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At least 541 records · Page 30Linked to original sources

PubMed2006

Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data.

Identification of transcriptional regulatory sites plays an important role in the investigation of gene regulation. For this propose, we designed and implemented a data warehouse to integrate multiple heterogeneous biological data sources with data types such as text-file, XML, image, MySQL database model, and Oracle database model. The utility of the biological data warehouse in predicting transcriptional regulatory sites of coregulated genes was explored using a synexpression group derived from a microarray study. Both of the binding sites of known transcription factors and predicted over-represented (OR) oligonucleotides were demonstrated for the gene group. The potential biological roles of both known nucleotides and one OR nucleotide were demonstrated using bioassays. Therefore, the results from the wet-lab experiments reinforce the power and utility of the data warehouse as an approach to the genome-wide search for important transcription regulatory elements that are the key to many complex biological systems.

Algorithms↗

PubMed2004

A multi-agent system architecture for geographic information gathering.

World Wide Web (WWW) is a vast repository of information, including a great deal of geographic information. But the location and retrieval of geographic information will require a significant amount of time and effort. In addition, different users usually have different views and interests in the same information. To resolve such problems, this paper first proposed a model of geographic information gathering based on multi-Agent (MA) architecture. Then based on this model, we construct a prototype system with GML (Geography Markup Language). This system consists of three tiers-Client, Web Server and Data Resource. Finally, we expatiate on the process of Web Server.

Algorithms↗

PubMed2002

New generation pharmacogenomic tools: a SNP linkage disequilibrium Map, validated SNP assay resource, and high-throughput instrumentation system for large-scale genetic studies.

Since public and private efforts announced the first draft of the human genome last year, researchers have reported great numbers of single nucleotide polymorphisms (SNPs). We believe that the availability of well-mapped, quality SNP markers constitutes the gateway to a revolution in genetics and personalized medicine that will lead to better diagnosis and treatment of common complex disorders. A new generation of tools and public SNP resources for pharmacogenomic and genetic studies--specifically for candidate-gene, candidate-region, and whole-genome association studies--will form part of the new scientific landscape. This will only be possible through the greater accessibility of SNP resources and superior high-throughput instrumentation-assay systems that enable affordable, highly productive large-scale genetic studies. We are contributing to this effort by developing a high-quality linkage disequilibrium SNP marker map and an accompanying set of ready-to-use, validated SNP assays across every gene in the human genome. This effort incorporates both the public sequence and SNP data sources, and Celera Genomics' human genome assembly and enormous resource ofphysically mapped SNPs (approximately 4,000,000 unique records). This article discusses our approach and methodology for designing the map, choosing quality SNPs, designing and validating these assays, and obtaining population frequency ofthe polymorphisms. We also discuss an advanced, high-performance SNP assay chemisty--a new generation of the TaqMan probe-based, 5' nuclease assay-and high-throughput instrumentation-software system for large-scale genotyping. We provide the new SNP map and validation information, validated SNP assays and reagents, and instrumentation systems as a novel resource for genetic discoveries.

Alleles↗

PubMed2005

Semantic challenges in database Federation: lessons learned.

In this project an integrated analysis of data from disparate surgery and anaesthesiology departmental information systems was carried out. Due to the lack of shared primary keys, a multi-stage "soft" matching method was implemented. Results of the matching steps are described in detail. Inconsistencies were shown to exist for identifying data, semantic definition of documentation content and documented data itself. Minimum requirements for interdisciplinary documentation in autonomous systems should include shared semantic definitions of documentation content as well as robust and regularly validated interfaces for identifying data.

Database Management Systems↗

PubMed1995

4.5 years of experience with an electronic patient record system at the University of Munich: PADS (Patient Archiving & Documentation System).

We demonstrate an Ethernet based local area network (LAN) with clinical workstations (Apple Macintosh). The patient archiving and documentation system (PADS) represents a computerized patient record system presently used in a university hospital's ICU, CCU, and oncology unit [1]. Since 1990, over 100 users have documented more than 6,000 patient admissions, equaling 30% of all inpatient admission in our hospital. Taking full advantage of the macintosh based graphical user interface (GUI), our system enables nurses and doctors to perform the following tasks: admission, medical history taking, physical examination, generation of problem lists and follow up notes, access to laboratory data and reports, and the semiautomatic generation of a discharge summary including full word processor capabilities. Furthermore, the system offers rapid, consistent, and complete automatic encoding of diagnoses following the International Classification of Disease (ICD - 9 CM; WHO). The system has links to other educational programs such as cardiac auscultation and image analysis. A MEDLINE literature search through a CD-ROM based system can be performed from within the system. CD-ROM based medical textbooks can be accessed as well. Users can customize their working environment and use any commercially available macintosh programs from within the main application. Additional options include: automatic background monitoring of users learning behavior, analyses and graphical display of numerous epidemiological, and healthcare related problems. Furthermore, sound and digital video can be recorded in our system. E had initially developed a relational database 4GL development tool in the rapid prototyping phase, and have since completed the next step of development: rewriting the complete application using C++ and Oracle. The user interface has hardly changed, maintaining the "look & feel" of the initial application and introducing the performance of a professional relational database management system (RDBMS). This system represents one in a line of modular departmental models which are being integrated to form a decentralized hospital information system (HIS) at the University of Munich. The proposed theater-style demonstration will walk the audience through the system simulating a true patient admission and work up.

Germany↗

PubMed1997

Evolution of the CANDA at Roche.

Computer-assisted NDAs (CANDAs) have evolved from an instrument that provides information to regulators to also providing information to internal researchers. They are still not as useful internally during the NDA process as they will be in the future. The portion of CANDA that allows summary, display, and query of the raw data is the most complicated part of the CANDA. Roche's current CANDA system, as well as the challenges in using, documenting, and validating such a system, is described, stressing the features that make it usable in-house. Roche's vision of the future is outlined, covering the strategies, targets, and expected savings.

Database Management Systems↗

PubMed2003

FPV: fast protein visualization using Java 3D.

MOTIVATION: Many tools have been developed to visualize protein structures. Tools that have been based on Java 3D((TM)) are compatible among different systems and they can be run remotely through web browsers. However, using Java 3D for visualization has some performance issues with it. The primary concerns about molecular visualization tools based on Java 3D are in their being slow in terms of interaction speed and in their inability to load large molecules. This behavior is especially apparent when the number of atoms to be displayed is huge, or when several proteins are to be displayed simultaneously for comparison. RESULTS: In this paper we present techniques for organizing a Java 3D scene graph to tackle these problems. We have developed a protein visualization system based on Java 3D and these techniques. We demonstrate the effectiveness of the proposed method by comparing the visualization component of our system with two other Java 3D based molecular visualization tools. In particular, for van der Waals display mode, with the efficient organization of the scene graph, we could achieve up to eight times improvement in rendering speed and could load molecules three times as large as the previous systems could. AVAILABILITY: EPV is freely available with source code at the following URL: http://www.cs.ucsb.edu/~tcan/fpv/

Computer Graphics↗

PubMed2004

Formalization of mouse embryo anatomy.

MOTIVATION: The Edinburgh Mouse Atlas and Gene Expression Database project has developed a digital atlas of mouse development to provide a spatio-temporal framework for spatially mapped data such as in situ gene expression and cell lineage. As part of this database, a mouse embryo anatomy ontology has been created. A formalization of this anatomy is required to document its precise semantics and how it is used in the context of the Mouse Atlas. RESULTS: The paper describes the existing anatomy ontology and formalizes aspects of it using a predicate logic based approach. It therefore provides a guide for users of the current version of the ontology, as well as the basis for a description of the anatomy using an ontology language, such as OWL, thus enabling future work on reasoning about the Mouse Atlas in the context of an intelligent gene expression bioinformatics workflow system. The logic has been implemented in a Prolog prototype. AVAILABILITY: The Mouse Atlas is available on-line at http://genex.hgu.mrc.ac.uk

Algorithms↗

PubMed2004

BioSilico: an integrated metabolic database system.

BioSilico is a web-based database system that facilitates the search and analysis of metabolic pathways. Heterogeneous metabolic databases including LIGAND, ENZYME, EcoCyc and MetaCyc are integrated in a systematic way, thereby allowing users to efficiently retrieve the relevant information on enzymes, biochemical compounds and reactions. In addition, it provides well-designed view pages for more detailed summary information. BioSilico is developed as an extensible system with a robust systematic architecture.

Database Management Systems↗

PubMed2005

[Adonco. A clinical-scientific database system for the acquisition and analysis of oncologic data in head and neck regions].

BACKGROUND: Our aim was to design and develop a computer database system for head and neck cancer patients for clinical and scientific use. METHODS: A relational database based on Filemaker Pro 6.0 was developed and integrated into our local network. Its precise and easy to handle interface should allow a quick overview of the patient's oncological data. An automatically generated letter was integrated to enhance patient care. For evaluation purposes, statistical analysis functions were incorporated. RESULTS: Over a 7 month period, about 300 patient records were available through the local network. The automated letter function and the well organized display resulted in more efficient patient care. Additionally, the quality of the information presented to referring physicians increased. Statistical analysis provided by the database was reliable and easy to export. CONCLUSIONS: We developed an oncology database for clinical and scientific use and integrated it into our patient documentation system. The combination of clinical and scientific features proved to be very effective in daily patient care routine and research.

Algorithms↗

PubMed1992

CD-ROM source data uploaded to the operating and storage devices of an IBM 3090 mainframe through a PC terminal.

A powerful method of processing MEDLINE and CINAHL source data uploaded to the IBM 3090 mainframe computer through an IBM/PC is described. Data are first downloaded from the CD-ROM's PC devices to floppy disks. These disks then are uploaded to the mainframe computer through an IBM/PC equipped with WordPerfect text editor and computer network connection (SONNGATE). Before downloading, keywords specifying the information to be accessed are typed at the FIND prompt of the CD-ROM station. The resulting abstracts are downloaded into a file called DOWNLOAD.DOC. The floppy disks containing the information are simply carried to an IBM/PC which has a terminal emulation (TELNET) connection to the university-wide computer network (SONNET) at the Ohio State University Academic Computing Services (OSU ACS). The WordPerfect (5.1) processes and saves the text into DOS format. Using the File Transfer Protocol (FTP, 130,000 bytes/s) of SONNET, the entire text containing the information obtained through the MEDLINE and CINAHL search is transferred to the remote mainframe computer for further processing. At this point, abstracts in the specified area are ready for immediate access and multiple retrieval by any PC having network switch or dial-in connection after the USER ID, PASSWORD and ACCOUNT NUMBER are specified by the user. The system provides the user an on-line, very powerful and quick method of searching for words specifying: diseases, agents, experimental methods, animals, authors, and journals in the research area downloaded. The user can also copy the TItles, AUthors and SOurce with optional parts of abstracts into papers under edition. This arrangement serves the special demands of a research laboratory by handling MEDLINE and CINAHL source data resulting after a search is performed with keywords specified for ongoing projects. Since the Ohio State University has a centrally founded mainframe system, the data upload, storage and mainframe operations are free.

CD-ROM↗

PubMed2003

GeneHuggers: database mining and application connectivity tools for subsequence analyses of the human genome.

UNLABELLED: GeneHuggers is a collection of program modules that enables precise selection of subsequence regions from records of the RefSeq human genome database. Subsequence regions can be selected based on diverse criteria, including feature addresses, annotations from LocusLink and UniGene, and results obtained from analyses with homologous subsequence detection programs. GeneHuggers provides functionality to the UNIX operating system that allows customized bioinformatics program development. AVAILABILITY: GeneHuggers source code is available under the GNU general public license and can be downloaded from ftp://ftp.scripps.edu/pub/genehuggers/gh.tar.gz

Abstracting and Indexing↗

PubMed2006

Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration.

BACKGROUND: There is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes. Similarly, a growing variety of bioinformatic programs are becoming available from many diverse sources, designed to identify a myriad of sequence patterns considered to have potential biological importance within inter-genic regions, genes, transcripts, and proteins. However, biologists require easy to use, uncomplicated tools to integrate this information, visualise and print gene annotations. Integrating this information usually requires considerable informatics skills, and comprehensive knowledge of the data format to make full use of this information. Tools are needed to explore gene model variants by allowing users the ability to create alternative transcript models using novel combinations of exons not necessarily represented in current database deposits of mRNA/cDNA sequences. RESULTS: Djinn Lite is designed to be an intuitive program for storing and visually exploring of custom annotations relating to a eukaryotic gene sequence and its modelled gene products. In particular, it is helpful in developing hypothesis regarding alternate splicing of transcripts by allowing the construction of model transcripts and inspection of their resulting translations. It facilitates the ability to view a gene and its gene products in one synchronised graphical view, allowing one to drill down into sequence related data. Colour highlighting of selected sequences and added annotations further supports exploration, visualisation of sequence regions and motifs known or predicted to be biologically significant. CONCLUSION: Gene annotating remains an ongoing and challenging task that will continue as gene structures, gene transcription repertoires, disease loci, protein products and their interactions become more precisely defined. Djinn Lite offers an accessible interface to help accumulate, enrich, and individualize sequence annotations relating to a gene, its transcripts and translations. The mechanism of transcript definition and creation, and subsequent navigation and exploration of features, are very intuitive and demand only a short learning curve. Ultimately, Djinn Lite can form the basis for providing valuable clues to plan new experiments, providing storage of sequences and annotations for dedication to customised projects. The application is appropriate for Windows 98-ME-2000-XP-2003 operating systems.

Alternative Splicing↗

PubMed2000

Requirements of a Web-based experiment management system.

Recent advances in tools for scientific data acquisition, visualization, and analysis have lead to growing information management problems for medical research laboratories. An exponential increase in the volume of data, combined with a proliferation of heterogeneous formats and autonomous systems, has driven the need for flexible and powerful Experiment Management Systems (EMS). This paper provides a detailed analysis of the informatics requirements of an EMS, and proposes a new type of middleware called an EMS-Building Environment (EMSBE), which enables the rapid development of web-based systems for managing laboratory data and workflow. We describe the Web-Interfacing Respository Manager (WIRM), an open-source application server for building customizable experiment management systems. WIRM is being used to manage several ongoing experiments, including a natural language processor of radiological findings, and an interdisciplinary project for studying brain function.

Clinical Laboratory Information Systems↗

PubMed2005

A Grid service for the interactive use of a parallel non-rigid registration algorithm of medical images.

OBJECTIVE: The goal of this work is to improve the usability of a non-rigid registration software for medical images. METHOD: We have built a registration grid service in order to use the interactivity of a visualization workstation and the computing power of a cluster. On the user side, the system is composed of a graphical interface that interacts in a complex and fluid manner with the registration software running on a remote cluster. CONCLUSION: Although the transmission of images back and forth between the computer running the user interface and the cluster running the registration service adds to the total registration time, it provides a user-friendly way of using the registration software without heavy infrastructure investments in hospitals. The system exhibits good performances even if the user is connected to the grid service through a low throughput network such as a wireless network interface or ADSL.

Algorithms↗

PubMed2005

Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures.

The structure of a closely integrated data warehouse is described that is designed to link different types and varying numbers of biological networks, sequence analysis methods and experimental results such as those coming from microarrays. The data schema is inspired by a combination of graph based methods and generalised data structures and makes use of ontologies and meta-data. The core idea is to consider and store biological networks as graphs, and to use generalised data structures (GDS) for the storage of further relevant information. This is possible because many biological networks can be stored as graphs: protein interactions, signal transduction networks, metabolic pathways, gene regulatory networks etc. Nodes in biological graphs represent entities such as promoters, proteins, genes and transcripts whereas the edges of such graphs specify how the nodes are related. The semantics of the nodes and edges are defined using ontologies of node and relation types. Besides generic attributes that most biological entities possess (name, attribute description), further information is stored using generalised data structures. By directly linking to underlying sequences (exons, introns, promoters, amino acid sequences) in a systematic way, close interoperability to sequence analysis methods can be achieved. This approach allows us to store, query and update a wide variety of biological information in a way that is semantically compact without requiring changes at the database schema level when new kinds of biological information is added. We describe how this datawarehouse is being implemented by extending the text-mining framework ONDEX to link, support and complement different bioinformatics applications and research activities such as microarray analysis, sequence analysis and modelling/simulation of biological systems. The system is developed under the GPL license and can be downloaded from http://sourceforge.net/projects/ondex/

Algorithms↗

PubMed1988

The knowledge workstation: an electronic environment for knowledge management.

This paper focuses on the creation of the IAIMS workstation in the context of the outcomes of a year-long IAIMS strategic planning process at the Johns Hopkins Medical Institutions (JHMI). These outcomes include a long-term institutional vision for a functional knowledge management environment, a JHMI IAIMS model, a strategic plan, and two model prototypes. The functional requirements and specific implementation strategies for the IAIMS workstation, the prototype for managing the knowledge base of the published biomedical literature, are discussed in detail.

Academic Medical Centers↗

PubMed2004

Multi-layered representation for cell signaling pathways.

To understand complex signaling pathways and networks, it is necessary to develop a formal and structured representation of the available information in a format suitable for analysis by software tools. Due to the complexity and incompleteness of the current biological knowledge about cell signaling, such a device must be able to represent cellular pathways at differing levels of details, one level of information abstract enough to convey an essential signaling flow while hiding its details and another level of information detailed enough to explain the underlying mechanisms that account for the signaling flow described at a more abstract level. We have defined a formal ontology for cell-signaling events that allows us to describe these cellular pathways at various levels of abstraction. Using this formal representation, ROSPath (reactive oxygen species-mediated signaling pathway) database system has been implemented and made available on the web (rospath.ewha.ac.kr). ROSPath is a database system for reactive oxygen species (ROS)-mediated cell signaling pathways and signaling processes in molecular detail, which facilitates a comprehensive understanding of the regulatory mechanisms in signaling pathways. ROSPath includes growth factor-, stress-, and cytokine-induced signaling pathways containing about 500 unique proteins (mostly mammalian) and their related protein states, protein complexes, protein complex states, signaling interactions, signaling steps, and pathways. It is a web-based structured repository of information on the signaling pathways of interest and provides a means for managing data produced by large-scale and high-throughput techniques such as proteomics. Also, software tools are provided for querying, displaying, and analyzing pathways, thus furnishing an integrated web environment for visualizing and manipulating ROS-mediated cell-signaling events.

Cell Physiological Phenomena↗