Construction of a data base for cobalt-59 nuclear magnetic resonance spectrometry

The TOOL-IR. PDB and COOD systems are compared for the construction of data bases for ⁵⁹Co-n.m.r. bibliographic and spectral data. The spectral data used are the chemical shifts from several different standards, and the line widths and coupling constants (if present). The PDB system is effective for storage and retrieval of bibliographic data, but the COOD system is better for the retrieval of spectral data, and for combination of data files on literature and chemical shifts.     

SDC experiences with large data bases.

SDC operates a large-data-base system that permits users all over the United States and in several foreign countries to search very large bibliographic files interactively, by means of a terminal and telephone connection. Developing extensive use of such systems requires not only technical considerations--such as proper selection and handling of data base elements--but also a massive educational effort, to help provide the large user community necessary to share the sizable costs of data base acquisition, file development, and storage. The growing acceptance of on-line retrieval services attests to the success of that effort, as well as to their inherent cost-effectiveness.     

Toxicology information systems: a historical perspective

Toxicology information systems have evolved swiftly from early, library-based bibliographic tools to advanced packages utilizing sophisticated computer and telecommunication technologies. These systems have evolved concurrently with the rapid expansion of the science of toxicology itself. Bibliographic files such as TOXLINE represent first attempts to handle the toxicology literature through on-line retrieval. Subsequent approaches applied the use of computers to provide literature-derived data, as in TDB or RTECS, or to capture data directly in the laboratory. Societal concerns about hazardous substances, manifested in legislation and regulations, have been responsible for the creation of many computerized systems. Advanced, integrated information management systems are being explored as a method of accessing a large number of independently maintained toxicology databases. Changes in information technologies such as the trend toward microcomputers and novel high-density storage devices will affect the future of toxicology information systems as will impending developments in toxicology itself related to biotechnology, analytical methodology, and alternatives to whole animal testing.     

Practical approach to archival and retrieval of analytical data in the laboratory

Today's analytical laboratory uses a large number of different instruments that are connected in networks. Together with increasing automation, data are produced at a rate that can easily reach gigabytes per month, which generates the problem of systematic archival. In addition, working under Good Laboratory Practice requires that archival of raw data be performed in such a way that they can be readily retrieved upon request, even years later. While systematic archival of data is already performed in most laboratories, it is the retrieval of saved information that is often far from straightforward. This paper describes a simple but systematic approach for both archival and retrieval of data files and related electronic documents. It consists of an unambiguous scheme for the naming of electronic files, an efficient backup strategy, a simple database holding information about any data acquired, and a convenient interface to this database that can be accessed from any workplace while assuring restricted access. The system is capable of handling several databases concurrently and is used in our facility to archive data from several workgroups. The use of freely available software such as the Linux operating system made it possible to implement a fast and stable solution at exceptionally low cost.     

Information theory applied to feature selection of binary-coded infrared spectra for automated interpretation by retrieval of reference data

A method is described for feature selection from infrared spectra, intended for identification of organic compounds by computer-aided retrieval of reference data contained in small files. Complete discrimination of the binary-coded spectra is achieved by selecting a minimum number of spectral features; the information content is used as the selection criterion. The selection procedure is applied to five data sets (saturated and unsaturated hydrocarbons, alcohols, ethers and aldehydes/ketones) involving some 400 spectra. Each spectrum is uniquely coded by using about 10% of the 140 spectral features (binary-coded peak positions) available originally. For the intensity, a threshold of 50% appears to be applicable in some cases. For coding the frequency or wavelength parameter, wavenumbers (cm^-1) are preferred to wavelengths (mm). The method takes into account the a priori probabilities of spectral features and their correlations. Results of a retrieval program for a few “unknown” spectra are given.     

Networking Mass Spectrometer Data Systems for Improved Productivity and Electronic Archiving of Data

Several Finngan-MAT mass spectrometer data systems were networked together to achieve the following two primary objectives: (1) to allow access to mass spectrometry data and data processing functions from remote locations without affecting simultaneous data acquisition at the instruments, and (2) to electronically archive mass spectrometry data at a central location on a high-capacity, fast-access device that allows rapid retrieval of archived data for all data processing operations at all locations. UNIX workstations, IBM PC/AT-compatible computers, and Data General Nova minicomputers were connected via Ethernet interfaces to allow rapid data transfer among all systems as well as X-Windows access to UNIX-based systems. Bridging techniques were used to isolate possible high-traffic areas of the network and to enable security measures for adequate protection of files. Additionally, serial connections were made through a Northern Telecom phone system to provide remote terminal access to the Data General Nova-based systems. Use of these connectivity techniques significantly improved productivity by allowing retrieval, processing, and printing of data from remote locations, such as office areas, without affecting data acquisition, processing, and printing performed simultaneously at the instruments. For archival purposes, data files are electronically stored on high-capacity magneto-optical disks for rapid retrieval. A highcapacity fixed disk is also available for centralized temporary data file storage. A Digital Equipment Corporation DECstation 2100 UNIX workstation was used as the file server for centralized data storage while being simultaneously utilized as the data system computer for one of the mass spectrometers. Utilization of this UNIX-based file server system in conjunction with Ethernet connectivity techniques provides a centralized, rapid-access, high-capacity, cost- and space-efficient method for electronic archival of mass spectrometry raw data recorded at all of the instruments.     

MOGADOC (Molecular Gas Phase Documentation) — An interactive computerised search/retrieval system

For 22 years the Section for Structure Documentation (SSD), University of Ulm, has provided a documentation service covering the literature of molecules studied in the gas phase by electron diffraction, microwave spectroscopy and other techniques. Much of the information which has been accumulated over these years has now been keyboarded to constitute a computerised database. An interactive search/retrieval system, MOGADOC, has been written using the SIMULA¹ language implemented on the UNIVAC 1100/82 computer at the University of Freiburg. MOGADOC enables the user to search the database on the basis of bibliographic, chemical and physical search terms.     

Spektren —a computer system for the identification and structure elucidation of organic compounds

The spectroscopic information system described consists of a data base of 30 000 nuclear magnetic resonance, infrared and mass spectracombined with a program containing functions for matching spectra and substructure search. Information retrieval with this program uses inverted files; sequential search and various functions for graphic and written output and updating are possible. Hardware configuration and data flow from spectrometers to an IBM 3032 computer are described. Results of matching spectra and substructure search and retrieval operations are presented.     

A comparative report on an on-line retrieval service employing two distinct software systems.

A subjective evaluation comparing the National Aeronautics and Space Administration RECON and National Library of Medicine ELHILL 2 on-line information retrieval systems is presented as they relate to the delivery of a major service dealing with a collection of toxicological bibliographic references (TOXLINE). Comparisons of file structure, response time, command language, system environment, and other relevant features are made based upon actual experience with both systems.     

FreeSolv: a database of experimental and calculated hydration free energies,with input files

This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz.     

化学结构正规编码及其信息处理功能

自从计算机在化学领域中应用以来,化学结构的正规编码已广泛用来作为一种化学文献的信息索引,它还在开发化学智能系统中发挥着重要作用。正规编码生成是以化学结构图的拓扑性质为基础的。本文首先概述编码的基本原理及其生成的方法,随后分析这种编码在当今文献数据库、化学反应数据库、分子设计以及合成反应路线规划等化学信息系统中的功能。     

CHEMLEARN: microcomputer-based training for CHEMLINE, an alternative to formal classroom training

CHEMLINE (CHEMical Dictionary OnLINE), the National Library of Medicine's online chemical dictionary file, is primarily used by librarians and information scientists to enhance the retrieval of bibliographic information associated with chemical substances. This paper will discuss CHEMLEARN, a microcomputer-based training program designed to provide inexpensive, easily accessible self-instruction as an alternative to formal classroom training in the use of CHEMLINE. CHEMLEARN allows novice users to learn at their own pace and with considerable program feedback. In addition, it provides the skilled searcher with a way to reinforce or recall previously learned search techniques without incurring online charges. CHEMLEARN may be used in place of formal training or as a precursor to or a refresher following formal training.     

MENTHOR,a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural,biologic, physical,or geometric properties

Summary MENTHOR is a database system for the storage and retrieval of three-dimensional coordinate and charge information on molecules as well as of traditional biological and physical properties. Our molecular graphics system retrieves from MENTHOR structural information in individual molecules and receptor map/macromolecular binding site hypotheses. Substructural searches of MENTHOR are used to find starting coordinates for molecular modeling and traditional database searches of MENTHOR identify compounds for which modeling is needed. It also forms the data to be searched with ALLADDIN, our substructure/geometric search program. MENTHOR expedites molecular modeling by organizing previous work and facilitating transmission of information between individuals. Examples from modeling of D-2 receptor agonists are shown.     

The NCI Drug Information System. 2. DIS Pre-Registry

The Pre-Registry Module of the Drug Information System (DIS) is a staging area through which all new compounds are passed prior to acquisition and testing. Several methods are available for the entry of structures into the Pre-Registry; all involve built-in data validation. Newly entered structures are examined by computer programs for structural novelty and potential for anticancer activity. For those compounds that proceed to acquisition, the various acquisition steps, such as letter writing and record updating, are performed automatically. When a sample is obtained, the entire Pre-Registry record is updated and moved forward into the permanent DIS chemistry files.     

Data,knowledge and method bases in chemical sciences. Part IV. Current status in databases

Computer readable databases have become an integral part of chemical research right from planning data acquisition to interpretation of the information generated. The databases available today are numerical, spectral and bibliographic. Data representation by different schemes--relational, hierarchical and objects--is demonstrated. Quality index (QI) throws light on the quality of data. The objective, prospects and impact of database activity on expert systems are discussed. The number and size of corporate databases available on international networks crossed manageable number leading to databases about their contents. Subsets of corporate or small databases have been developed by groups of chemists. The features and role of knowledge-based or intelligent databases are described.     

The assessment of radiochemical separation procedures by means of computational techniques

The behaviour of 66 radio-ions towards 11 exchangers and 11 solutions under standardized experimental conditions has been evaluated and classified in order to have the possibility of a rapid assessment of radiochemical separation procedures. Two systems of utilizing the bulk of data obtained have been devised and employed. The first is based on the use of a deck of cards similar to those used for fast retrieval of bibliographic information, in which the behaviour of ions is coded by means of punched holes; the second is based on the treatment of the data by means of an electronic computer. The operational modes of the two systems and examples of their practical applications are presented.     

AGGREGATES: Finding structures in simulation results of solutions

Molecular Dynamic and Monte‐Carlo simulations are widely used to investigate the structure and physical properties of solids and liquids at a molecular level. Tools to extract the most relevant information from the obtained results are, however, in considerable demand. One such tool, the program AGGREGATES, is described in this work. Based on distance criteria, the program searches trajectory files for the presence of molecular clusters and computes several statistical and shape properties for these structures. Tools designed to investigate the local organization and the molecular conformations in the clusters are also available. Among these, it is introduced a new approach to perform a First Shell Analysis, by looking for the presence of atomic contacts between molecules. These elements are particularly useful to obtain information on molecular assembly processes (such as the nucleation of crystals or colloidal particles) or to investigate polymorphism in organic compounds. The program features are illustrated here through the investigation of the 4′‐hydroxyacetophenone + ethanol system. © 2017 Wiley Periodicals, Inc.     

Adsorption and adsorptive separations: A review and bibliographical update (1994)

This paper provides a review of the 1994 journal literature and complete bibliography concerned with adsorptive separations. The references are taken from the 45 most important chemical engineering journals. This paper provides an update to the literature as provided in previous bibliographic papers (Ray 1990; 1991; 1995). References for membranes and membrane-type separations (for 1992–1993) were the subject of a separate bibliographic paper (Ray 1994), due to the number of papers now published on this topic each year. A review and bibliography paper covering 1994 for membranes has been submitted for publication. Bibliographic papers covering traditional unit operations (Ray 1992; 1993; 1994; 1994) and supercritical extraction (Ray 1994) have been published. A bibliography of the chemical engineering journal literature from 1967–1988 has been published by the author (Ray 1990), and can provide access to a wider range of topics. A complete bibliographic listing of the chemical engineering journal literature from 1989 to 1994 (with subsequent six-monthly updates) is available on a CD-ROM database (Published by Royal Melbourne Institute of Technology) and full details can be obtained from the author.     

Cytochrome P450 Database

Abstract

This paper describes a specialized database dedicated exclusively to the cytochrome P450 superfamily. The system provides the impression of superfamily's nomenclature and describes structure and function of different P450 enzymes. Information on P450-catalyzed reactions, substrate preferences, peculiarities of induction and inhibition is available through the database management system. Also the source genes and appropriate translated proteins can be retrieved together with corresponding literature references.

Developed programming solution provides the flexible interface for browsing, searching, grouping and reporting the information. Local version of database manager and required data files are distributed on a compact disk. Besides, there is a network version of the software available on Internet. The network version implies the original mechanism. which is useful for the permanent online extension of the data scope.     

Information Database on Internal pH Gradients in Chromatofocusing

An information database on internal pH gradients in chromatofocusing was developed. The Windows 95/98/NT–based database contains information on model and experimental pH gradients and has a user-friendly interface for information retrieval and new data input. The database also contains two embedded programs: CF for simulating pH gradients by experimental conditions and ABC for rapidly calculating particular sections in gradient profiles. Examples of the use of embedded programs are given, and experimental and model pH gradients are compared.