Interactive computer supported tumor registry in the state of Rhode Island.

A new interactive computerized tumor registry has been established for the state of Rhode Island. The registry is implemented with new data base software which features a pagination scheme with rapid retrieval of non-coded variable data. The types of data stored are discussed as well as the computer system and methods of data entry storage and retrieval.     

GeVaDSs - decision support system for novel Genetic Vaccine development process

ABSTRACT: BACKGROUND: The lack of a uniform way for qualitative and quantitative evaluation of vaccine candidates under development led us to set up a standardized scheme for vaccine efficacy and safety evaluation. We developed and implemented molecular and immunology methods, and designed support tools for immunization data storage and analyses. Such collection can create a unique opportunity for immunologists to analyse data delivered from their laboratories. RESULTS: We designed and implemented GeVaDSs (Genetic Vaccine Decision Support system)- an interactive system for efficient storage, integration, retrieval and representation of data. Moreover, GeVaDSs allows for relevant association and interpretation of data, and thus for knowledge-based generation of testable hypotheses of vaccine responses. CONCLUSIONS: GeVaDSs has been tested by several laboratories in Europe, and proved its usefulness in vaccine analysis. Case study of its application is presented in the additional files. The system is available at: http://gevads.cs.put.poznan.pl/preview/ (login: viewer, password: password).     

IRAP — A system for the retrieval and analysis of orthopaedic implant data

An interactive computer system for the storage, retrieval and analysis of standardized clinical and material characterization data associated with orthopaedic implants is described. The system consists basically of four independent modules. The essence of the system centers on the cross-referencing capabilities which are virtually unlimited. The system has been designed for use by non-computer trained personnel.     

Computerization of data capture for mouse skin painting studies

An interactive data input, storage, retrieval and treatment system for mouse skin painting studies is described. The system was implemented on a Hewlett-Packard (HP)1000-F computer under RTE IVB operating system using FORTRAN IV. The program's simple design means that it can be run easily by unskilled personnel.     

新版DELTA系统在植物分类学中的应用——以羊茅属研究为例

DELTA系统是针对分类学研究开发的综合性多功能软件包。新版DELTA系统在运行环境、程序、指令、界面、操作方式及中文字符处理等重要功能上比旧版本均有较大改进。作为国际分类学数据库数据交换标准,应用该系统可以规范分类学描述,对研究中所有常用性状进行识别和处理,自动生成各个研究对象分类学特征描述并对其进行详尽的相似性和差异性比较,对性状特征和分类单元进行注释和图像示例,将数据转换为数量分类学或分支分类学所需格式以生成树状图,自动生成检索表,建成基于本地和网络的交互式专家辅助鉴定系统等。DELTA系统作为植物分类学研究的常用手段和工具是非常适合及大有帮助的。     

处理植物分类学描述语言的国际标准——DELTA系统

DELTA系统是澳大利亚Dallwitz等人经过多年研究发出的一套用于分类学描述语言编码的国际标准。本文对该系统的主要功能,即自然语言描述、检索表、数据矩阵的自动生成、标本鉴定和信息检索以及分支分类运算和表征分类运算所需数据格式的转换等做了综述性介绍,以期促进该软件在我国广大植物分类学工作者中的推广与使用。     

A program for handling data obtained by ‘blind’ histopathological evaluations

An interactive data input, storage, retrieval and treatment system (LAMES) is described for use in histophatological studies where pathologists evaluate tissues without any identification (termed evaluations which are ‘blind’). The system produces the mean values of individual groups within an experiment, and results of statistical comparisons between the groups. The system was implemented on a Hewlett-Packard (HP) 1000-F minicomputer operating under RTE-6/VM, and was written using FORTRAN IV.     

A microcomputer based program for the storage and retrieval of experimental animal information

A microcomputer based program for the storage and selective retrieval of experimental animal information has been developed for use on any system which runs under CP/M system software. The program has been designed to be completely conversational, to communicate with the user in French, English, or Spanish, and to allow the user to define the data format and the alphanumeric coding scheme.     

Towards organizing health knowledge on community-based health services

Online community-based health services accumulate a huge amount of unstructured health question answering (QA) records at a continuously increasing pace. The ability to organize these health QA records has been found to be effective for data access. The existing approaches for organizing information are often not applicable to health domain due to its domain nature as characterized by complex relation among entities, large vocabulary gap, and heterogeneity of users. To tackle these challenges, we propose a top-down organization scheme, which can automatically assign the unstructured health-related records into a hierarchy with prior domain knowledge. Besides automatic hierarchy prototype generation, it also enables each data instance to be associated with multiple leaf nodes and profiles each node with terminologies. Based on this scheme, we design a hierarchy-based health information retrieval system. Experiments on a real-world dataset demonstrate the effectiveness of our scheme in organizing health QA into a topic hierarchy and retrieving health QA records from the topic hierarchy.     

A rapid retrieval tool for operating on large, flat archive files

Computer-aided sequencing and analysis facilities need to efficientlysearch flat archive files. Retrieval by e-mail or network serverconnections can become impractical in cases where large numbersof selected entries need to be accessed. Public versions ofthese archives can be retrieved via ftp and installed on a localhard disk as an alternative to network-based retrieval. Afterinstallation, a scheme is required for rapid access of the archivethat is consistent with the other production needs of the sequencingfacility. We have developed a retrieval system for entries insidea flat-file database. The system works for any flat-file databasesystem such as those used in the public DNA and protein archives.     

Pharmacophoric pattern matching in files of 3D chemical structures: evaluation of search performance

A computerized retrieval system is described which allows the interactive identification of pharmacophoric patterns in 3D chemical structures. A query pharmacophore in the system is matched against a file of structures using a three-stage retrieval mechanism. The initial search involves a rapid bit-string matching operation using screens denoting the presence or absence of interatomic distances that lie within certain predefined ranges. These ranges are selected by an analysis of the frequencies of occurrence of interatomic distances in the data file that is being searched. The second stage involves the generation of all interatomic distances in potentially matching structures in the file to ascertain whether all of the query distances are present. If this is the case, a final search is carried out to determine whether these distances are in the correct geometric orientation to each other; this search involves a novel matching algorithm based upon the set reduction techniques used for substructure searching in files of 2D chemical structures. The evaluation of the system has involved the searching of several pharmacophoric patterns against a 12 728-compound subset of the Cambridge Crystallographic Data Bank. Measurements of the numbers of structures matching at each of the three levels of search show that the system provides a highly efficient means of identifying structures containing a query pharmacophore.     

A tabular learning structure with an adaptable k-d tree for relaxation of the curse of dimensionality

Memory-based learning schemes are characterized by their memorization of observed events. A memory-based learning scheme either memorizes the collected data directly or reorganizes such information and stores it distributively into a tabular memory. For the tabular type, the system requires a training process to determine the contents of the associative memory. This training process helps filter out zero-mean noise. Since the stored data are associated to pre-assigned input locations, memory management and data retrieval are easier and more efficient. Despite these merits, a drawback of tabular schemes is the difficulty in applying it to high-dimensional problems due to the curse of dimensionality. As the input dimensionality increases, the number of quantized elements in the input space increases at an exponential rate and that causes a huge demand of memory. In this paper, a dynamic tabular structure is proposed for possible relaxation of such a demand. The memorized data are organized as part of a k-d tree. Nodes in the tree, called vertices, correspond to some regularly assigned input points. Memory resource is allocated only at locations where it is needed. Being able to easily compute the vertex positions helps reduce the searching cost in data retrieval. In addition, the learning process is able to expand the tree structure into one covering the problem domain. With memory allocated based on demand, memory consumption becomes closely related to task complexity instead of input dimensionality, and is minimized. Algorithms for structure construction and training are presented in this paper. Simulation results demonstrate that the memory can be efficiently utilized. The developed scheme offers a solution for high-dimensional learning problems with a manageable size of effective input domain.     

The fitting of dynamic models to observed data

The question of how to fit a general cubic model of a multicomponent, interactive growth system to observed data is addressed. A multidimensional-polynomial type of regression analysis is used, with a least-squares criterion. By testing the scheme on a problem with known solution, the way in which the accuracy of the results varies with the number of datum points used is investigated in an heuristic manner.     

A knowledgebase system to enhance scientific discovery: Telemakus

BACKGROUND: With the rapid expansion of scientific research, the ability to effectively find or integrate new domain knowledge in the sciences is proving increasingly difficult. Efforts to improve and speed up scientific discovery are being explored on a number of fronts. However, much of this work is based on traditional search and retrieval approaches and the bibliographic citation presentation format remains unchanged. METHODS: Case study. RESULTS: The Telemakus KnowledgeBase System provides flexible new tools for creating knowledgebases to facilitate retrieval and review of scientific research reports. In formalizing the representation of the research methods and results of scientific reports, Telemakus offers a potential strategy to enhance the scientific discovery process. While other research has demonstrated that aggregating and analyzing research findings across domains augments knowledge discovery, the Telemakus system is unique in combining document surrogates with interactive concept maps of linked relationships across groups of research reports. CONCLUSION: Based on how scientists conduct research and read the literature, the Telemakus KnowledgeBase System brings together three innovations in analyzing, displaying and summarizing research reports across a domain: (1) research report schema, a document surrogate of extracted research methods and findings presented in a consistent and structured schema format which mimics the research process itself and provides a high-level surrogate to facilitate searching and rapid review of retrieved documents; (2) research findings, used to index the documents, allowing searchers to request, for example, research studies which have studied the relationship between neoplasms and vitamin E; and (3) visual exploration interface of linked relationships for interactive querying of research findings across the knowledgebase and graphical displays of what is known as well as, through gaps in the map, what is yet to be tested. The rationale and system architecture are described and plans for the future are discussed.     

3D HUMAN MOTION RETRIEVAL BASED ON HUMAN HIERARCHICAL INDEX STRUCTURE

With the development and wide application of motion capture technology, the captured motion data sets are becoming larger and larger. For this reason, an efficient retrieval method for the motion database is very important. The retrieval method needs an appropriate indexing scheme and an effective similarity measure that can organize the existing motion data well. In this paper, we represent a human motion hierarchical index structure and adopt a nonlinear method to segment motion sequences. Based on this, we extract motion patterns and then we employ a fast similarity measure algorithm for motion pattern similarity computation to efficiently retrieve motion sequences. The experiment results show that the approach proposed in our paper is effective and efficient.     

Visualizations for taxonomic and phylogenetic trees

MOTIVATION: Despite substantial efforts to develop and populate the back-ends of biological databases, front-ends to these systems often rely on taxonomic expertise. This research applies techniques from human-computer interaction research to the biodiversity domain. RESULTS: We developed an interactive node-link tool, TaxonTree, illustrating the value of a carefully designed interaction model, animation, and integrated searching and browsing towards retrieval of biological names and other information. Users tested the tool using a new, large integrated dataset of animal names with phylogenetic-based and classification-based tree structures. These techniques also translated well for a tool, DoubleTree, to allow comparison of trees using coupled interaction. Our approaches will be useful not only for biological data but as general portal interfaces.     

MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites

The three-dimensional environments of ligand binding sites have been derived from the parsing and loading of the PDB entries into a relational database. For each bound molecule the biological assembly of the quaternary structure has been used to determine all contact residues and a fast interactive search and retrieval system has been developed. Prosite pattern and short sequence search options are available together with a novel graphical query generator for inter-residue contacts. The database and its query interface are accessible from the Internet through a web server located at: http://www.ebi.ac.uk/msd-srv/msdsite.     

PGV - Prokaryotic Genome Viewer

Recent sequencing of genomes of several microorganisms provides an opportunity to have access to huge volumes of data stored in various databases. This has resulted in the development of various computational and visualization tools to aid in retrieval and analysis of data. Development of user friendly genome data mapping and visualization tools facilitates researchers to closely examine various features of genes and make inferences from the displayed data efficiently. PGV - Prokaryotic Genome Viewer is a Java based web application tool capable of generating high quality interactive circular chromosome maps. With simple mouse roll over tasks on the interested region on the displayed map, the user is provided with features such as feature labeling, multi-fold zooming, image rotation and hyperlinking to different information resources. The tool is capable of instantaneously generating maps using user-supplied sequence data.