[More support and better information to rare disabilities' groups. A competence center and a factual database is to be established].
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Centralized Hospital Services↗
SEARCH · Search PubMed
Results for “Databases, Factual”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
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[Creation of evidence-based practice guidelines and the monetary charges to access factual databases].
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Databases, Factual↗
[Factual databases in bioorganic chemistry. Analytical review].
The main scientific sequence databases of interest for researchers working in the field of bioorganic chemistry are reviewed. Information is given concerning possibilities for rapid access and efficient search for needed information, postal and e-mail addresses, and literature sources in which these databases are comprehensively described.
Amino Acid Sequence↗
The Visible Human Project: a resource for anatomical visualization.
The National Library of Medicine (NLM) has long been a world leader in the archiving and distribution of the print-based images of biology and medicine. NLM has also been a pioneer in the use of computer systems to encode and distribute textual knowledge of the life sciences. NLM's Long Range Planning effort of 1985-86 foresaw a coming era where NLM's Bibliographic and factual database services would be complemented by libraries of digital images, distributed over high speed computer networks and by high capacity physical media. The NLM Planning Panel on Electronic Imaging recommended that NLM should undertake the building a digital image library consisting of computerized tomography (CT) and magnetic resonance (MR) images, and cryosection images of a representative, carefully selected and prepared male and female cadaver--the "Visible Human ProjectJ." The male and female Visible Human data sets are now being made available through a license agreement with the NLM. The data sets are supporting a wide range of educational, diagnostic, treatment planning, and commercial uses. The value of this international resource in the public domain increases through its application. Its utility will continue to grow as related databases are attached to it, and as more attributes are given to its image elements.
Anatomy, Cross-Sectional↗
Searching fee and non-fee toxicology information resources: an overview of selected databases.
Toxicology profiles organize information by broad subjects, the first of which affirms identity of the agent studied. Studies here show two non-fee databases (ChemFinder and ChemIDplus) verify the identity of compounds with high efficiency (63% and 73% respectively) with the fee-based Chemical Abstracts Registry file serving well to fill data gaps (100%). Continued searching proceeds using knowledge of structure, scope and content to select databases. Valuable sources for information are factual databases that collect data and facts in special subject areas organized in formats available for analysis or use. Some sources representative of factual files are RTECS, CCRIS, HSDB, GENE-TOX and IRIS. Numerous factual databases offer a wealth of reliable information; however, exhaustive searches probe information published in journal articles and/or technical reports with records residing in bibliographic databases such as BIOSIS, EMBASE, MEDLINE, TOXLINE and Web of Science. Listed with descriptions are numerous factual and bibliographic databases supplied by 11 producers. Given the multitude of options and resources, it is often necessary to seek service desk assistance. Questions were posed by telephone and e-mail to service desks at DIALOG, ISI, MEDLARS, Micromedex and STN International. Results of the survey are reported.
Bibliographies as Topic↗
PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine.
BACKGROUND: The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-readable format. We hypothesized that the formidable task-size of backfilling the database could be reduced by using Support Vector Machine technology to first locate interaction information in the literature. We present an information extraction system that was designed to locate protein-protein interaction data in the literature and present these data to curators and the public for review and entry into BIND. RESULTS: Cross-validation estimated the support vector machine's test-set precision, accuracy and recall for classifying abstracts describing interaction information was 92%, 90% and 92% respectively. We estimated that the system would be able to recall up to 60% of all non-high throughput interactions present in another yeast-protein interaction database. Finally, this system was applied to a real-world curation problem and its use was found to reduce the task duration by 70% thus saving 176 days. CONCLUSIONS: Machine learning methods are useful as tools to direct interaction and pathway database back-filling; however, this potential can only be realized if these techniques are coupled with human review and entry into a factual database such as BIND. The PreBIND system described here is available to the public at http://bind.ca. Current capabilities allow searching for human, mouse and yeast protein-interaction information.
Algorithms↗
Information systems to support medical practice and scientific discovery.
In many educational applications of the computer, systems are designed to contain information or knowledge that is to be conveyed to the student or user via an interactive learning scheme. In contrast, most NLM systems strive merely to increase the user's access to the broad range of published scientific literature, or to link the user to appropriate factual databases. Providing or enhancing access is, of course, made more difficult than in didactic systems because of the relatively large size of the files that make up the bibliographic and factual databases. For example, the MEDLARS files contain over 12 million records, made up of roughly thirty billion online characters. Users send electronic queries to these files on-line via commercial value-added networks (24 hrs/day, 365 days/year), in total about 4 million queries per year. Of the 4 million, approximately half of the queries were (in the opinion of the users polled) prompted by questions that arose in caring for a particular patient. The remaining 2 million queries concerned research, teaching, and public policy.
Biotechnology↗
A stereochemically accurate chemical substance database based on the systematic names of organic compounds. 1. Low molecular weight organic compounds.
A chemical substance database, containing chemical structures generated automatically from their IUPAC systematic names, is described. The structure generation program can convert the names of natural products, peptides, and stereochemically complex names into stereochemically correct connection tables. More than 300,000 commonly encountered compounds are stored in the database and are publicly accessible through the JOIS-F online system, which also offers mass spectral, thermochemical, and other factual databases.
Algorithms↗
CHIRBASE, a molecular database for the separation of enantiomers by chromatography.
A selected review on the separation of the stereoisomers of menthol by gas chromatography serves to demonstrate a new approach to tackle the increasing number of publications on enantiomer separation. The graphical molecular database CHIRBASE covers information (structural, bibliographic and chromatographic data) on liquid chromatography, supercritical fluid chromatography and gas chromatography. CHIRBASE is based on standard database software, thus meeting the requirements of "state of the art" information management in the chemical and pharmaceutical industries and academia. The scrutiny required to create and maintain a factual database revealed that the information content of the contemporary literature with respect to chromatographic data requires improvement.
Chromatography↗
The copyrightability of factual compilations such as databases containing medical records.
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Copyright↗
[Information sources on carcinogenic agents].
This work comprises lists of publications and computer data bases available at the Scientific Information Department, The Nofer Institute of Occupational Medicine, Lodz, Poland, containing information on cancer risks resulting from exposure to carcinogenic agents. The following publications have been described: IARC Monographs on the Evaluation of Carcinogenic Risk to Humans; Official lists of carcinogens valid in individual countries; a periodical--Survey of compounds which have been tested for carcinogenic activity; a guide--The Annual Report on Carcinogens, a series on Carcinogens in the Occupational Environment, comprising Information Cards and Monographs; a guide on Carcinogenic Agents, and computer databases, including the INCAR, IRIS, IRPTC, RTECS CHEMINFO factual databases and the CANCER-CD, MEDLINE, TOXLINE, NIOSHTIC and MEDIP bibliographic (or reference) databases. The presented publications and databases may prove helpful in searching for data on identifying and preventing the adverse health effects of environmental and occupational exposure to carcinogens.
Carcinogens↗
Testing HIV molecular biology in in silico physiologies.
The natural and medical sciences have strongly benefitted from technological advances that help to create and store more raw information than can be effectively processed. In particular, this rapid growth has created a strong need for a flexible and far-reaching approach to cross-database simulation. The paper uses a highly simplified example, called the 'TinyMouse' simulator, to explain the design and functioning of interactive cross-database simulators that can be applied to prototype experiments with animal models of human disease, such as the hu-SCID mouse model for the Acquired Immune Deficiency Syndrome (AIDS). Work in progress is discussed to extend 'TinyMouse' into 'CyberMouse', an informational organism that synthesizes factual databases of the murine neuroendocrine-immune system.
Animals↗
Protein Circular Dichroism Data Bank (PCDDB): data bank and website design.
The Protein Circular Dichroism Data Bank (PCDDB) is a new deposition data bank for validated circular dichroism spectra of biomacromolecules. Its aim is to be a resource for the structural biology and bioinformatics communities, providing open access and archiving facilities for circular dichroism and synchrotron radiation circular dichroism spectra. It is named in parallel with the Protein Data Bank (PDB), a long-existing valuable reference data bank for protein crystal and NMR structures. In this article, we discuss the design of the data bank structure and the deposition website located at http://pcddb.cryst.bbk.ac.uk. Our aim is to produce a flexible and comprehensive archive, which enables user-friendly spectral deposition and searching. In the case of a protein whose crystal structure and sequence are known, the PCDDB entry will be linked to the appropriate PDB and sequence data bank files, respectively. It is anticipated that the PCDDB will provide a readily accessible biophysical catalogue of information on folded proteins that may be of value in structural genomics programs, for quality control and archiving in industrial and academic labs, as a resource for programs developing spectroscopic structural analysis methods, and in bioinformatics studies.
Circular Dichroism↗
The Italian XLMR bank: a clinical and molecular database.
Mental retardation (MR) is a nonprogressive condition characterized by a significant impairment of intellectual capabilities with deficit of cognitive and adaptive functioning and onset before 18 years. Mental retardation occurs in about 2 to 3% of the general population and it is estimated that 25 to 35% of the cases may be due to genetic causes. Among these "genetic" MR, 25 to 30% are probably due to mutations in a gene on the X chromosome (X-linked mental retardation, XLMR). Given the genetic heterogeneity of XLMR, the availability of a considerable number of patients with accurate phenotypic classification is a crucial factor for research. The X-linked Mental Retardation Italian Network, which has been active since 2003, has collected detailed clinical information and biological samples from a vast number of MR patients. Collected samples and clinical information are inserted within the XLMR bank, a comprehensive molecular and clinical web-based database available at the address http://xlmr.unisi.it. The database is organized in three distinct parts. Part I and II contain several electronic schedules to register information on the family, the phenotypic description, the photographs, and a 20 sec movie of the patient. Part III allows the registration of molecular analyses performed on each case; samples and clinical data are usable via password-restricted access. Clinical and molecular centers interested in joining the network may request a password by simply contacting the Medical Genetics of the University of Siena. The XLMR bank is an innovative biological database that allows the collection of molecular and clinical data, combines descriptive and iconographic resources, and represents a fundamental tool for researchers in the field of mental retardation.
Computer Security↗
Analysis of the wheat and Puccinia triticina (leaf rust) proteomes during a susceptible host-pathogen interaction.
Wheat leaf rust is caused by the fungus Puccinia triticina. The genetics of resistance follows the gene-for-gene hypothesis, and thus the presence or absence of a single host resistance gene renders a plant resistant or susceptible to a leaf rust race bearing the corresponding avirulence gene. To investigate some of the changes in the proteomes of both host and pathogen during disease development, a susceptible line of wheat infected with a virulent race of leaf rust were compared to mock-inoculated wheat using 2-DE (with IEF pH 4-8) and MS. Up-regulated protein spots were excised and analyzed by MALDI-QqTOF MS/MS, followed by cross-species protein identification. Where possible MS/MS spectra were matched to homologous proteins in the NCBI database or to fungal ESTs encoding putative proteins. Searching was done using the MASCOT search engine. Remaining unmatched spectra were then sequenced de novo and queried against the NCBInr database using the BLAST and MS BLAST tools. A total of 32 consistently up-regulated proteins were examined from the gels representing the 9-day post-infection proteome in susceptible plants. Of these 7 are host proteins, 22 are fungal proteins of known or hypothetical function and 3 are unknown proteins of putative fungal origin.
Amino Acid Sequence↗
SPLASH: systematic proteomics laboratory analysis and storage hub.
In the field of proteomics, the increasing difficulty to unify the data format, due to the different platforms/instrumentation and laboratory documentation systems, greatly hinders experimental data verification, exchange, and comparison. Therefore, it is essential to establish standard formats for every necessary aspect of proteomics data. One of the recently published data models is the proteomics experiment data repository [Taylor, C. F., Paton, N. W., Garwood, K. L., Kirby, P. D. et al., Nat. Biotechnol. 2003, 21, 247-254]. Compliant with this format, we developed the systematic proteomics laboratory analysis and storage hub (SPLASH) database system as an informatics infrastructure to support proteomics studies. It consists of three modules and provides proteomics researchers a common platform to store, manage, search, analyze, and exchange their data. (i) Data maintenance includes experimental data entry and update, uploading of experimental results in batch mode, and data exchange in the original PEDRo format. (ii) The data search module provides several means to search the database, to view either the protein information or the differential expression display by clicking on a gel image. (iii) The data mining module contains tools that perform biochemical pathway, statistics-associated gene ontology, and other comparative analyses for all the sample sets to interpret its biological meaning. These features make SPLASH a practical and powerful tool for the proteomics community.
Database Management Systems↗
Characterization of bovine seminal plasma by proteomics.
Previous investigations of bovine seminal plasma (BSP) have revealed the identities of the three major proteins, BSP-PDC109, BSP-A3 and BSP-30 kDa, which together constitute about half of the total protein, as well as about 30 of the minor proteins. Analyses of BSP by 2-DE have revealed about 250 protein spots, suggesting that much of the BSP proteome remains undescribed. In this study, BSP has been analyzed by 2-D LC-based and SDS-PAGE-based proteomic methods. Ninety-nine proteins were identified, including 49 minor proteins that have not previously been described in seminal plasma of any species.
Animals↗