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Medical information related to human immunodeficiency virus (HIV) infection is highly diverse, and the practicing physician or researcher may find specific information difficult to locate. To provide timely access to medical information on topics related to the acquired immunodeficiency syndrome (AIDS), several computer-based products have recently been developed. Some are available from vendors of online information systems, whereas others are available only on CD-ROM or floppy disk. We review several computer-based products. AIDSLINE is the most comprehensive bibliographic index, AIDSTRIALS contains specific information about ongoing unpublished investigational studies, and AIDS Knowledge Base from San Francisco General Hospital is an up-to-date electronic textbook covering all aspects of AIDS. COMPACT LIBRARY: AIDS operates on a microcomputer and combines several databases, including full-text AIDS-related articles from nine major medical journals. AIDS References from the Bureau of Hygiene and Tropical Diseases provides critical analysis of publications worldwide. Although smaller in size than AIDSLINE, about one third of the publications covered by this resource are not covered by AIDSLINE.
The analysis of expression signatures is a powerful tool for the classification of cancer and other tissue samples. Several protocols and platforms are available on the market, and these lead to both confirmatory and complementary results. We review the main processing techniques for cross-platform comparisons and the different tissue sources for cancer profiling. Some examples and the cross-interpretation of bibliographic data related to prostate cancer are also presented.
AffinDB is a database of affinity data for structurally resolved protein-ligand complexes from the Protein Data Bank (PDB). It is freely accessible at http://www.agklebe.de/affinity. Affinity data are collected from the scientific literature, both from primary sources describing the original experimental work of affinity determination and from secondary references which report affinity values determined by others. AffinDB currently contains over 730 affinity entries covering more than 450 different protein-ligand complexes. Besides the affinity value, PDB summary information and additional data are provided, including the experimental conditions of the affinity measurement (if available in the corresponding reference); 2D drawing, SMILES code and molecular weight of the ligand; links to other databases, and bibliographic information. AffinDB can be queried by PDB code or by any combination of affinity range, temperature and pH value of the measurement, ligand molecular weight, and publication data (author, journal and year). Search results can be saved as tabular reports in text files. The database is supposed to be a valuable resource for researchers interested in biomolecular recognition and the development of tools for correlating structural data with affinities, as needed, for example, in structure-based drug design.
Molecular and morphological aspects are traditionally opposed in life sciences. Systematics, however, has long used molecular tools for evolutionary purposes and might be the place to unify those two elements of biology, even though up until recently, such methodologies were incompatible and opposed. Morphological studies suffer from a lesser recognition and a largely inferior access to credits and renewal of personnel, because of the length of time and level of specialization required to produce morpho-anatomy based work. Databasing might be a way to simplify and speed up morphological studies. The use of databases is spreading in systematics, from bibliography to collection catalogs and localisation, to sequence banks. The example of Acanthomorpha examplifies this with the construction of a database gathering bibliographical and anatomical data so as to avoid repeating previous work. Molecular phylogenies cannot be explored alone; they need to be compared with morphological analyses.
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). There may be multiple promoter entries for a single gene. The underlying experimental evidence comes from journal articles and, starting from release 73, from 5' ESTs of full-length cDNA clones used for so-called in silico primer extension. Access to promoter sequences is provided by pointers to TSS positions in nucleotide sequence entries. The annotation part of an EPD entry includes a description of the type and source of the initiation site mapping data, links to other biological databases and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Web-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria and to navigate to related databases exploiting different cross-references. Tools for analysing sequence motifs around TSSs defined in EPD are provided by the signal search analysis server. EPD can be accessed at http://www.epd. isb-sib.ch.
The development of communication and the possibility of its dissemination to the biomedical documentation by means of the Internet network are producing changes in the traditional way of conceiving scientific publications. Two initiatives, derived from this new framework, are analyzed in this article. These are the Pubmed Central, the initiative of NCBI, intended to create a reservoir of biomedical literature, with free access, on-line, and the Cochrane Library which, through its different databases, is aimed at offering practitioners reasonable replies to frequent clinical questions. A new model of clinical documentation is arising from a combination of both: on the one hand, rational indexing and accessibility of the literature, and on the other, the analysis of information produced to generate relevant clinical knowledge.
Two reports of the Commission on bibliography are published. The first, by Henry Lowood, concerns the Workshop on bibliographic control of sources for the history of science, technology, and medicine held in Trento in September 1992; the second, by Wesley M. Stevens, is a survey of computer-assisted catalogues of pre-1600 manuscripts.
In order to find rules for the secondary structure prediction of proteins which describe the (sequentially) long-range interactions in sheet structures methods of applied graph theory were used. The so called beta graph which describes the sheet topology was defined for every protein in the Brookhaven Data Bank containing beta sheets. The resemblance of proteins at that topological level is discussed, and four notations and graphic representations of sheets which describe the sequential and topological neighborhoods of the strands were derived. This description level supports the usage of data structures which allow the implementation of efficient algorithms for the analysis and comparison of beta structures in proteins. A computer program for the representation and retrieval of bibliographic data and beta sheet structures was implemented. Some examples for substructure search illustrate the usefulness of the program. Two graphic catalogues were compiled: one contains all beta graphs of PDB proteins and the other all occurring different greek key descriptions.
Recent research studies describe typical information-seeking behavior of doctors, nurses, and other health care providers. This review identifies and analyzes thirty-nine studies and nine reviews published since 1990. The researchers are from many disciplines and often work in multi-disciplinary teams. They have used both quantitative and qualitative methods to gather self-report and observational data. In spite of the increased availability of online bibliographic and full-text sources in this decade, health care providers are using the same sources they used twenty years ago. Self-report studies usually show a higher use of published literature than of advice from colleagues; observational studies usually show the opposite.
Projects on informatics at the School of Medicine of the University of Chile are being brought about in accordance with both its institutional goals and present trends in technology. Prominent among the latter are the widespread distribution of autonomous processing power represented by low-cost computers and the ease of communication at local and worldwide levels. Our main project has been the design and start of a computer network that integrates the School's Departments and the geographically dispersed teaching hospitals. The principal services provided by the network are local and international electronic mail, access to data bases, and emulation of mainframe terminals (eg, to run remotely a mainframe's statistics software). Automated bibliographic search has been made available both through remote access to Medline data base and through local usage of compact disc (CD-ROM) versions. Since our network is open, it should become a forceful mean of assisting and integrating the biomedical community throughout the country.
Online Mendelian Inheritance In Man (OMIM) is a public database of bibliographic information about human genes and genetic disorders. Begun by Dr. Victor McKusick as the authoritative reference Mendelian Inheritance in Man, it is now distributed electronically by the National Center for Biotechnology Information (NCBI). Material in OMIM is derived from the biomedical literature and is written by Dr. McKusick and his colleagues at Johns Hopkins University and elsewhere. Each OMIM entry has a full text summary of a genetic phenotype and/or gene and has copious links to other genetic resources such as DNA and protein sequence, PubMed references, mutation databases, approved gene nomenclature, and more. In addition, NCBI's neighboring feature allows users to identify related articles from PubMed selected on the basis of key words in the OMIM entry. Through its many features, OMIM is increasingly becoming a major gateway for clinicians, students, and basic researchers to the ever-growing literature and resources of human genetics.
News of the death of biomedical journals seem premature. Revamped traditional scientific journals remain highly valued sources and vehicles of information, critical debate, and knowledge. Some analyses seem to place a disproportionate emphasis on technological and formal issues, as compared to the importance ascribed to matters of power. Not all journals must necessarily have a large circulation. There are many examples of efficient, high-quality journals with a great impact on relatively small audiences for whom the journal is thought-provoking, useful, and pleasant to read. How can we achieve a better understanding of an article s spectrum of impacts? A certain mixing of three distinct entities (journals, articles, and authors) has often pervaded judgments. Data used by the Institute for Scientific Information present weaknesses in their accuracy. The two-year limit for citations to count towards the bibliographic impact factor favors "fast-moving", "basic" biomedical disciplines and is less appropriate for public health studies. Increasing attention is given to the specific number of citations received by each individual article. It is possible to make progress towards more valid, accurate, fair, and relevant assessments.
Evaluation of research activity is extremely important but remains a complex domain. There's no standardized methods and evaluation is often based on the scientific publications. It is easy to identify, for a researcher, all the publications realized over a given period of time. At the level of an important establishment like an University Hospital, with about 500 researchers, this sort of inventory is very difficult to realize: we have to list the researchers, to list their publications, to determine the quality of articles produced, to store retrieved data and to calculate summary statistics. We have developed a full-Web prototype, using free software which, for a given researchers' list, interrogates the Pubmed server, downloads the found references and stores them in a local database. They are then enriched with local data which allow the realization of more or less complex analyses, the automatic production of reports, or keyword search. This tool is very easy to use, allowing for immediate analysis of publications of a researcher or a research team. This tool will allow to identify those active teams to be maintained or emergent teams to be supported. It will also allow to compare candidate profiles for appointments to research posts.
Electronic information resources are proliferating, library collections are increasingly accessible via the Internet, and the number of end users who access library resources remotely is on the rise. Changes in user behavior drives a corresponding change in the way instructional programs must be delivered to meet the needs of remote library users. This paper discusses some technologies currently available for remote instruction, assesses their use, and offers views on future trends.
Libraries are adding electronic resources of all kinds at an increasing pace to provide service to users outside the library and around the world. To meet this new demand, libraries are turning more and more to the use of online tutorials as a valuable means of providing instruction on how to access and use important resources. This article describes the Health Sciences Library and Biocommunications Center's work and experiences while creating tutorials, the ideas used, and ways the work was evaluated.
Scientific productivity of the CAMS members was analyzed according to the number of papers published in periodicals covered by international Medline and Science Citation Index data bases from 1986 to 1990. Results showed the mean scientific productivity per CAMS member, and the relationship between scientific productivity and age, field of medicine or respective biomedical discipline. The pattern of scientific productivity was also found to change, when analyzed according to Medline or SCI data bases in separate.
OBJECTIVE: The purpose of this study was to index the contents of the pre-MEDLINE American Journal of Roentgenology into a database that could then be accessed over the World Wide Web. CONCLUSION: The database is composed of more than 8,000 citations from the years 1914 (volume 1) to 1965 (volume 95). Using a Web browser, a user can search the database by year, volume, title word, page, or author. Results are returned sorted by year and page number in a bibliographic format. The database is accessed approximately 200 times per month.