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PubMed1998

Advanced query mechanisms for biological databases.

Existing query interfaces for biological databases are either based on fixed forms or textual query languages. Users of a fixed form-based query interface are limited to performing some pre-defined queries providing a fixed view of the underlying database, while users of a free text query language-based interface have to understand the underlying data models, specific query languages and application schemas in order to formulate queries. Further, operations on application-specific complex data (e.g., DNA sequences, proteins), which are usually provided by a variety of software packages with their own format requirements and peculiarities, are not available as part of, nor integrated with biological query interfaces. In this paper, we describe generic tools that provide powerful and flexible support for interactively exploring biological databases in a uniform and consistent way, that is via common data models, formats, and notations, in the framework of the Object-Protocol Model (OPM). These tools include (i) a Java graphical query construction tool with support for automatic generation of Web query forms that can be either used for further specifying conditions, or can be saved and customized; (ii) query processors for interpreting and executing queries that may involve complex application-specific objects, and that could span multiple heterogeneous databases and file systems; and (iii) utilities for automatic generation of HTML pages containing query results, that can be browsed using a Web browser. These tools avoid the restrictions imposed by traditional fixed-form query interfaces, while providing users with simple and intuitive facilities for formulating ad-hoc queries across heterogeneous databases, without the need to understand the underlying data models and query languages.

Animals↗
PubMed1992

A BASIC algorithm for calculating the postmortem interval from arthropod successional data.

A computer algorithm, implemented in the BASIC language, is presented for calculating the postmortem interval (PMI) from arthropod successional data. Entomology-assisted determination of the PMI promises to be a reliable technique in cases of homicide, suicide, accidental death, and unattended death due to natural causes. The program requires, as input, the identity of arthropod taxa recovered from human remains in a death scene investigation and machine-readable data on carrion-associated arthropod taxa and their known successional patterns of activity for the same geographical area. The program performs rapid comparisons of these lists and, on output, calculates an upper and lower estimate of the PMI, identifies the definitive taxa for these limits, and determines if the remaining corpse taxa have known successional patterns that are consistent for this estimate. An alternate output is provided if one or more corpse taxa do not overlap all the others at any single time in the succession. In that event, the user is prompted to recheck the identity of the non-overlapping taxon or taxa or reevaluate the environmental circumstances surrounding the case in question. Results of the analysis are saved to an ASCII file for output to a printer for making paper copies useful for the entomologist's Case Study Final Report. This program may make possible wider use of this technique in law enforcement and medical investigator offices that utilize both forensic entomologist expertise and IBM PCs (or compatible computers).

Accidents↗
PubMed1996

An object-oriented class library for medical software development.

The objective of this research is the development of a Medical Object Library (MOL) consisting of reusable, inheritable, portable, extendable C++ classes that facilitate rapid development of medical software at reduced cost and increased functionality. The result of this research is a library of class objects that range in function from string and hierarchical file handling entities to high level, procedural agents that perform increasingly complex, integrated tasks. A system built upon these classes is compatible with any other system similarly constructed with respect to data definitions, semantics, data organization and storage. As new objects are built, they can be added to the class library for subsequent use. The MOL is a toolkit of software objects intended to support a common file access methodology, a unified medical record structure, consistent message processing, standard graphical display facilities and uniform data collection procedures. This work emphasizes the relationship that potentially exists between the structure of a hierarchical medical record and procedural language components by means of a hierarchical class library and tree structured file access facility. In doing so, it attempts to establish interest in and demonstrate the practicality of the hierarchical medical record model in the modern context of object oriented programming.

Humans↗
PubMed1999

The Biopolymer Markup Language.

SUMMARY: An XML derived from a data model designed to be a hierarchical representation of an organism has been specified and a browser to use this language has been developed. AVAILABILITY: The language definition is available in HTML form at http://www.proteometrics.com/BIOML/. The BioML browser is available on request from the author.

Biopolymers↗
PubMedDate not supplied

[CISMeF: catalog and index of French-speaking medical sites].

The Internet has now become a major source of health information. The aim of CISMeF is to catalogue and index the main French-speaking sites and documents concerning health. This project was initiated by Rouen University Hospital. Its URL is http://www.chu-rouen.fr/cismef. CISMeF covers all areas of health care and medical sciences, and is indexed both alphabetically and according to subject. It was set up on a Sun workstation under the Sun UNIX operating system and is entirely based on static HTML. By May 1999, the number of sites and documents indexed was already over 6,500, with a mean of 75 new sites added each week. CISMeF is updated via a five-step process: resource collection, filtering, description, classification, and indexing. The Net Scoring criteria are used to assess the quality of health information on the Internet. These criteria concern eight categories: credibility, content, links, design, interactivity, quantitative aspects, ethics and accessibility. CISMeF uses two standard tools to organize information: the MeSH (medical subject heading) thesaurus from the Medline reference database (National Library of Medicine, USA) and the Dublin core metadata format. The sites and documents included in CISMeF are described using the following elements from the Dublin core project: title, author or creator, subject and keywords, description, publisher, date, resource type, format, identifier, and language.

Abstracting and Indexing↗
PubMed1993

Grammatical formalization of metabolic processes.

In the field of biotechnology and medicine it is of interest to model and simulate metabolic processes. The usual methods to model metabolic pathways are chemical descriptions and differential equations. Moreover, the graph theoretical aspect is discussed and the development of expert systems is in process. In this paper we present the formalization of metabolic processes. Our formalization is based on the theory of formal languages. This formalization is called genetic grammar and represents an expansion of the Semi-Thue-System.

Computer Simulation↗
PubMed1996

Implications of the Java language on computer-based patient records.

The growth of the utilization of the World Wide Web (WWW) as a medium for the delivery of computer-based patient records (CBPR) has created a new paradigm in which clinical information may be delivered. Until recently the authoring tools and environment for application development on the WWW have been limited to Hyper Text Markup Language (HTML) utilizing common gateway interface scripts. While, at times, this provides an effective medium for the delivery of CBPR, it is a less than optimal solution. The server-centric dynamics and low levels of interactivity do not provide for a robust application which is required in a clinical environment. The emergence of Sun Microsystems' Java language is a solution to the problem. In this paper we examine the Java language and its implications to the CBPR. A quantitative and qualitative assessment was performed. The Java environment is compared to HTML and Telnet CBPR environments. Qualitative comparisons include level of interactivity, server load, client load, ease of use, and application capabilities. Quantitative comparisons include data transfer time delays. The Java language has demonstrated promise for delivering CBPRs.

Computer Communication Networks↗
PubMed1978

Computer-assisted analysis of written language: assessing the written language of deaf children.

Methods for assessing the written language of deaf students are reviewed. The merits and shortcomings of various objective indicators that have traditionally been used are discussed. These include various measures of total output, such as total number of words or sentences, and simple measures of diversity of usage such as the type-token ratio. There have been several attempts in recent years to include objective measures of syntactic complexity as part of an overall language assessment program. The use of a computer to assist teachers in the derivation of such syntactic measures is described. Two illustrative examples are provided. The first shows how the computer system performs a detailed syntactic analysis on a typical sentence taken from the written language of a deaf child. The second example shows how the system provides a summary analysis of several sentences in a theme. A statistical count of the syntactic forms used in the written language sample is provided at the end of the analysis.

Adolescent↗
PubMed1998

The globalization of crystallographic knowledge.

The rapid growth of the World Wide Web provides major new opportunities for distributed databases, especially in macromolecular science. A new generation of technology, based on structured documents (SD), is being developed which will integrate documents and data in a seamless manner. This offers experimentalists the chance to publish and archive high-quality data from any discipline. Data and documents from different disciplines can be combined and searched using technology such as eXtensible Markup Language (XML) and its associated support for hypermedia (XLL), metadata (RDF) and stylesheets (XSL). Opportunities in crystallography and related disciplines are described.

Crystallography↗
PubMed1996

The "SentiWeb" method for exploring a database on the Net.

Return of information is one of the main goals of any public health information system. About 25,000 maps and 10,000 graphs may be obtained from the time-series collected in the database of the French Communicable Diseases Network (FCDN). Furthermore, this huge epidemiological atlas is updated each week. What is the optimal way of returning such information? This report discloses the strategies used for enhancing the access facilities to the FCDN database for any users, particularly those without specific training in epidemiology or database query language. The technical options implemented in the SentiWeb server (http:/(/)www.b3e.jussieu.fr) are discussed.

Communicable Diseases↗
PubMedDate not supplied

Computer languages and operating systems. What they are and how they work.

Programs (software) make a computer's circuits (hardware) perform useful work. This article reviews briefly how computers are programmed, beginning with the storage of data and program instructions. A simple description of how a computer executes a sequence of instructions (program) is followed by the basic concepts of machine-language and assembly-language programming. An overview of higher-level computer languages and a description of the distinction between systems and applications programs are also included.

Computers↗
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↗
PubMed2002

The Bio* toolkits--a brief overview.

Bioinformatics research is often difficult to do with commercial software. The Open Source BioPerl, BioPython and Biojava projects provide toolkits with multiple functionality that make it easier to create customised pipelines or analysis. This review briefly compares the quirks of the underlying languages and the functionality, documentation, utility and relative advantages of the Bio counterparts, particularly from the point of view of the beginning biologist programmer.

Computational Biology↗
PubMed2004

MuSiC: a tool for multiple sequence alignment with constraints.

SUMMARY: MuSiC is a web server to perform the constrained alignment of a set of sequences, such that the user-specified residues/nucleotides are aligned with each other. The input of the MuSiC system consists of a set of protein/DNA/RNA sequences and a set of user-specified constraints, each with a fragment of residue/nucleotide that (approximately) appears in all input sequences. The output of MuSiC is a constrained multiple sequence alignment in which the fragments of the input sequences whose residues/nucleotides exhibit a given degree of similarity to a constraint are aligned together. The current MuSiC system is implemented in Java language and can be accessed via a simple web interface. AVAILABILITY: http://genome.life.nctu.edu.tw/MUSIC

Algorithms↗
PubMed1997

The GRAIL concept modelling language for medical terminology.

The GALEN representation and integration language (GRAIL) has been developed to support effective clinical user interfaces and extensible re-usable models of medical terminology. It has been used successfully to develop the prototype GALEN common reference (CORE) model for medical terminology and for a series of projects in clinical user interfaces within the GALEN and PEN&PAD projects. GRAIL is a description logic or frame language with novel features to support part-whole and other transitive relations and to support the GALEN modelling style aimed at re-use and application independence. GRAIL began as an experimental language. However, it has clarified many requirements for an effective knowledge representation language for clinical concepts. It still has numerous limitations despite its practical successes. The GRAIL experience is expected to form the basis for future languages which meet the same requirements but have greater expressiveness and more soundly based semantics. This paper provides a description and motivation for the GRAIL language and gives examples of the modelling paradigm which it supports.

Artificial Intelligence↗