoS Computational Biology  2008;4(10):e1000204.
Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.
PMCID: PMC2568856  PMID: 18974831
11.  Good old days? 
Alternative models of subsidizing scholarly publishing and dissemination have germinated and gathered momentum in the fertile soil of dissatisfaction. Like the stubborn spring dandelion that needs but a small crack in the sidewalk to flower boldly, the first flowers of Open Access in library literature, including Biomedical Digital Libraries, have sensed their opportunity to change the existing paradigm of giving away our scholarship and intellectual property, only to buy it back for the privilege of knowing it can be read. Will biomedical digital library and informatics researchers understand their role in a new era of Open Access simply by desiring an immediate uninhibited global audience and recognizing the necessity of open access peer-reviewed literature to become self-sufficient?
PMCID: PMC1097712  PMID: 15829010
12.  Purchasing online journal access for a hospital medical library: how to identify value in commercially available products 
Medical practice today requires evaluating large amounts of information which should be available at all times. This information is found most easily in a digital form. Some information has already been evaluated for validity (evidence based medicine sources) and some is in unevaluated form (paper and online journals). In order to improve access to digital information, the School of Clinical Medicine and Research at the University of the West Indies and Queen Elizabeth Hospital decided to enhance the library by offering online full text medical articles and evidence based medicine sources. The aim of this paper is to evaluate the relative value of online journal commercial products available for a small hospital and medical school library.
Three reference standards were chosen to represent the ideal list of core periodicals for a broad range of medical care: 2 Brandon/Hill selected lists of journals for the small medical library (BH and BH core) and the academic medical library core journal collection chosen for the Florida State University College of Medicine Medical Library. Six commercially available collections were compared to the reference standards and to the current paper journal subscription list as regards to number of journals matched and cost per journal matched. Ease of use and presence of secondary sources were also considered.
The cost per journal matched ranged from US $ 3194 to $ 81. Because of their low subscription prices, the Biomedical Reference Collection and Proquest products were the most cost beneficial. However, they provided low coverage of the ideal lists (12 – 17% and 21–32% respectively) and contained significant embargoes on current editions, were not user friendly and contained no secondary sources. The Ovid Brandon/Hill Plus Collection overcame these difficulties but had a much higher cost-benefit range while providing higher coverage of the ideal lists (14–47%).
After considering costs, benefits, ease of use, embargoes, presence of secondary sources (ACP Journal Club, DARE), the Ovid Brandon/Hill Plus Collection was the best choice for our hospital considering our budget. However, the option to individually select our own journal list from Ovid and pay per journal has a certain appeal as well.
PMCID: PMC1533853  PMID: 16836760
13.  The MEDLARS Project at the UCLA Biomedical Library *† 
The National Library of Medicine has established at the Biomedical Library, UCLA, a remote MEDLARS search station. The agreement between the libraries provided that the Biomedical Library in cooperation with the UCLA Health Sciences Computing Facility would reprogram MEDLARS for the IBM 7094 computer, provide personnel to be trained in machine searching at NLM, and engage in a pilot demonstration of search service to the medical staff of UCLA. This paper describes the place of the search section in the organization of the Biomedical Library and the training of personnel at NLM (the article by Garvis in this issue of the Bulletin relates the problems encountered in making two different computer systems compatible). Search service had not begun when this paper was written; it was scheduled to begin late in 1965. Plans for the future include the enlargement of the UCLA MEDLARS staff and extension of search service to a larger geographical area.
PMCID: PMC198363  PMID: 5901354
14.  AHEC library services: from circuit rider to virtual librarian 
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.
PMCID: PMC35258  PMID: 11055304
15.  Image Acquisition Context 
Objective: To support clinically relevant indexing of biomedical images and image-related information based on the attributes of image acquisition procedures and the judgments (observations) expressed by observers in the process of image interpretation.
Design: The authors introduce the notion of “image acquisition context,” the set of attributes that describe image acquisition procedures, and present a standards-based strategy for utilizing the attributes of image acquisition context as indexing and retrieval keys for digital image libraries.
Methods: The authors' indexing strategy is based on an interdependent message/terminology architecture that combines the Digital Imaging and Communication in Medicine (DICOM) standard, the SNOMED (Systematized Nomenclature of Human and Veterinary Medicine) vocabulary, and the SNOMED DICOM microglossary. The SNOMED DICOM microglossary provides context-dependent mapping of terminology to DICOM data elements.
Results: The capability of embedding standard coded descriptors in DICOM image headers and image-interpretation reports improves the potential for selective retrieval of image-related information. This favorably affects information management in digital libraries.
PMCID: PMC61345  PMID: 9925229
16.  PMD2HD – A web tool aligning a PubMed search results page with the local German Cancer Research Centre library collection 
Web-based searching is the accepted contemporary mode of retrieving relevant literature, and retrieving as many full text articles as possible is a typical prerequisite for research success. In most cases only a proportion of references will be directly accessible as digital reprints through displayed links. A large number of references, however, have to be verified in library catalogues and, depending on their availability, are accessible as print holdings or by interlibrary loan request.
The problem of verifying local print holdings from an initial retrieval set of citations can be solved using Z39.50, an ANSI protocol for interactively querying library information systems. Numerous systems include Z39.50 interfaces and therefore can process Z39.50 interactive requests. However, the programmed query interaction command structure is non-intuitive and inaccessible to the average biomedical researcher. For the typical user, it is necessary to implement the protocol within a tool that hides and handles Z39.50 syntax, presenting a comfortable user interface.
PMD2HD is a web tool implementing Z39.50 to provide an appropriately functional and usable interface to integrate into the typical workflow that follows an initial PubMed literature search, providing users with an immediate asset to assist in the most tedious step in literature retrieval, checking for subscription holdings against a local online catalogue.
PMD2HD can facilitate literature access considerably with respect to the time and cost of manual comparisons of search results with local catalogue holdings. The example presented in this article is related to the library system and collections of the German Cancer Research Centre. However, the PMD2HD software architecture and use of common Z39.50 protocol commands allow for transfer to a broad range of scientific libraries using Z39.50-compatible library information systems.
PMCID: PMC1187866  PMID: 15982415
17.  Development of genomic resources for the prairie vole (Microtus ochrogaster): construction of a BAC library and vole-mouse comparative cytogenetic map 
BMC Genomics  2010;11:70.
The prairie vole (Microtus ochrogaster) is a premier animal model for understanding the genetic and neurological basis of social behaviors. Unlike other biomedical models, prairie voles display a rich repertoire of social behaviors including the formation of long-term pair bonds and biparental care. However, due to a lack of genomic resources for this species, studies have been limited to a handful of candidate genes. To provide a substrate for future development of genomic resources for this unique model organism, we report the construction and characterization of a bacterial artificial chromosome (BAC) library from a single male prairie vole and a prairie vole-mouse (Mus musculus) comparative cytogenetic map.
We constructed a prairie vole BAC library (CHORI-232) consisting of 194,267 recombinant clones with an average insert size of 139 kb. Hybridization-based screening of the gridded library at 19 loci established that the library has an average depth of coverage of ~10×. To obtain a small-scale sampling of the prairie vole genome, we generated 3884 BAC end-sequences totaling ~2.8 Mb. One-third of these BAC-end sequences could be mapped to unique locations in the mouse genome, thereby anchoring 1003 prairie vole BAC clones to an orthologous position in the mouse genome. Fluorescence in situ hybridization (FISH) mapping of 62 prairie vole clones with BAC-end sequences mapping to orthologous positions in the mouse genome was used to develop a first-generation genome-wide prairie vole-mouse comparative cytogenetic map. While conserved synteny was observed between this pair of rodent genomes, rearrangements between the prairie vole and mouse genomes were detected, including a minimum of five inversions and 16 inter-chromosomal rearrangements.
The construction of the prairie vole BAC library and the vole-mouse comparative cytogenetic map represent the first genome-wide modern genomic resources developed for this species. The BAC library will support future genomic, genetic and molecular characterization of this genome and species, and the isolation of clones of high interest to the vole research community will allow for immediate characterization of the regulatory and coding sequences of genes known to play important roles in social behaviors. In addition, these resources provide an excellent platform for future higher resolution cytogenetic mapping and full genome sequencing.
PMCID: PMC2824727  PMID: 20109198
18.  Suppressive Subtractive Hybridization of and Differences in Gene Expression Content of Calcifying and Noncalcifying Cultures of Emiliania huxleyi Strain 1516 
The marine coccolithophorid Emiliania huxleyi is a cosmopolitan alga intensely studied in relation to global carbon cycling, biogeochemistry, marine ecology, and biomineralization processes. The biomineralization capabilities of coccolithophorids have attracted the attention of scientists interested in exploiting this ability for the development of materials science and biomedical and biotechnological applications. Although it has been well documented that biomineralization in E. huxleyi is promoted by growth under phosphate-limited conditions, the genes and proteins that govern the processes of calcification and coccolithogenesis remain unknown. Suppressive subtractive hybridization (SSH) libraries were constructed from cultures grown in phosphate-limited and phosphate-replete media as tester and driver populations for reciprocal SSH procedures. Positive clones from each of the two libraries were randomly selected, and dot blotting was performed for the analysis of expression patterns. A total of 513 clones from the phosphate-replete library and 423 clones from the phosphate-limited library were sequenced, assembled, and compared to sequences in GenBank using BLASTX. Of the 103 differentially expressed gene fragments from the phosphate-replete library, 34% showed significant homology to other known proteins, while only 23% of the 65 differentially expressed gene fragments from the phosphate-limited library showed homology to other proteins. To further assess mRNA expression, real-time RT-PCR analysis was employed and expression profiles were generated over a 14-day time course for three clones from the phosphate-replete library and five clones from the phosphate-limited library. The fragments isolated provide the basis for future cloning of full-length genes and functional analysis.
PMCID: PMC1087533  PMID: 15870347
19.  Development and Implementation of a Web-Enabled 3D Consultation Tool for Breast Augmentation Surgery Based on 3D-Image Reconstruction of 2D Pictures 
Producing a rich, personalized Web-based consultation tool for plastic surgeons and patients is challenging.
(1) To develop a computer tool that allows individual reconstruction and simulation of 3-dimensional (3D) soft tissue from ordinary digital photos of breasts, (2) to implement a Web-based, worldwide-accessible preoperative surgical planning platform for plastic surgeons, and (3) to validate this tool through a quality control analysis by comparing 3D laser scans of the patients with the 3D reconstructions with this tool from original 2-dimensional (2D) pictures of the same patients.
The proposed system uses well-established 2D digital photos for reconstruction into a 3D torso, which is then available to the user for interactive planning. The simulation is performed on dedicated servers, accessible via Internet. It allows the surgeon, together with the patient, to previsualize the impact of the proposed breast augmentation directly during the consultation before a surgery is decided upon. We retrospectively conduced a quality control assessment of available anonymized pre- and postoperative 2D digital photographs of patients undergoing breast augmentation procedures. The method presented above was used to reconstruct 3D pictures from 2D digital pictures. We used a laser scanner capable of generating a highly accurate surface model of the patient’s anatomy to acquire ground truth data. The quality of the computed 3D reconstructions was compared with the ground truth data used to perform both qualitative and quantitative evaluations.
We evaluated the system on 11 clinical cases for surface reconstructions and 4 clinical cases of postoperative simulations, using laser surface scan technologies showing a mean reconstruction error between 2 and 4 mm and a maximum outlier error of 16 mm. Qualitative and quantitative analyses from plastic surgeons demonstrate the potential of these new emerging technologies.
We tested our tool for 3D, Web-based, patient-specific consultation in the clinical scenario of breast augmentation. This example shows that the current state of development allows for creation of responsive and effective Web-based, 3D medical tools, even with highly complex and time-consuming computation, by off-loading them to a dedicated high-performance data center. The efficient combination of advanced technologies, based on analysis and understanding of human anatomy and physiology, will allow the development of further Web-based reconstruction and predictive interfaces at different scales of the human body. The consultation tool presented herein exemplifies the potential of combining advancements in the core areas of computer science and biomedical engineering with the evolving areas of Web technologies. We are confident that future developments based on a multidisciplinary approach will further pave the way toward personalized Web-enabled medicine.
PMCID: PMC3374529  PMID: 22306688
Medical informatics computing; computer-assisted surgery; imaging, three-dimensional
20.  An essay on reflection. 
From the vantage point of her personal experience, the author examines milestones since the 1960s which have changed the medical library profession and helped shape the Medical Library Association. The advent of automation, including cataloging with OCLC and online literature searching through the SUNY Biomedical Communication Network, was a dramatic event that transformed the work and priorities of librarians, fulfilling the dreams of earlier visionaries. The application of technology in libraries led to an increased demand for education and training for librarians. The Medical Library Association responded with continuing education programs, and a series of important reports influenced how the association filled its role in professional development. Legislation providing federal funding, such as the Medical Library Assistance Act, resulted in a period of expansion for libraries and their services. The Medical Library Association has developed a legislative agenda to influence action in areas such as copyright. In the future, health sciences librarians must take a leadership role.
PMCID: PMC226363  PMID: 9578947
21.  A Macroscopic and Microscopic Biomedical Image Processing System 
This paper summarizes the current status of a biomedical image processing system being developed in the Biomedical Engineering Program, University of Iowa. This system consists of an EyeCom® II picture digitizer and display, a PDP 11/34 minicomputer with peripherals, a light table and a microscope, and the associate image processing software. The capability of the present system, both hardware and software, is described in detail. Some current biomedical applications using this system along with illustrations are given. Two of the future developments: dynamic imaging and true color imaging are also outlined.
PMCID: PMC2581153
22.  Digital analysis of cDNA abundance; expression profiling by means of restriction fragment fingerprinting 
BMC Genomics  2002;3:7.
Gene expression profiling among different tissues is of paramount interest in various areas of biomedical research. We have developed a novel method (DADA, Digital Analysis of cDNA Abundance), that calculates the relative abundance of genes in cDNA libraries.
DADA is based upon multiple restriction fragment length analysis of pools of clones from cDNA libraries and the identification of gene-specific restriction fingerprints in the resulting complex fragment mixtures. A specific cDNA cloning vector had to be constructed that governed missing or incomplete cDNA inserts which would generate misleading fingerprints in standard cloning vectors. Double stranded cDNA was synthesized using an anchored oligo dT primer, uni-directionally inserted into the DADA vector and cDNA libraries were constructed in E. coli. The cDNA fingerprints were generated in a PCR-free procedure that allows for parallel plasmid preparation, labeling, restriction digest and fragment separation of pools of 96 colonies each. This multiplexing significantly enhanced the throughput in comparison to sequence-based methods (e.g. EST approach). The data of the fragment mixtures were integrated into a relational database system and queried with fingerprints experimentally produced by analyzing single colonies. Due to limited predictability of the position of DNA fragments on the polyacrylamid gels of a given size, fingerprints derived solely from cDNA sequences were not accurate enough to be used for the analysis. We applied DADA to the analysis of gene expression profiles in a model for impaired wound healing (treatment of mice with dexamethasone).
The method proved to be capable of identifying pharmacologically relevant target genes that had not been identified by other standard methods routinely used to find differentially expressed genes. Due to the above mentioned limited predictability of the fingerprints, the method was yet tested only with a limited number of experimentally determined fingerprints and was able to detect differences in gene expression of transcripts representing 0.05% of the total mRNA population (e.g. medium abundant gene transcripts).
PMCID: PMC99051  PMID: 11882253
23.  Library as place: results of a delphi study 
Objective: An expert consensus on the future of the library as place was developed to assist health sciences librarians in designing new library spaces.
Method: An expert panel of health sciences librarians, building consultants, architects, and information technologists was asked to reflect on the likelihood, desirability, timing, and impact on building design of more than seventy possible changes in the use of library space.
Results: An expert consensus predicted that the roles librarians play and the way libraries are used will substantially change. These changes come in response to changes in technology, scholarly communication, learning environments, and the health care economy.
Conclusions: How health sciences library space is used will be far less consistent by 2015, as space becomes more tailored to institutional needs. However, the manner in which health sciences libraries develop and deliver services and collections will drastically change in the next decade. Libraries will continue to exist and will provide support for knowledge management and clinical trials, provide access to digital materials, and play a host of other roles that will enable libraries to emerge as institutional change agents.
PMCID: PMC1175798  PMID: 16059421
24.  Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data 
Journal of Biomedical Semantics  2013;4(Suppl 1):S5.
The World Wide Web has become a dissemination platform for scientific and non-scientific publications. However, most of the information remains locked up in discrete documents that are not always interconnected or machine-readable. The connectivity tissue provided by RDF technology has not yet been widely used to support the generation of self-describing, machine-readable documents.
In this paper, we present our approach to the generation of self-describing machine-readable scholarly documents. We understand the scientific document as an entry point and interface to the Web of Data. We have semantically processed the full-text, open-access subset of PubMed Central. Our RDF model and resulting dataset make extensive use of existing ontologies and semantic enrichment services. We expose our model, services, prototype, and datasets at
The semantic processing of biomedical literature presented in this paper embeds documents within the Web of Data and facilitates the execution of concept-based queries against the entire digital library. Our approach delivers a flexible and adaptable set of tools for metadata enrichment and semantic processing of biomedical documents. Our model delivers a semantically rich and highly interconnected dataset with self-describing content so that software can make effective use of it.
PMCID: PMC3804025  PMID: 23734622
25.  The Unified Medical Language System (UMLS): integrating biomedical terminology 
Nucleic Acids Research  2004;32(Database issue):D267-D270.
The Unified Medical Language System ( is a repository of biomedical vocabularies developed by the US National Library of Medicine. The UMLS integrates over 2 million names for some 900 000 concepts from more than 60 families of biomedical vocabularies, as well as 12 million relations among these concepts. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank. In addition to data, the UMLS includes tools for customizing the Metathesaurus (MetamorphoSys), for generating lexical variants of concept names (lvg) and for extracting UMLS concepts from text (MetaMap). The UMLS knowledge sources are updated quarterly. All vocabularies are available at no fee for research purposes within an institution, but UMLS users are required to sign a license agreement. The UMLS knowledge sources are distributed on CD-ROM and by FTP.
PMCID: PMC308795  PMID: 14681409

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