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PubMedDate not supplied

The publication speed of information in bibliographic chemical databases.

The quality of bibliographic databases depends very much on the reliably fast follow-up of the pertinent literature. We have studied this quality feature of two important chemical bibliographic databases: Chemical Abstracts (CA) and Analytical Abstracts (AA). The follow-up rate (speed of information) of these databases has been determined with respect to 10 core journals in analytical chemistry. On the average the performance of Chemical Abstracts has been good over the past decade, while the formerly poor performance of Analytical Abstracts has improved considerably. Some quite unexpected nonuniformities can, however, still be detected in the publication time distributions of both databases.

Journal Article↗
PubMedDate not supplied

Chemical descriptors with distinct levels of information content and varying sensitivity to differences between selected compound databases identified by SE-DSE analysis.

Analysis of the variability of molecular descriptors in large compound databases has recently been carried out using both the Shannon entropy (SE) and differential Shannon entropy (DSE) concepts that reduce descriptor distributions to their information content (SE analysis) and detect intrinsic differences between descriptor settings in compound databases (DSE analysis). Here it is shown that a combination of SE and DSE calculations, termed SE-DSE analysis, makes it possible to identify molecular descriptors most sensitive to systematic differences in databases consisting of synthetic, drug-like, and natural molecules. Descriptors with consistently high information content are detected, and database-specific differences are quantified. Different sets of only very few descriptors were found to be most responsive to principal differences between synthetic, natural, and drug-like molecules. Descriptors with DSE values furthest away from zero are likely to best distinguish between compounds with different characteristics. SE-DSE analysis also reveals that a number of descriptors are not sensitive to compound class-specific features, despite their complexity and consistently high information content.

Journal Article↗
PubMedDate not supplied

Representation of the molecular topology of cyclical structures by means of cycle graphs. 2. Application to clustering of chemical databases.

The great size of chemical databases and the high computational cost required in the atom-atom comparison of molecular structures for the calculation of the similarity between two chemical compounds necessitate the proposal of new clustering models with the aim of reducing the time of recovery of a set of molecules from a database that satisfies a range of similarities with regard to a given molecule pattern. In this paper we make use of the information corresponding to the cycles existing in the structure of molecules as an approach for the classification of chemical databases. The clustering method here proposed is based on the representation of the topological structure of molecules stored in chemical databases through its corresponding cycle graph. This method presents a more appropriate behavior for others described in the bibliography in which the information corresponding to the cyclicity of the molecules is also used.

Journal Article↗
PubMedDate not supplied

Comparing the information content of two large olfactory databases.

The expert's subjectivity in establishing an olfactory description can produce wide discrepancies in different databases listing the odor profile of identical compounds. A representative example is obtained by comparing the odorous compounds included in the "Perfumery Materials and Performance 2001" (PMP2001) database and in Arctander's books (1960 and 1969). To better assess this problem, classification models obtained by using the adaptive fuzzy partition method were established on subsets of these databases distributed into the same olfactory classes. The robustness and the prediction power of these models give a powerful criterion for evaluating the "quality" of their information content and for deciding which is the most trustable database.

Journal Article↗
PubMedDate not supplied

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.

Journal Article↗
PubMed2000

New approach to molecular docking and its application to virtual screening of chemical databases

This paper describes the validation of a molecular docking method and its application to virtual database screening. The code flexibly docks ligand molecules into rigid receptor structures using a tabu search methodology driven by an empirically derived function for estimating the binding affinity of a protein-ligand complex. The docking method has been tested on 70 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. The lowest energy geometry produced by the docking protocol is within 2.0 A root mean square of the experimental binding mode for 79% of the complexes. The method has been applied to the problem of virtual database screening to identify known ligands for thrombin, factor Xa, and the estrogen receptor. A database of 10,000 randomly chosen "druglike" molecules has been docked into the three receptor structures. In each case known receptor ligands were included in the study. The results showed good separation between the predicted binding affinities of the known ligand set and the database subset.

Journal Article↗
PubMed1999

Lead generation using pharmacophore mapping and three-dimensional database searching: application to muscarinic M(3) receptor antagonists.

By using a pharmacophore model, a geometrical representation of the features necessary for molecules to show a particular biological activity, it is possible to search databases containing the 3D structures of molecules and identify novel compounds which may possess this activity. We describe our experiences of establishing a working 3D database system and its use in rational drug design. By using muscarinic M(3) receptor antagonists as an example, we show that it is possible to identify potent novel lead compounds using this approach. Pharmacophore generation based on the structures of known M(3) receptor antagonists, 3D database searching, and medium-throughput screening were used to identify candidate compounds. Three compounds were chosen to define the pharmacophore: a lung-selective M(3) antagonist patented by Pfizer and two Astra compounds which show affinity at the M(3) receptor. From these, a pharmacophore model was generated, using the program DISCO, and this was used subsequently to search a UNITY 3D database of proprietary compounds; 172 compounds were found to fit the pharmacophore. These compounds were then screened, and 1-[2-(2-(diethylamino)ethoxy)phenyl]-2-phenylethanone (pA(2) 6.67) was identified as the best hit, with N-[2-(piperidin-1-ylmethyl)cycohexyl]-2-propoxybenz amide (pA(2) 4. 83) and phenylcarbamic acid 2-(morpholin-4-ylmethyl)cyclohexyl ester (pA(2) 5.54) demonstrating lower activity. As well as its potency, 1-[2-(2-(diethylamino)ethoxy)phenyl]-2-phenylethanone is a simple structure with limited similarity to existing M(3) receptor antagonists.

Animals↗
PubMed2002

Does size really matter--using a decision tree approach for comparison of three different databases from the medical field of acute appendicitis.

Decision trees have been successfully used for years in many medical decision making applications. Transparent representation of acquired knowledge and fast algorithms made decision trees one of the most often used symbolic machine learning approaches. This paper concentrates on the problem of separating acute appendicitis, which is a special problem of acute abdominal pain, from other diseases that cause acute abdominal pain by use of an decision tree approach. Early and accurate diagnosing of acute appendicitis is still a difficult and challenging problem in everyday clinical routine. An important factor in the error rate is poor discrimination between acute appendicitis and other diseases that cause acute abdominal pain. This error rate is still high, despite considerable improvements in history-taking and clinical examination, computer-aided decision-support, and special investigation such as ultrasound. We investigated three databases of different size with cases of acute abdominal pain to complete this task as successful as possible. The results show that the size of the database does not necessary directly influence the success of the decision tree built on it. Surprisingly we got the best results from the decision trees built on the smallest and the biggest database, where the database with medium size (relative to the other two) was not so successful. Despite this we were able to produce decision tree classifiers that were capable of producing correct decisions on test data sets with accuracy up to 84%, sensitivity to acute appendicitis up to 90%, and specificity up to 80% on the same test set.

Acute Disease↗
PubMed1997

Development of computerized storage facilities for twin data: a relational database system for a twin register.

Many twin registers hold information on flat file systems such as those provided by statistical packages or spreadsheets. Demographic details may be maintained separately from data collected in multiple different studies, leading to considerable problems with data consistency, redundancy, and integration. Ad hoc requests may be difficult. Implementation of a relational database system permits storage and maintenance of all records, simple data entry and validation procedures, linking of information from different projects with security of access, and the flexibility to provide rapid answers to ad hoc enquiries using standard Structured Query Language (SQL). Twin data provide a challenge for relational database design which rests on the technique of normalization and the use of unique identifiers to access associated groups of variables; for twins, "uniqueness" must preserve identification of both the pair and the individual twin subjects in the data structure to enable flexible access to and analysis of the data. An application on the Institute of Psychiatry Volunteer Twin Register (IOPVTR) database is described, through reference to one study of a sample of the twins, with simulated data. We show how a balance of adherence to database design principles and attention to ongoing clerical and research procedures has been used to produce an integrated, flexible, and open-ended system.

Data Collection↗
PubMed2000

Outcomes of coronary artery bypass grafting: a 3 year analysis using the Society of Thoracic Surgeons Database.

BACKGROUND: Accurate risk factor analysis is a critical element in contemporary cardiac surgical practice. In the USA, the Society of Thoracic Surgeons Database allows institutions and individual surgeons to carry out detailed patient risk assessment and to review their cardiac surgical outcomes in a comparative fashion. METHODS: To evaluate outcomes of isolated coronary artery bypass grafting, data from all patients operated upon at the Alfred Hospital, Melbourne, Australia, over a 3 year period were entered into the Society of Thoracic Surgeons Database. RESULTS: Our results (mortality and morbidity) compared favourably with those contained within this large international database. CONCLUSION: It is hoped that a similar Australasian database can be established to facilitate a meaningful local risk assessment and a comparative analysis of outcomes of cardiac surgical procedures.

Journal Article↗
PubMed2001

Why Australia needs a Cardiac Procedures Database.

The development of a national cardiac procedures database is in the interest of many groups: cardiac surgeons and interventional cardiologists, participating hospital units, patients, governments, health insurance funds and industry. To date, information about short-term outcomes of coronary interventions has been fragmented and uncoordinated at state and national levels. Long-term outcomes have not yet been systematically addressed in Australia. A highly desirable objective is the development of a dataset of information that is pertinent to the Australian context, with common minimum datasets for surgery and percutaneous intervention. Information will gain added value if it is linked to other national databases such as the National Death Index. Also, risk adjustment should be used to improve the value of outcome data. Development of a 'common' Cardiac Procedures Database, in turn, should lead to improved health policy and better health management in an area that currently runs at significant cost. Thus, provided due care is taken to protect the privacy of stakeholders, maintain quality control and entry of only valid information into the database, the resulting outcome will benefit all interested parties; clinicians, hospitals, patients and the wider Australian community.

Journal Article↗
PubMed1987

The use of a computerised database for the diagnosis of a rare neurological syndrome.

A database which runs on an office microcomputer is being developed for the diagnosis of genetically determined neurological disorders. At present about 1100 conditions with their clinical features and 3000 references are stored in the database. We discuss a family with 3 sibs affected by a unique neurological disorder and show how the database is used. The 3 sibs, 4, 5 and 10 years old, show the same clinical course characterized by congenital cataracts, microcephaly, hypotonia, mental retardation, pyramidal signs and choreoathetoid movements starting in early childhood. The parents are first cousins of Bangladeshi origin. This condition does not appear in published report and is not listed in the database. It can therefore be concluded that the sibs have a unique autosomal recessive disorder.

Athetosis↗
PubMed2003

Metric-space indexes as a basis for scalable biological databases.

Biochemical databases will be best served by the development of new specialized database management systems whose storage managers are based on metric-space indexing techniques and the development a database query languages that embody semantics derived from biochemical models of similarity and evolution. Important biochemical data types cannot be effectively mapped to low dimensional coordinate systems on which O(log n) indexing methods rely. It is clear from an abundance of bioinformatic discoveries that biochemical data is not random and exhibits interesting structure with respect to clustering. Metric-space indexing exploits a data set's intrinsic clustering to speed the execution of similarity queries, even when the data cannot be mapped to a coordinate system. Database management systems that seamlessly integrate semantically rich query languages with a metric-storage and retrieval mechanism will allow biologists to simply and concisely develop informatic studies that have traditionally been large and labor intensive.

Computational Biology↗
PubMed1993

SIGNAL SCAN 3.0: new database and program features.

SIGNAL SCAN is a program that utilizes a transcription factor database to find potential transcription factor binding sites in DNA sequences. The program is now in its third version. The SIGNAL SCAN transcription factor database format has changed and the program output format has been improved. New features allow the user to update the SIGNAL SCAN database automatically, to retrieve original journal citations and to develop user signal databases. The program now uses an indexing algorithm, improving scanning speed by a factor of 3. SIGNAL SCAN is now network compatible and is available for IBM-compatible PC, Unix and VMS platforms.

Algorithms↗
PubMed1983

A DNA recombinant database management system.

A set of computer programs is described which constitutes a clone database management system. Maintenance of the database and the stocks of material is designed to be under the control of one person or group of people, who may insert, delete or modify data entries, and who may interrogate the database as to which stocks are in need of checking. The system is organised in such a way that information is freely and speedily available to all users. Database entries may be accessed by name or key word.

Animals↗
PubMedDate not supplied

Clarification of the database concept.

Our concern is that nursing databases be structured to improve the efficiency of decision-making in nursing. The selection of database management systems that are compatible with the computer resources in a majority of settings is important to methodology. To facilitate methodological development, we encourage the inclusion of information in the nursing literature that details the investments in personnel, equipment, and facilities required to develop computerized databases. In the current state of affairs, determining the personnel and budgets for the development, update, and maintenance of computerized databases and related data management systems is somewhat like trying to pin the tail on the donkey while blindfolded. However some of the frustrations encountered at the start of new endeavors can be lessened if we share our experiences in project management as we report findings from our work.

Computers↗

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