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The current status and future outlook of macromolecular structure databases and information handling, with particular reference to European databases, are reviewed. Issues concerning the efficiency with which data are represented, validated, archived and accessed are discussed in view of the fast growing body of information on structures of biological macromolecules.
OBJECTIVE: To design a diagnostic protocol that uses appropriate techniques, including ultrasonography, to assess cardiovascular health and detect primary cardiac diseases in gorillas and to establish a database of reference values for cardiac measurements in clinically normal gorillas. DESIGN: Prospective study. ANIMALS: 5 adult male lowland gorillas from 11 to 18 years old. PROCEDURE: A complete cardiac evaluation was performed on anesthetized gorillas, including physical examination, thoracic radiography, electrocardiography, echocardiography, blood pressure determination, CBC, serum biochemical analyses, and serologic assay for viral diseases. Standard cardiac measurements were made from images collected during ultrasonography. RESULTS: Cardiac measurements derived from ultrasonographic images were consistent with those considered normal in human beings. Results of other diagnostic tests were also considered normal. CLINICAL IMPLICATIONS: Cardiac disease is the primary cause of mortality in old captive gorillas. The technique used here provided excellent evaluation of cardiac function. Use of these techniques will allow early detection of cardiac disease, making treatment or medical management possible.
OBJECTIVE: To assess the data quality of septicemia and sepsis registration in a hospital discharge registry in the County of Northern Jutland, Denmark. DESIGN: Comparison of data from the discharge registry of an 880-bed, public, urban hospital in the County of Northern Jutland with data from a computerized bacteremia database at the regional department of clinical microbiology. SETTING: Urban hospital with approximately 45,000 admissions per year. PATIENTS: The study included 406 episodes of bacteremia in the bacteremia database and 83 discharges with the diagnosis of septicemia registered in the hospital discharge registry between January 1, 1994, and December 31, 1994. INTERVENTIONS: None. RESULTS: Eighteen episodes were registered in both the hospital discharge registry and the bacteremia database. Using the bacteremia database as reference standard, the sensitivity for the diagnosis of septicemia in the hospital discharge registry was 4.4% (18/406; 95% confidence intervals [CI95, 2.4%-6.4%]). By review of hospital records, we estimated the positive predictive value of septicemia registration in the hospital discharge registry as 21.7% (18/83; CI95, 12.8%-30.5%). No blood culture had been obtained in 44.4% (36/81; CI95, 33.6%-55.3%) of the cases with a discharge diagnosis of septicemia. In 33.3% (27/81; CI95, 23.1%-43.6%), the discharge diagnosis of septicemia was given, although blood cultures were negative. CONCLUSIONS: The hospital discharge registry revealed numerous misclassifications, and the system was found not suited for surveillance of, or research in, bacteremia at present.
Papyrus is an inexpensive bibliographic database which provides some features not found in other similar packages. Its flexibility in handling references of many types and formats, its capacity for integration with manuscripts prepared with word processors, its capacity for importing references from national databases and its ability to perform microcosmic literature searches are attractive features. Because Papyrus has tackled a complex task, mastery of the intricacies of the program may present a substantial challenge to novice computer users. Although the manipulation of an existing customized bibliographic database would seem to be attractive for any researcher or author who prepares manuscripts for publication, the optimal use of the program also requires an extensive commitment of time and labor for the initial entry of all pertinent references into the database. While this could be accomplished gradually in conjunction with the preparation of individual manuscripts, the creation of a complete file of references could require hundreds of hours of labor. Individual authors, as well as larger research groups, should be prepared for this type of commitment before acquiring the Papyrus system.
STUDY OBJECTIVE: To evaluate the ability of seven widely known herbal references and electronic databases to answer questions about herbal products asked at drug information centers. DESIGN: Cross-sectional study. SETTING: Five academic and institutional drug information centers. METHODS: Fifty-seven herbal-related questions were obtained from academic and institutional drug information centers. Seven herbal references and electronic databases were evaluated for their ability to answer these 57 questions: The Complete German Commission E Monographs: Therapeutic Guide to Herbal Medicines, 1st edition; Physicians' Desk Reference (PDR) for Herbal Medicines, 2001 edition; Tyler's Honest Herbal: A Sensible Guide to the Use of Herbs and Related Remedies, 4th edition; The Lawrence Review of Natural Products, 2001; Natural Medicines Comprehensive Database (electronically updated, 2001); The Natural Pharmacist (electronically updated, 2001); and AltMedDex (electronically updated, 2001). RESULTS: Natural Medicines Comprehensive Database outperformed all other products evaluated, providing direct answers to 61% of questions. AltMedDex and The Natural Pharmacist performed similarly to one another, answering 49% and 44% of questions, respectively. The Lawrence Review of Natural Products, PDR for Herbal Medicines, The Complete German Commission E Monographs, and Tyler's Honest Herbal were the least helpful in providing direct answers to the questions (24%, 21%, 11%, and 9%, respectively). CONCLUSION: Natural Medicines Comprehensive Database, AltMedDex, and The Natural Pharmacist outperformed all other evaluated herbal references and electronic databases in their ability to answer questions about herbal products posed in clinical practice.
The objective of the Vegetal Estrogens in Nutrition and the Skeleton (VENUS) project was to evaluate existing data on dietary exposure to compounds with oestrogenic and anti-oestrogenic effects present in plant foods as constituents or contaminants, and to identify and disseminate in vitro and in vivo methodologies to analyse the effects of such compounds on bone. To permit the assessment of exposure to isoflavones in European populations (Italy, the UK, Ireland, The Netherlands), the VENUS database of phyto-oestrogen levels in foods was established. Data on the isoflavone (genistein and daidzein) content of 791 foods, including almost 300 foods commonly consumed in Europe, were collected. Levels of coumestrol, formononetin and biochanin A in a limited number of foods were also included. Lignan levels (secoisolariciresinol and matairesinol) in 158 foods were incorporated into the database, which also contains information on the references sourced for the compositional data, on the analytical methods used by each author and on the number of foods analysed in each reference. The VENUS database was constructed in Microsoft Access 2000, which is widely available as part of Microsoft Office Professional. This paper outlines the procedures used for the selection and evaluation of existing literature data for incorporation into the database. In addition, the design of the database is described, along with the data entry and quality control procedures used in its construction. Limitations of the data are discussed and guidelines for its use are provided.
Substance identification by infrared spectroscopy is performed by comparison of the experimental spectrum with a reference spectrum from a printed compilation or a database. If the analyzed compound can not be found in a database the corresponding reference spectrum has to be simulated. In order to achieve this, several reasonable candidates of structures for the compound at hand have to be conceived and for all these, infrared spectra have to be developed. The simulated spectrum that is most similar to the experimental suggests the correct structure. A rapid spectrum prediction method based on neural networks has been developed that supplies reference spectra for any organic compound. The scope and limitations of this method will be discussed on a test set of 16 compounds representing a broad range of organic chemistry.
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include format and content enhancements, cross-references to additional databases, new documentation files and improvements to TrEMBL, a computer-annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDSs) in the EMBL Nucleotide Sequence Database, except the CDSs already included in SWISS-PROT. We also describe the Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT. SWISS-PROT is available at: http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/
An isoelectric focusing method using thin-layer agarose gel has been developed for wheat gliadin. Using flat-bed units with a third electrode, up to 72 samples per gel may be analyzed. Advantages over traditional acid polyacrylamide gel electrophoresis methodology include: faster run times, nontoxic media, and greater sample capacity. The method is suitable for fingerprinting or purity testing of wheat varieties. Using digital images captured by a flat-bed scanner, a 4-band reference system using isoelectric points was devised. Software enables separated bands to be assigned pI values based upon reference tracks. Precision of assigned isoelectric points is shown to be on the order of 0.02 pH units. Captured images may be stored in a computer database and compared to unknown patterns to enable an identification. Parameters for a match with a stored pattern may be adjusted for pI interval required for a match, and number of best matches.
The Library of the Health Sciences at the University of Illinois at Chicago obtained a grant from the Illinois State Library to implement a statewide demonstration project that would provide consumer health information (CHI) using InfoTrac's Health Reference Center CD-ROM database. The goals of the project were to cooperate with targeted public libraries and clinics in providing CHI at the earliest point of need; to provide access to the database via a dial-up network server and a toll-free telephone number; and to work with targeted sites on database training, core CHI reference sources, and referral procedures. This paper provides background information about the project; describes the major systems and technical issues encountered; and discusses the outcomes, impact, and envisioned enhancements.
We derive an expectation maximization algorithm for maximum-likelihood training of substitution rate matrices from multiple sequence alignments. The algorithm can be used to train hidden substitution models, where the structural context of a residue is treated as a hidden variable that can evolve over time. We used the algorithm to train hidden substitution matrices on protein alignments in the Pfam database. Measuring the accuracy of multiple alignment algorithms with reference to BAliBASE (a database of structural reference alignments) our substitution matrices consistently outperform the PAM series, with the improvement steadily increasing as up to four hidden site classes are added. We discuss several applications of this algorithm in bioinformatics.
Biomedical databases are an important source of information for health technology assessment. However, there is considerable variation in the costs of accessing commercial databases. We sought to measure the quality, amount of overlap, and costs of information retrieved from two of the main database sources--MEDLINE and EMBASE. Librarians at two health technology assessment agencies ran a total of eight literature searches on various medical technologies, using both databases. All search results were independently reviewed by two researchers. The researchers were asked to identify relevant references and to rank each of these according to a level of evidence scale. The results were tabulated to show the number of references identified by each database, the number of relevant references ranked by level of evidence, and the number of these references that were unique to one or the other database. The cost of retrieving references from each source was also calculated. Each database contained relevant references not available in the other. Because of the longer time lag for indexing in MEDLINE, many of the references that originally appeared to be unique to EMBASE were subsequently available in MEDLINE as well. Since our study was conducted, MEDLINE has been made available worldwide, free of charge, via the Internet. Hence, the cost difference between the databases is now even greater. However, notwithstanding the costs, it appears that literature searches that rely on only one or the other database will inevitably miss pertinent information.
The Prostate Gene Database (PGDB: http://www.ucsf.edu/pgdb) is a curated and integrated database of genes or genomic loci related to the human prostate and prostatic diseases. Currently, PGDB covers genes involved in a number of molecular and genetic events of the prostate including gene amplification, mutation, gross deletion, methylation, polymorphism, linkage and over-expression, as published in the literature. Genes that are specifically expressed in prostate, as evidenced by analysis of data from expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), are also included. There are a total of 165 unique entries in the database. Users can either browse or query the PGDB through a web interface. For each gene, in addition to basic gene information and rich cross-references to other databases, inclusive and relevant literature references are provided to support the inclusion of the gene in the database. Detailed expression data calculated from the UniGene and SAGEmap databases are also presented.
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Recent efforts have focused on exhaustive cross-referencing to the EMBL nucleotide sequence database, and on the improvement of the WWW-based user interfaces and data retrieval mechanisms. EPD can be accessed at http://www.epd.isb-sib.ch
OBJECTIVE: This study aims to evaluate the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for species identification of human Capnocytophaga and to confirm results by whole-genome sequencing. METHODS: Six reference strains, representing human Capnocytophaga species and one taxon, and a total of 126 clinical strains, selected based on their biochemical profiles from a large collection of preliminarily identified Capnocytophaga isolates, were analyzed. RESULTS: Of those, 125 strains (94%) were identified at least at the genus level (log score variation of 1.7-1.999), while 52 strains (39%) were identified at the species level with a cut-off score of ≥2.0. Eight strains (6%) remained unidentified with a log score of <1.69. C. leadbetteri and Capnocytophaga genospecies AHN8471 strains were accurately identified at the genus level. Minor identification errors were observed in three cases: C. leadbetteri (n=1), C. ochracea (n=2), and Capnocytophaga genospecies AHN8471 (n=38). MALDI-TOF MS was unable to distinguish between C. sputigena and Capnocytophaga genospecies AHN8471 at the species level but clustered them together in the Main Spectra Profile (MSP) dendrogram. CONCLUSIONS: MALDI-TOF MS shows promise as a diagnostic tool for identifying human Capnocytophaga species when correct taxonomy and sufficient reference strains are available in the database. Based on the close phenotypic, ribosomal, and genotypic structures, we propose to establish the term "C. sputigena group" encompassing C. sputigena, Capnocytophaga genospecies AHN8471, and other related Capnocytophaga variants. Nevertheless, updating and expanding the MALDI-TOF MS reference database is essential to improve identification accuracy.
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of experimentally characterised eukaryotic POL II promoters. The underlying definition of a promoter is that of a transcription initiation site. All information presented in EPD results from an independent evaluation of primary experimental data shown in the biological literature. Sequences flanking transcription initiation sites are indirectly given by pointers to EMBL sequences. The annotation part of a promoter entry includes description of the promoter-defining evidence, cross-references to other databases, and bibliographic references. Being designed as a resource for comparative sequence analysis, EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets. The database is available through the World Wide Web at URL http://cmpteam4.unil.ch
Electronic databases corresponding to most of the world's currently published literature and many other types of information are publicly available through online systems. Scientific databases that give references for publications are numerous and widely used; scientific numeric databases that are open to the public are far fewer and less used. Online retrieval systems are becoming easier to use as a result of the introduction of artificial intelligence techniques and user-friendly front ends and gateways. Issues related to electronic databases include public-private sector competition, transborder data flow, copyright, downloading, and the changing roles in database generation and processing.
OBJECTIVE: To compare nine on-line bibliographic databases to obtain bibliographic references on specific drug interactions. DESIGN: Seven bibliographic databases were selected for their ability to provide information concerning drug interactions: EMBASE, MEDLINE, TOXLINE, BIOSIS, Chemical Abstracts (CAS), PHARMLINE, and International Pharmaceutical Abstracts (IPA). Two French on-line bibliographic databases (i.e., PASCAL, BIBLIOGRAPHIF) were also tested to compare them with the other international databases. Twenty drug interactions were selected randomly using the journal Reactions Weekly 1993. MAIN OUTCOMES MEASURES: The total number of references, the number of potentially relevant references, the number of case report references, the number of unique references in the total number of references, and the number of unique references between potentially relevant references were analyzed by using the Friedman two-way ANOVA by ranks. For each database, relevance and relative recall were calculated. RESULTS: For the total number of references, EMBASE was significantly more comprehensive then all other databases (p < 0.05). EMBASE had a significantly greater number of potentially relevant references than IPA, PHARMLINE, CAS, and BIBLIOGRAPHIF (p < 0.05). For the total number of case report references, only one significant difference, between EMBASE and BIBLIOGRAPHIF (p < 0.05), was observed. MEDLINE and TOXLINE had the lowest cost per potentially relevant reference. CONCLUSIONS: To obtain bibliographic references on drug interactions, the first step should be to search MEDLINE or TOXLINE; the second step, for completeness, should be to search EMBASE.