MODULEWRITER: a program for automatic generation of database interfaces

MODULEWRITER is a PERL object relational mapping (ORM) tool that automatically generates database specific application programming interfaces (APIs) for SQL databases. The APIs consist of a package of modules providing access to each table row and column. Methods for retrieving, updating and saving entries are provided, as well as other generally useful methods (such as retrieval of the highest numbered entry in a table). MODULEWRITER provides for the inclusion of user-written code, which can be preserved across multiple runs of the MODULEWRITER program.     

A database for QA/QC in neutron activation analysis and gamma-ray spectrometry

A database has been designed for storing, retrieving and analyzing information about samples, experimental conditions and results obtained by neutron activation analysis and gamma-ray spectrometry. It has been created using Microsoft ACCESS 2002 under a Windows operating system. The database has been designed not only for saving information but also for quality assurance and quality control purposes. The structure of the relational design has been discussed and demonstrated with a new graphical feature of ACCESS 2002 called PIVOTCHART.     

Efficient substructure searching of large chemical libraries: the ABCD chemical cartridge

Efficient substructure searching is a key requirement for any chemical information management system. In this paper, we describe the substructure search capabilities of ABCD, an integrated drug discovery informatics platform developed at Johnson & Johnson Pharmaceutical Research & Development, L.L.C. The solution consists of several algorithmic components: 1) a pattern mapping algorithm for solving the subgraph isomorphism problem, 2) an indexing scheme that enables very fast substructure searches on large structure files, 3) the incorporation of that indexing scheme into an Oracle cartridge to enable querying large relational databases through SQL, and 4) a cost estimation scheme that allows the Oracle cost-based optimizer to generate a good execution plan when a substructure search is combined with additional constraints in a single SQL query. The algorithm was tested on a public database comprising nearly 1 million molecules using 4,629 substructure queries, the vast majority of which were submitted by discovery scientists over the last 2.5 years of user acceptance testing of ABCD. 80.7% of these queries were completed in less than a second and 96.8% in less than ten seconds on a single CPU, while on eight processing cores these numbers increased to 93.2% and 99.7%, respectively. The slower queries involved extremely generic patterns that returned the entire database as screening hits and required extensive atom-by-atom verification.     

JChem: Java applets and modules supporting chemical database handling from web browsers

A Java based development tool for building portable chemical information systems is presented. The system contains applets for constructing web-based interfaces and classes that add structure handling to relational databases. Custom applications built with JChem can combine SQL and structural queries.     

PlantPIs--an interactive web resource on plant protease inhibitors

PlantPIs is a web querying system for a database collection of plant protease inhibitors data. Protease inhibitors in plants are naturally occurring proteins that inhibit the function of endogenous and exogenous proteases. In this paper the design and development of a web framework providing a clear and very flexible way of querying plant protease inhibitors data is reported. The web resource is based on a relational database, containing data of plants protease inhibitors publicly accessible, and a graphical user interface providing all the necessary browsing tools, including a data exporting function. PlantPIs contains information extracted principally from MEROPS database, filtered, annotated and compared with data stored in other protein and gene public databases, using both automated techniques and domain expert evaluations. The data are organized to allow a flexible and easy way to access stored information. The database is accessible at http://www.plantpis.ba.itb.cnr.it/.     

JenPep: a novel computational information resource for immunobiology and vaccinology

JenPep is a relational database containing a compendium of thermodynamic binding data for the interaction of peptides with a range of important immunological molecules: the major histocompatibility complex, TAP transporter, and T cell receptor. The database also includes annotated lists of B cell and T cell epitopes. Version 2.0 of the database is implemented in a bespoke postgreSQL database system and is fully searchable online via a perl/HTML interface (URL: http://www.jenner.ac.uk/JenPep).     

Computer Handling of Chemical and Biological Data of Traditional Chinese Medicines

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StructSorter: a method for continuously updating a comprehensive protein structure alignment database

Advances in protein crystallography and homology modeling techniques are producing vast amounts of high resolution protein structure data at ever increasing rates. As such, the ability to quickly and easily extract structural similarities is a key tool in discovering important functional relationships. We report on an approach for creating and maintaining a database of pairwise structure alignments for a comprehensive database comprising the PDB and homology models for the human and select pathogen genomes. Our approach consists of a novel, multistage method for determining pairwise structural similarity coupled with an efficient clustering protocol that approximates a full NxN assessment in a fraction of the time. Since biologists are commonly interested in recently released structures, and the homology models built from them, an automatically updating database of structural alignments has great value. Our approach yields a querying system that allows scientists to retrieve databank-wide protein structure similarities as easily as retrieving protein sequence similarities via BLAST or PSI-BLAST. Basic, noncommercial access to the database can be requested at https://tip.eidogen-sertanty.com/.     

IR SPECTRA RETRIEVAL FOR INORGANIC COMPOUNDS AND MINERALS——FEATURE SELECTION AND DATA COMPRESSION

Spectral feature channels are selected based on the optimization theory and by makinguse of Shannon's formula with main effective wavenumber regions ranging from 1600 cm~(-1)to 400 cm~(-1). Ten characteristic codes are sufficient for retrieving a spectrum using the spec-tral data re-compressed in the selected channels. Results of retrieving 50 substances includ-ed in the databank show that the accuracy and the precision of the system are 1.00 and 0.85respectively. Results of retrieving substances not included in the databank show a credibleinterpretative capacity of the system. The average time for retrieving a spectrum is ca.0. 98s.     

CheD: chemical database compilation tool, Internet server, and client for SQL servers

An efficient program, which runs on a personal computer, for the storage, retrieval, and processing of chemical information, is presented, The program can work both as a stand-alone application or in conjunction with a specifically written Web server application or with some standard SQL servers, e.g., Oracle, Interbase, and MS SQL. New types of data fields are introduced, e.g., arrays for spectral information storage, HTML and database links, and user-defined functions. CheD has an open architecture; thus, custom data types, controls, and services may be added. A WWW server application for chemical data retrieval features an easy and user-friendly installation on Windows NT or 95 platforms.     

Implementation of a two-dimensional electrophoresis-related laboratory information processing system: database aspects.

A laboratory information processing system (LIPS) has been developed to provide support for various laboratory activities related to two-dimensional electrophoresis. In this paper we present the relational schema for each level of activity and the application development of LIPS, in terms of the relational database management system being used. We also discuss our experience with the current system.     

A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships

The rapid expansion of structural information for protein-ligand binding sites is potentially an important source of information in structure-based drug design and in understanding ligand cross reactivity and toxicity. We have developed a large database of ligand binding sites extracted automatically from the Protein Data Bank. This has been combined with a method for calculating binding site similarity based on geometric hashing to create a relational database for the retrieval of site similarity and binding site superposition. It contains an all-against-all comparison of binding sites and holds known protein-ligand binding sites, which are made accessible to data mining. Here we demonstrate its utility in two structure-based applications: in determining site similarity and in aiding the derivation of a receptor-based pharmacophore model. The database is available from http://www.bioinformatics.leeds.ac.uk/sb/.     

中草药微量元素数据的数据库管理

中草药微量元素数据库收集有四百多种常用中草药六十多种元素的测定数据，具有检索、打印、统计等多种功能，对逐步建立中草药微量元素背景值，促进中草药微量元素的研究具有重要的作用。     

Automation of analysis of airborne radionuclides observed in Canadian CTBT radiological monitoring networks using LINSSI

Linux System for Spectral Information (LINSSI¹) is a SQL database and established under Linux. Currently it is compatible with HPGe gammaspectra analysis software UniSampo, Shaman and Aatami. Based on this database and software, an automated analysis pipeline has been setup for Canadian CTBT radiological monitoring networks. This paper has investigated the performance of this pipeline in its capabilities and reliabilities of rapid small peak search, nuclide identification, and radionuclide activity concentration evaluation. Up to now, more than 80 thousand daily monitoring gamma-spectra have been automatically received and processed, the results have been stored in database. The pipeline nuclide detection limits is satisfied for environmental radiation monitoring and nuclear emergency preparedness.     

Web-based spectrum analysis software for photon activation analysis

Photon activation analysis (PAA) includes extensive data evaluation that is sensitive to error. In order to save time and minimize human error, a new computer program—photon activation analysis system (PAAS)—was designed, built and implemented using the SQL language and Asp.net technology to analyze PAA data. Given peak information from PAA spectra and aided by a photonuclear data library, the program identifies the product isotopes, recognizes the possible nuclear reactions, and evaluates the concentration of target elements. Uncertainties of concentrations are estimated using standard error propagation techniques. The program can be accessed conveniently anywhere the internet is available and gives a fast and reliable determination of the trace elemental content of samples. Furthermore, this program also allow one to search its database for the information of general photonuclear reactions (e.g. energy lines, line intensities, target and product nuclides, photonuclear reactions, cross sections, natural abundance, etc.) and estimating the activity even before the activation begins. By switching the nuclide libraries, the program could also be expanded to neutron activation analysis and charged particle activation analysis (CPAA) without any difficulty. This program can be a versatile tool for the daily use of the nuclear and radiochemistry laboratories that conduct activation analysis.     

MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications

As the speed with which proteomic labs generate data increases along with the scale of projects they are undertaking, the resulting data storage and data processing problems will continue to challenge computational resources. This is especially true for shotgun proteomic techniques that can generate tens of thousands of spectra per instrument each day. One design factor leading to many of these problems is caused by storing spectra and the database identifications for a given spectrum as individual files. While these problems can be addressed by storing all of the spectra and search results in large relational databases, the infrastructure to implement such a strategy can be beyond the means of academic labs. We report here a series of unified text file formats for storing spectral data (MS1 and MS2) and search results (SQT) that are compact, easily parsed by both machine and humans, and yet flexible enough to be coupled with new algorithms and data-mining strategies.     

Workshop on two-dimensional gel protein databases.

A workshop on two-dimensional gel electrophoresis (2-DE) protein database, organized by the Committee on Data for Science and Technology (CODATA) of the International Council of Scientific Unions Task Group on Biological Macromolecules, was held at the CODATA Secretariat in Paris on March 9, 1992. Eleven scientists from eight different countries represented various aspects of 2-DE analysis--namely, cellular protein database development and protein microsequencing methodologies. The purpose of the workshop was to explore means of integrating the rapidly expanding body of information on 2-DE resolved proteins from different laboratories. A major proposal emanating from the workshop was the establishment of an intermediary or "relational" 2-DE gel protein database. This intermediary database, which would catalogue pertinent information on 2-DE resolved proteins (experimental source, 2-DE loci, biological information, etc.) could be an adjunct to, and accessed through, the existing international protein sequence databanks. It would function as a pointer for researchers to the individual 2-DE protein databases where primary and more specialized 2-DE data would be housed.     

A database-centric virtual chemistry system

We describe an Oracle database application for general use within virtual chemistry. The application functions as a central hub and repository for chemical data with interfaces to external calculators. It deals with the general problems of merging data from disparate sources and with scheduling of computational tasks for parallel or sequential execution in a mixed environment. The central database is used for the storage of input, intermediary, and final data as well as for job control. A calculation job is split into distinct tasks, or units of work, which are put in a queue. Tasks are dequeued and handled by specialized calculators. These calculators are in-house or commercial programs for which adaptor modules for connection to the database must be written. Tasks are handled in a transactional fashion, so that uncompleted or failed tasks are left in the queue. This makes the system stable to many types of disturbances. Sorting, filtering, and merging operations are handled by the database itself. Usage is very general, but some specific examples are (1) as a back end for a chemical property calculator Web page, (2) in an automated quantitative structure-activity relationship system, and (3) in virtual screens.     

A problem-oriented analysis of database models.

Which is the most convenient database model considering specific applications? The goal of this paper is to try to answer this question by the use of a chemical example. Examples of requests describe the problems of insertion, deletion, and updating; these requests are analyzed for the hierarchical model and are expressed in a relational language defined by the authors and in Socrate for the network model.     

Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation

We have developed a method that uses energetic analysis of structure-based fragment docking to elucidate key features for molecular recognition. This hybrid ligand- and structure-based methodology uses an atomic breakdown of the energy terms from the Glide XP scoring function to locate key pharmacophoric features from the docked fragments. First, we show that Glide accurately docks fragments, producing a root mean squared deviation (RMSD) of <1.0 Å for the top scoring pose to the native crystal structure. We then describe fragment-specific docking settings developed to generate poses that explore every pocket of a binding site while maintaining the docking accuracy of the top scoring pose. Next, we describe how the energy terms from the Glide XP scoring function are mapped onto pharmacophore sites from the docked fragments in order to rank their importance for binding. Using this energetic analysis we show that the most energetically favorable pharmacophore sites are consistent with features from known tight binding compounds. Finally, we describe a method to use the energetically selected sites from fragment docking to develop a pharmacophore hypothesis that can be used in virtual database screening to retrieve diverse compounds. We find that this method produces viable hypotheses that are consistent with known active compounds. In addition to retrieving diverse compounds that are not biased by the co-crystallized ligand, the method is able to recover known active compounds from a database screen, with an average enrichment of 8.1 in the top 1% of the database.