Database archiving

WWW NDT/UT Library of 250 sites with its abstracts in sections Institutes. Societies. Applications, Databases/Archives, Standards. NDT Maps of Germany/Canada/Israel... 

Khan, A., Warner, H., Brown, W. (2000). Symptom reduction and suicide risk in patients treated with placebo in antidepressant clinical trials An analysis of the Food and Drug Administration database. Archives of General Psychiatry, 57, 311-317. 

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

Derwent Information Ltd. Derwent Information Ltd., previously known as Derwent PubHcations Ltd., changed its name in the 1990s to reflect more accurately the fact that its products go far beyond traditional pubHcations. Derwent provides a wide spectmm of information products and services, many of them relating to patents. Derwent also produces important databases (qv) of nonpatent information from the pharmaceutical and agncultural chemical Hterature. These products and services encompass alerting tools for current awareness, systems for retrospective search and retneval, and means for document deHvery and archiving. 

The LIMS software is essentially a database for tracking, reporting, and archiving lab data as well as scheduling and guiding lab activities. Graphical and statistical treatment of data for improved process control (qv) as well as preparation of certificates of analysis (COA) for the customer are some of the other features of a comprehensive LIMS package (30). 

Mass storage device. Typically, fixed-head hard disk drives are used to store ac tive data, including on-line and historical databases and non-memory-resident programs. Memory-resident programs are stored to allow loading at system startups. The tape drives are used for archives and backups. 

Historical DataBase Subsystem We have discussed the use of on-hne databases. An historical database is built similar to an on-line database. Unlike their on-line counterparts, the information stored in a historical database is not normally accessed directly by other subsystems for process control and monitoring. Periodic reports and longterm trends are generated based on the archived data. The reports are often used for long-term planning and system performance evaluations such as statistical process (quality) control. The trends may be used to detect process drifts or to compare process variations at different times. 

The historical data is sampled at user-specified intervals. A typical process plant contains a large number of data points, but it is not feasible to store data for all points at all times. The user determines if a data point should be included in the list of archive points. Most systems provide archive-point menu displays. The operators are able to add or delete data points to the archive point hsts. The samphng periods are normally some multiples of their base scan frequencies. However, some systems allow historical data samphng of arbitraiy intei vals. This is necessaiy when intermediate virtual data points that do not have the scan frequency attribute are involved. The archive point lists are continuously scanned bv the historical database software. On-line databases are polled for data. The times of data retrieval are recorded with the data ootained. To consei ve storage space, different data compression techniques are employed by various manufacturers. 

As already stated above, the database has been developed using ISIS software. The program operation is very simple, and about 30 min to learn the particular commands of this structure-searching program. ISIS provides both storage and retrieval of chemical structures. It is also possible to store text and numeric data into database entries. Because molecular structures are searchable in many ways, ISIS software is an excellent tool for exploiting data, and not simply archiving it. 

Databases are the lingua franca—the common language—of bioinformatics. Although the kind of data archived may vary, nonetheless, the use, creation, and manipulation of databases remains the most critical feature of modern-day bioinformatics, both as a discipline in its own right and as a support for... 

A key factor in determining an ROI on the basis of increased efficiencies is to be able to apply metrics to the existing processes commonly this requires measurement of the process before the implementation of a new system and then a corresponding measurement of the process after implementation. In the case of ELN systems, this information can also be supplemented through the use of the ELN database itself, for example, by looking at the number of completed experiments created per scientist per week. These data can then be compared with an historical analysis of data from paper notebook archives on scientific productivity by similar groups. 

Experiments may need to be viewed or presented 30 or 40 years after they are saved in a database. For instance, a lawyer may ask for experimental documents to defend a company in a product liability lawsuit. An important requirement here is that the document format should be independent of the application used to create the information, and that ideally the long-term archive format should not be based on a proprietary technology. This is a... 

What is the relationship of the single file to the database Demonstrate the functionality to accurately and readily retrieve archival records throughout the record retention period (e.g., backup and restore or archive/ retrieve or other). Include ... 

The Human Gene Mutation Database http //archive.uwcm.ac.uk/ uwcm/ mg/hgmdO.html... 

Chemical Physics Preprint Database. This database [81] is a fully automated electronic archive and distribution server intended to provide a means for rapid and efficient preprint distribution within the international theoretical chemical physics community. A preprint is a copy of a paper that has been submitted for publication. This database has been designed to be a useful and freely available tool for education and research. It allows investigators to submit and retrieve electronic copies of preprints via the Internet. Access for retrieval and listing of papers in the database is possible through WWW servers, anonymous ftp, or e-mail. Currently research papers are submitted to the databases via e-mail. This project is a joint effort by the Department of Chemistry at Brown University and the Theoretical Chemistry and Molecular Physics Group at the Los Alamos National Laboratory. The homepage of Chemical Physics Preprint Database is http // www.chem.brown.edu/chem-ph.html. (For a more... 

Our specimen database also contains additional parameters that are used to control the data collection process and to provide archival information to each data file written by the collection process. The console display for editing the specimen database is of the "fill in the form" type and the user revises the parameters for each specimen position (including the zeroth) as required. New parameter values are checked for validity at the time they are entered. All other parameters retain the values they possessed during the previous set of analyses. Thus, only minor changes are needed to program for a set of samples similar to the previous ones. All records in the database can be cleared if the analytical conditions are markedly different. 

Field, H.I., Fenyo, D., Beavis, R.C. (2002). RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics 2, 36 17. 

H. I. Field, D. Fenyo, and R. C. Beavis. RADARS, a Bioinformatics Solution that Automates Proteome Mass Spectral Analysis, Optimises Protein Identification, and Archives Data in a Relational Database. Proteomics, 2, no. 1 (2002) 36-47. 

Search engine of the National Center for Biotechnology Information, including a few databases PubMed (MEDLINE biomedical literature), PubMed Central (free digital archive of life sciences journal literature), Books, OMIM (Online Mendelian Inheritance in Man, a catalog of genetically linked diseases),... 

The experimental exploration and confirmation of protein functions are relatively slow processes and always require dedicated experiments. The analysis of protein-protein associations as such improved remarkably in quality and speed. This is accompanied by the creation of new databases that will reflect the network of interacting proteins (the Protein Function and Metabolic Pathway project, http //bioinformer.ebi. ac.uk 80/newsletter/archives/4/pfmp.html, and the Biomolecular Interaction Network Database project http //bioinfo.mshri.on.ca/ BIND/). These activities contribute to the idea that cellular mechanisms can be better understood when they are seen as a multicomponent networked process. 

The protein sequence databases are the most comprehensive source of information on proteins. The goal of this chapter is to describe the different protein sequence databases available to researchers. It is necessary to distinguish between universal databases that cover proteins from all species and specialized data collections that store information about specific families or groups of proteins, or about the proteins of a specific organism. Two categories of universal protein sequence databases can be discerned simple archives of sequence data and annotated databases in which additional information has been added to the sequence record. The next section describes the Protein Information Resource (PIR), the oldest protein sequence database SWISS-PROT, an annotated universal sequence database and TrEMBL, the supplement of... 

The assembly of large screening libraries for HTS requires the development of archival and retrieval systems that can handle solid compounds and compound solutions in microtubes or in plates in either the 96 or the 384 format. Barcodes are used to identify each sample vial, tube, or plate. Databases record which samples are available, what type of sample it is, and how much is available. All solid samples are prepared first as stock (master) solutions ( around 5 mg/mL in DMSO) in 2-D bar-coded tubes that are then aliquotted to plates and processed as described earlier. The tubes and plates are usually made of polypropylene for compatibility with DMSO. DMSO is the industry standard solvent for screening libraries because many of the archived compounds are not soluble in water at 5 mg/mL. DMSO, an organic solvent, also has a favorable combination of biological... 

The documentation of all the available types of data in the archives was done and tabulated to decide which information could be verified. Tournigan incorporated only those holes in the database which could be verified from original documentation. 

Astronomical data is archived and released in the form of images (maps and outlines) and spectra (distribution of photons as a function of their energy). Duly classified, these constitute a huge database. The problem then is to give physical and astrophysical meaning to these cosmic archives, via an interpretation within the framework of the most relevant physical theory. 

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