systems integration

Summary

Summary: The procedures involved in combining separately developed modules, components, or subsystems so that they work together as a complete system. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

Top Publications

  1. pmc TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
    V Matys
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 34:D108-10. 2006
  2. pmc The Ensembl genome database project
    T Hubbard
    The Wellcome Trust Sanger Institute and European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 30:38-41. 2002
  3. pmc Reactome knowledgebase of human biological pathways and processes
    Lisa Matthews
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 37:D619-22. 2009
  4. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
  5. pmc VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
    Zhenjun Hu
    Center for Advanced Genomic Technology, Program in Bioinformatics, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 37:W115-21. 2009
  6. pmc WikiPathways: pathway editing for the people
    Alexander R Pico
    Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA
    PLoS Biol 6:e184. 2008
  7. pmc BioGRID: a general repository for interaction datasets
    Chris Stark
    Ontario Cancer Institute, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9
    Nucleic Acids Res 34:D535-9. 2006
  8. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:D5-15. 2009
  9. pmc WebGestalt: an integrated system for exploring gene sets in various biological contexts
    Bing Zhang
    Graduate School in Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Nucleic Acids Res 33:W741-8. 2005
  10. ncbi State of the nation in data integration for bioinformatics
    Carole Goble
    School of Computer Science, University of Manchester, Oxford Road, Manchester M139PL, UK
    J Biomed Inform 41:687-93. 2008

Detail Information

Publications309 found, 100 shown here

  1. pmc TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
    V Matys
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 34:D108-10. 2006
    ..The here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html...
  2. pmc The Ensembl genome database project
    T Hubbard
    The Wellcome Trust Sanger Institute and European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 30:38-41. 2002
    ..The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops...
  3. pmc Reactome knowledgebase of human biological pathways and processes
    Lisa Matthews
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Nucleic Acids Res 37:D619-22. 2009
    ..Reactome's data content and software can all be freely used and redistributed under open source terms...
  4. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
    ..We conclude with a discussion of how the open-source nature of the project has contributed to the development effort...
  5. pmc VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
    Zhenjun Hu
    Center for Advanced Genomic Technology, Program in Bioinformatics, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 37:W115-21. 2009
    ..Both algorithms take account of network topology (i.e. correlations between genes based on various sources of evidence). VisANT is freely available at http://visant.bu.edu...
  6. pmc WikiPathways: pathway editing for the people
    Alexander R Pico
    Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA
    PLoS Biol 6:e184. 2008
  7. pmc BioGRID: a general repository for interaction datasets
    Chris Stark
    Ontario Cancer Institute, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9
    Nucleic Acids Res 34:D535-9. 2006
    ..User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID...
  8. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:D5-15. 2009
    ..Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  9. pmc WebGestalt: an integrated system for exploring gene sets in various biological contexts
    Bing Zhang
    Graduate School in Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Nucleic Acids Res 33:W741-8. 2005
    ..Exploration of all the 48 gene sets using WebGestalt is available for the public at http://genereg.ornl.gov/webgestalt/wg_enrich.php...
  10. ncbi State of the nation in data integration for bioinformatics
    Carole Goble
    School of Computer Science, University of Manchester, Oxford Road, Manchester M139PL, UK
    J Biomed Inform 41:687-93. 2008
    ..The paper expands on that talk. We attempt to place some perspective on past efforts, highlight the reasons for success and failure, and indicate some pointers to the future...
  11. pmc miRGator: an integrated system for functional annotation of microRNAs
    Seungyoon Nam
    Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea
    Nucleic Acids Res 36:D159-64. 2008
    ..Currently, miRGator, available at: http://genome.ewha.ac.kr/miRGator/, supports the human and mouse genomes...
  12. pmc E-MSD: an integrated data resource for bioinformatics
    S Velankar
    Macromolecular Structure Database Group E MSD, EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:D262-5. 2005
    ..This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group...
  13. pmc Pathguide: a pathway resource list
    Gary D Bader
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 460, New York, NY 10021, USA
    Nucleic Acids Res 34:D504-6. 2006
    ..Pathguide is useful as a starting point for biological pathway analysis and for content aggregation in integrated biological information systems...
  14. pmc The EMBRACE web service collection
    Steve Pettifer
    School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK
    Nucleic Acids Res 38:W683-8. 2010
    ..embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions...
  15. pmc R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases
    Alexey V Antonov
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute for Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 38:W78-83. 2010
    ..R spider provides a user-friendly dialog-driven web interface for several model organisms and supports most available gene identifiers. R spider is freely available at http://mips.helmholtz-muenchen.de/proj/rspider...
  16. pmc A series of PDB related databases for everyday needs
    Robbie P Joosten
    Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
    Nucleic Acids Res 39:D411-9. 2011
    ..All these systems are updated weekly. The data sets can be used for the analysis of properties of protein structures in areas ranging from structural genomics, to cancer biology and protein design...
  17. ncbi Standards to support information systems integration in anatomic pathology
    Christel Daniel
    ADICAP INSERM, UMR_S 872 eq20 and Université Paris Descartes, Paris, France
    Arch Pathol Lab Med 133:1841-9. 2009
    ....
  18. ncbi Bio2RDF: towards a mashup to build bioinformatics knowledge systems
    François Belleau
    Centre de Recherche du CHUL, Universite Laval, 2705 Boulevard Laurier, Que, Canada G1V4G2
    J Biomed Inform 41:706-16. 2008
    ..The Bio2RDF repository can be queried at http://bio2rdf.org...
  19. pmc ConsensusPathDB--a database for integrating human functional interaction networks
    Atanas Kamburov
    Max Planck Institute for Molecular Genetics, Ihnestr 63 73, 14195 Berlin, Germany
    Nucleic Acids Res 37:D623-8. 2009
    ..The ConsensusPathDB database is available at: http://cpdb.molgen.mpg.de...
  20. ncbi Visualizing biological data-now and in the future
    Seán I O'Donoghue
    European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Methods 7:S2-4. 2010
    ..For most users, a key challenge is to benefit from the deluge of data without being overwhelmed by it. This challenge is still largely unfulfilled and will require the development of truly integrated and highly useable tools...
  21. ncbi A Chado case study: an ontology-based modular schema for representing genome-associated biological information
    Christopher J Mungall
    Lawrence Berkeley National Laboratory, Lawrence Berkeley National Lab, Mail Stop 64R0121, Berkeley, CA 94720, USA
    Bioinformatics 23:i337-46. 2007
    ..Our question was whether we could create a relational database schema that would be successfully reused...
  22. pmc MaGe: a microbial genome annotation system supported by synteny results
    David Vallenet
    Atelier de Génomique Comparative, CNRS UMR8030, 2 rue Gaston Cremieux, 91057 Evry, Cedex, France
    Nucleic Acids Res 34:53-65. 2006
    ..In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria). MaGe can be accessed at http://www.genoscope.cns.fr/agc/mage...
  23. pmc inGAP: an integrated next-generation genome analysis pipeline
    Ji Qi
    Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA
    Bioinformatics 26:127-9. 2010
    ..All the detected SNPs/indels can be further evaluated by a graphical editor in our pipeline. inGAP also provides functions of multiple genomes comparison and assistance of bacterial genome assembly...
  24. pmc From genomics to chemical genomics: new developments in KEGG
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 34:D354-7. 2006
    ..Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps...
  25. pmc ToxoDB: an integrated Toxoplasma gondii database resource
    Bindu Gajria
    Department of Biology, Department of Genetics, Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
    Nucleic Acids Res 36:D553-6. 2008
    ..ToxoDB has matured significantly since its initial release. Here we outline the numerous updates with respect to the data and increased functionality available on the website...
  26. pmc The HGNC Database in 2008: a resource for the human genome
    Elspeth A Bruford
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    Nucleic Acids Res 36:D445-8. 2008
    ..genenames.org, with direct links to the searchable HGNC database and other related database resources, such as the HCOP orthology search tool and manually curated gene family webpages...
  27. ncbi RNAshapes: an integrated RNA analysis package based on abstract shapes
    Peter Steffen
    Faculty of Technology and, Bielefeld University, 33594 Bielefeld, Germany
    Bioinformatics 22:500-3. 2006
    ..Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach...
  28. pmc Lists2Networks: integrated analysis of gene/protein lists
    Alexander Lachmann
    Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA
    BMC Bioinformatics 11:87. 2010
    ..In addition, linking high-content multilayered experimental results with prior biological knowledge can be useful for identifying functional themes and form novel hypotheses...
  29. ncbi Standardized and flexible health data management with an archetype driven EHR system (EHRflex)
    Anton Brass
    Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Germany
    Stud Health Technol Inform 155:212-8. 2010
    ..These can be exchanged with other people and systems when needed. EHRflex introduces EHR standards into the clinical routine delivering a technical platform which works directly on archetype based data...
  30. ncbi Model driven development of clinical information sytems using openEHR
    Koray Atalağ
    Department of Computer Science, The University of Auckland, New Zealand
    Stud Health Technol Inform 169:849-53. 2011
    ..This might provide guidance for other developers and form evidence required for the adoption of these standards for vendors and national programs alike...
  31. pmc Archetype-based conversion of EHR content models: pilot experience with a regional EHR system
    Rong Chen
    Department of Biomedical Engineering, Linkoping University, Linkoping, Sweden
    BMC Med Inform Decis Mak 9:33. 2009
    ..This study was designed to investigate the feasibility of representing EHR content models from a regional EHR system as openEHR archetypes and inversely to convert archetypes to the proprietary format...
  32. ncbi Achieving clinical statement interoperability using R-MIM and archetype-based semantic transformations
    Ozgur Kilic
    Department of Computer Engineering, Middle East Technical University, 06531 Ankara, Turkey
    IEEE Trans Inf Technol Biomed 13:467-77. 2009
    ..Finally, we show how to transform Health Level Seven clinical statement instances to EHRcom clinical statement instances and vice versa by using the generated mapping definitions...
  33. pmc The RIKEN integrated database of mammals
    Hiroshi Masuya
    RIKEN BioResource Center, Tsukuba, Japan
    Nucleic Acids Res 39:D861-70. 2011
    ....
  34. pmc STRING: known and predicted protein-protein associations, integrated and transferred across organisms
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 33:D433-7. 2005
    ..STRING currently holds 730,000 proteins in 180 fully sequenced organisms, and is available at http://string.embl.de/...
  35. pmc Integration of tools for binding archetypes to SNOMED CT
    Erik Sundvall
    Department of Biomedical Engineering, Linkoping University, 581 85 Linkoping, Sweden
    BMC Med Inform Decis Mak 8:S7. 2008
    ..This paper presents an archetype editor with support for manual or semi-automatic creation of bindings between archetypes and terminology systems...
  36. pmc CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge
    Jessica Ahmed
    Charite University Medicine Berlin, Institute for Physiology, Structural Bioinformatics Group, Thielallee 71, 14195 Berlin, Germany
    Nucleic Acids Res 39:D960-7. 2011
    ..CancerResource addresses the spectrum of research on compound-target interactions in natural sciences as well as in individualized medicine; CancerResource is available at: http://bioinformatics.charite.de/cancerresource/...
  37. pmc GlycomeDB - integration of open-access carbohydrate structure databases
    René Ranzinger
    German Cancer Research Center DKFZ, Core Facility Molecular Structural Analysis, Im Neuenheimer Feld 280, Heidelberg, Germany
    BMC Bioinformatics 9:384. 2008
    ..For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases...
  38. pmc An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependence
    Satya S Sahoo
    Kno e sis Center, Wright State University, Dayton, OH, USA
    J Biomed Inform 41:752-65. 2008
    ..In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base...
  39. pmc Tools for comparative protein structure modeling and analysis
    Narayanan Eswar
    Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143 2240, USA
    Nucleic Acids Res 31:3375-80. 2003
    ....
  40. pmc KEGG for linking genomes to life and the environment
    Minoru Kanehisa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
    Nucleic Acids Res 36:D480-4. 2008
    ..KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers...
  41. pmc Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks
    Allan Peter Davis
    Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
    Nucleic Acids Res 37:D786-92. 2009
    ..This wealth of chemical-gene-disease information yields testable hypotheses for understanding the effects of environmental chemicals on human health. CTD is freely available at http://ctd.mdibl.org...
  42. pmc Taverna: a tool for building and running workflows of services
    Duncan Hull
    School of Computer Science, University of Manchester, M13 9PL, UK
    Nucleic Acids Res 34:W729-32. 2006
    ..These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from http://taverna.sourceforge.net/...
  43. ncbi Combining multiple microarray studies and modeling interstudy variation
    Jung Kyoon Choi
    Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 371 1 Guseong dong Yuseong gu, Daejeon 305 701, Korea
    Bioinformatics 19:i84-90. 2003
    ..We also developed an alternative modeling procedure based on a Bayesian approach, which would offer flexibility and robustness compared to the classical procedure...
  44. pmc Protégé: a tool for managing and using terminology in radiology applications
    Daniel L Rubin
    Section of Medical Informatics, Stanford University, MSOB X 215, 251 Campus Drive, Stanford, CA 94305, USA
    J Digit Imaging 20:34-46. 2007
    ..In this report, we describe Protégé's features and its particular advantages in the radiology domain in the creation, maintenance, and use of radiology terminology...
  45. pmc An information integration theory of consciousness
    Giulio Tononi
    Department of Psychiatry, University of Wisconsin, Madison, USA
    BMC Neurosci 5:42. 2004
    ..For example, why do specific parts of the brain contribute specific qualities to our conscious experience, such as vision and audition?..
  46. ncbi Workflow management of content-based image retrieval for CAD support in PACS environments based on IHE
    Petra Welter
    Department of Medical Informatics, RWTH Aachen University, Germany
    Int J Comput Assist Radiol Surg 5:393-400. 2010
    ..One essential factor in this setting is scheduling. Applied and proved with modalities and the acquisition of images for a long time, we now establish scheduling with CBIR...
  47. ncbi Data security assurance in CAD-PACS integration
    Zheng Zhou
    Image Processing and Informatics IPI Laboratory, Radiology Department, University of Southern California, Marina del Rey, CA 90292, USA
    Comput Med Imaging Graph 31:353-60. 2007
    ..Combining this method with traditional one-dimensional digital signature technique for protecting CAD results, we provide a complete integrity assurance solution for a CAD application integrated with a PACS...
  48. ncbi Enterprise-wide PACS: beyond radiology, an architecture to manage all medical images
    David Bandon
    Service of Medical Informatics, University Hospitals of Geneva, Switzerland
    Acad Radiol 12:1000-9. 2005
    ..To address the various situations encountered in the imaging specialties, the traditional architecture used for the radiology department has to evolve...
  49. ncbi CAD-PACS integration tool kit based on DICOM secondary capture, structured report and IHE workflow profiles
    Zheng Zhou
    Image Processing and Informatics IPI Laboratory, Radiology Department, University of Southern California, Marina del Rey, CA 90292, USA
    Comput Med Imaging Graph 31:346-52. 2007
    ....
  50. pmc Ten key principles for successful health systems integration
    Esther Suter
    Health Systems and Workforce Research Unit, Alberta Health Services, Calgary Health Region
    Healthc Q 13:16-23. 2009
    ..The literature does not contain a one-size-fits-all model or process for successful integration, nor is there a firm empirical foundation for specific integration strategies and processes...
  51. ncbi Integrating 'omic' information: a bridge between genomics and systems biology
    Hui Ge
    Dana Farber Cancer Institute and Department of Genetics, Harvard Medical School, SM858, 44 Binney Street, Boston, MA 02115, USA
    Trends Genet 19:551-60. 2003
    ..Here, we review the recent development of strategies for such integration and we argue that these will be important for a systems approach to modular biology...
  52. pmc Identifying transcriptional regulatory sites in the human genome using an integrated system
    Hsien Da Huang
    Department of Biological Science and Technology and Institute of Bioinformatics, National Chiao Tung University, Hsin Chu 300, Taiwan
    Nucleic Acids Res 32:1948-56. 2004
    ..The integrated system is now available at http://rgsminer. csie.ncu.edu.tw/...
  53. pmc ERGR: An ethanol-related gene resource
    An Yuan Guo
    Department of Psychiatry and Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
    Nucleic Acids Res 37:D840-5. 2009
    ..More functions will also be added. ERGR has a user-friendly web interface with browse and search functions at multiple levels. It is freely available at http://bioinfo.vipbg.vcu.edu/ERGR/...
  54. pmc Prediction of drug-target interaction networks from the integration of chemical and genomic spaces
    Yoshihiro Yamanishi
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Bioinformatics 24:i232-40. 2008
    ..Therefore, there is a strong incentive to develop new methods capable of detecting these potential drug-target interactions efficiently...
  55. pmc Impact of a computer-aided detection (CAD) system integrated into a picture archiving and communication system (PACS) on reader sensitivity and efficiency for the detection of lung nodules in thoracic CT exams
    Luca Bogoni
    Siemens Healthcare, Malvern, PA 19355, USA
    J Digit Imaging 25:771-81. 2012
    ..1 s, after localizing it in the original image series. The integration of CAD into PACS increases reader sensitivity with minimal impact on interpretation time and supports such implementation into daily clinical practice...
  56. ncbi The integration of medical images with the electronic patient record and their web-based distribution
    H Munch
    German Cancer Research Center, Medical and Biological Informatics Division, Im Neuenheimer Feld 280, D 69120 Heidelberg, Germany
    Acad Radiol 11:661-8. 2004
    ..This integration has been successfully tested using three different commercial RIS and HIS products...
  57. ncbi Digital imaging and electronic patient records in pathology using an integrated department information system with PACS
    Thomas Kalinski
    Institute of Pathology, Otto von Guericke University, Magdeburg, Germany
    Pathol Res Pract 198:679-84. 2002
    ..Moreover, we evaluate the current situation and future prospects for PACS in pathology...
  58. pmc Exchange of computable patient data between the Department of Veterans Affairs (VA) and the Department of Defense (DoD): terminology mediation strategy
    Omar Bouhaddou
    Veterans Affairs, VA Salt Lake City Office of Information, 550 Foothill Drive, Salt Lake City, Utah 84113, USA
    J Am Med Inform Assoc 15:174-83. 2008
    ..Stable and mature standards, mediation strategies, and a close relationship between healthcare institutions and Standards Development Organizations are recommended to achieve and maintain semantic interoperability in a clinical setting...
  59. pmc The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
    Richard G Côté
    EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nucleic Acids Res 36:W372-6. 2008
    ..Improvements have been made to both OLS query interfaces, based on user feedback and requirements, to improve usability and service interoperability and provide novel ways to perform queries...
  60. pmc ApiDB: integrated resources for the apicomplexan bioinformatics resource center
    Cristina Aurrecoechea
    Center for Tropical and Emerging Global Diseases, Athens, GA, USA
    Nucleic Acids Res 35:D427-30. 2007
    ..Through the ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases...
  61. ncbi An e-consent-based shared EHR system architecture for integrated healthcare networks
    Joachim Bergmann
    Technical University of Braunschweig, Institute for Medical Informatics, Muehlenpfordtstr 23, 38106 Braunschweig, Germany
    Int J Med Inform 76:130-6. 2007
    ..Our work aims on specification and development of a virtual shared health record architecture using a patient-centred integration and authorization model...
  62. ncbi UniProt archive
    Rasko Leinonen
    EMBL Outstation, The European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 20:3236-7. 2004
    ..UniParc contains only protein sequences and database cross-references; all other information must be retrieved from the source databases...
  63. pmc Automated mapping of pharmacy orders from two electronic health record systems to RxNorm within the STRIDE clinical data warehouse
    Penni Hernandez
    Center for Clinical Informatics, Stanford University, Stanford, CA, USA
    AMIA Annu Symp Proc 2009:244-8. 2009
    ..5 million pharmacy orders showed that the system could accurately assign pharmacy orders in over 96% of cases. This paper describes the algorithm and discusses some of the causes of failures in mapping to RxNorm...
  64. ncbi Design and implementation of a health data interoperability mediator
    Mu Hsing Kuo
    School of Health Information Science, The University of Victoria, BC, Canada
    Stud Health Technol Inform 155:101-7. 2010
    ..A routine admission notification data exchange scenario is used to test the efficiency and feasibility of the proposed mediator. The study results show that the proposed mediator can make health information exchange more efficient...
  65. ncbi Digital pathology in Europe: coordinating patient care and research efforts
    Marcial Garcia Rojo
    Hospital General de Ciudad Real, 13005 Ciudad Real, Spain
    Stud Health Technol Inform 150:997-1001. 2009
    ..Nowadays, further discussion is needed on the adequacy of current existing technical solutions, including for instance quality of images obtained by scanners, or the efficiency of image analysis applications...
  66. pmc NONCODE: an integrated knowledge database of non-coding RNAs
    Changning Liu
    Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
    Nucleic Acids Res 33:D112-5. 2005
    ..0) contains 5339 non-redundant sequences from 861 organisms, including eukaryotes, eubacteria, archaebacteria, virus and viroids. Access is free for all users through a web interface at http://noncode.bioinfo.org.cn...
  67. pmc VBASE2, an integrative V gene database
    Ida Retter
    Department of Experimental Immunology, German Research Centre for Biotechnology, Mascheroder Weg 1, D 38124 Braunschweig, Germany
    Nucleic Acids Res 33:D671-4. 2005
    ..VBASE2 can be accessed either by a web-based text query or by a sequence similarity search with the DNAPLOT software. VBASE2 is available at http://www.vbase2.org, and the DAS server is located at http://www.dnaplot.com/das...
  68. pmc A balanced evaluation perspective: picture archiving and communication system impacts on hospital workflow
    Rogier van de Wetering
    Department of Information and Computing Sciences, Utrecht University, Centrumgebouw Noord, Padualaan 14, De Uithof, 3584 CH, Utrecht, The Netherlands
    J Digit Imaging 19:10-7. 2006
    ..Results show that PACS did improve hospital workflow considerably and that the organizational alignment of PACS in hospitals is an important critical success factor...
  69. pmc Integr8 and Genome Reviews: integrated views of complete genomes and proteomes
    Paul Kersey
    The EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:D297-302. 2005
    ..Integr8 also allows the users to customize their own interactive analysis, and to download both customized and prepared datasets for their own use. Integr8 is available at http://www.ebi.ac.uk/integr8...
  70. pmc ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics
    Hee Joon Chung
    Seoul National University Biomedical Informatics, Seoul National University College of Medicine, Seoul 110 799, Republic of Korea
    Nucleic Acids Res 32:W460-4. 2004
    ..ArrayXPath produces Javascript-enabled SVGs for web-enabled interactive visualization of pathways integrated with gene-expression profiles...
  71. ncbi Systems biology: integrating technology, biology, and computation
    Leroy Hood
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Mech Ageing Dev 124:9-16. 2003
    ..These two themes will dominate 21st century biology and medicine. I will discuss these changes and indicate how they may interface with with the process of aging...
  72. ncbi Data integration: challenges for drug discovery
    David B Searls
    Bioinformatics Division, Genetics Research, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, P O Box 1539, King of Prussia, Pennsylvania 19406, USA
    Nat Rev Drug Discov 4:45-58. 2005
    ....
  73. ncbi A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
    Matthew Bellew
    LabKey Software, Seattle, WA 98109, USA
    Bioinformatics 22:1902-9. 2006
    ....
  74. ncbi yOWL: an ontology-driven knowledge base for yeast biologists
    Natalia Villanueva-Rosales
    School of Computer Science, Carleton University, Ottawa, Ont, Canada K1S5B6
    J Biomed Inform 41:779-89. 2008
    ..Based on yeast data obtained from the Saccharomyces Genome Database and UniProt, we discuss the challenges encountered during the building of the knowledge base and how they were overcome...
  75. ncbi Architectural approach to eHealth for enabling paradigm changes in health
    B Blobel
    eHealth Competence Center, University Hospital Regensburg, Franz Josef Strauss Allee 11, 93053 Regensburg, Germany
    Methods Inf Med 49:123-34. 2010
    ....
  76. pmc New challenges in gene expression data analysis and the extended GEPAS
    Javier Herrero
    Bioinformatics Unit, Biotechnology Programme, Centro Nacional de Investigaciones Oncologicas, Melchor Fernandez Almagro, 3, E 28029 Madrid, Spain
    Nucleic Acids Res 32:W485-91. 2004
    ..The web-based pipeline for microarray gene expression data, GEPAS, is available at http://gepas.bioinfo.cnio.es...
  77. ncbi From XML to RDF: how semantic web technologies will change the design of 'omic' standards
    Xiaoshu Wang
    Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon St Suite 303, Charleston, South Carolina 29403 5720, USA
    Nat Biotechnol 23:1099-103. 2005
    ..In the present article, we discuss why semantic web technologies, as recommended by the World Wide Web consortium (W3C), expand current data standard technology for biological data representation and management...
  78. ncbi Protein network inference from multiple genomic data: a supervised approach
    Y Yamanishi
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan
    Bioinformatics 20:i363-70. 2004
    ..In this context, the problem of inferring a global protein network for a given organism, using all available genomic data about the organism, is quickly becoming one of the main challenges in current computational biology...
  79. pmc OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI
    Johann Lenffer
    Biotechnology Research Institute and Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia
    Nucleic Acids Res 34:D599-601. 2006
    ..ncbi.nlm.nih.gov/entrez/query.fcgi?db=omia). Curation of OMIA data by researchers working on particular species and disorders has also been enabled...
  80. pmc VisANT: data-integrating visual framework for biological networks and modules
    Zhenjun Hu
    Program in Bioinformatics and Systems Biology, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 33:W352-7. 2005
    ..VisANT is distributed freely via the web at http://visant.bu.edu and can also be downloaded for individual use...
  81. pmc Integrating data from legacy systems using object linking and embedding technology: development of a reporting system for heavy metal poisoning results
    S C Lin
    Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
    J Am Med Inform Assoc 7:357-60. 2000
    ..The system provides a model for a relatively easy solution for laboratories and other groups that need a way to integrate standard data sets that are distributed across legacy systems...
  82. pmc Semantic integration to identify overlapping functional modules in protein interaction networks
    Young Rae Cho
    Department of Computer Science and Engineering, State University of New York, Buffalo, NY, USA
    BMC Bioinformatics 8:265. 2007
    ..The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module detection algorithms...
  83. pmc An integrated approach to the prediction of domain-domain interactions
    Hyunju Lee
    Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
    BMC Bioinformatics 7:269. 2006
    ..The availability of many diverse biological data sets provides an opportunity to discover the underlying domain interactions within protein interactions through an integration of these biological data sets...
  84. pmc PathSys: integrating molecular interaction graphs for systems biology
    Michael Baitaluk
    San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
    BMC Bioinformatics 7:55. 2006
    ....
  85. pmc Human protein reference database--2006 update
    Gopa R Mishra
    Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
    Nucleic Acids Res 34:D411-4. 2006
    ....
  86. pmc GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface
    Alexander Loss
    German Cancer Research Centre, Central Spectroscopic Department, B090 Im Neuenheimer Feld 280, D 69120 Heidelberg, Germany
    Nucleic Acids Res 34:W733-7. 2006
    ..The service is available at www.glycosciences.de/sweetdb/start.php?action=form_shift_estimation...
  87. pmc sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes
    Jonathan Livny
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, 136 Harrison Avenue, Boston, MA 02111, USA
    Nucleic Acids Res 33:4096-105. 2005
    ..Our findings suggest that sRNAPredict can be used to efficiently identify novel sRNAs even in bacteria for which promoter consensus sequences are not available...
  88. pmc The CAP cancer protocols--a case study of caCORE based data standards implementation to integrate with the Cancer Biomedical Informatics Grid
    Jonathan Tobias
    Department of Pathology, University of California at Los Angeles School of Medicine, Los Angeles, CA, USA
    BMC Med Inform Decis Mak 6:25. 2006
    ..The College of American Pathologists (CAP) cancer protocols and checklists are an important reporting standard in pathology, for which no complete electronic data standard is currently available...
  89. ncbi goCluster integrates statistical analysis and functional interpretation of microarray expression data
    Gunnar Wrobel
    Biozentrum and Swiss Institute of Bioinformatics, Klingelbergstrasse 50 70, CH 4056 Basel, Switzerland
    Bioinformatics 21:3575-7. 2005
    ..goCluster extends this concept by providing a modular framework that facilitates integration of statistical and functional microarray data analysis with data interpretation...
  90. pmc Plant protein annotation in the UniProt Knowledgebase
    Michel Schneider
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, University of Geneva, 1211 Geneva 4, Switzerland
    Plant Physiol 138:59-66. 2005
    ....
  91. ncbi Dasty and UniProt DAS: a perfect pair for protein feature visualization
    Philip Jones
    EMBL Outstation European Bioinformatics Institute EBI, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:3198-9. 2005
    ....
  92. ncbi The role of informatics in the coordinated management of biological resources collections
    Paolo Romano
    Bioinformatics and Structural Proteomics, National Cancer Research Institute, Genoa, Italy
    Appl Bioinformatics 4:175-86. 2005
    ....
  93. pmc Integrating protein annotation resources through the Distributed Annotation System
    Páll Isólfur Olason
    Center for Biological Sequence, Analysis BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Nucleic Acids Res 33:W468-70. 2005
    ..ebi.ac.uk/das-srv/uniprot/das) at the European Bioinformatics Institute. Other DAS data sources for protein annotation will be added as they become available...
  94. ncbi LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources
    Rachel Karchin
    Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, CA 94143, USA
    Bioinformatics 21:2814-20. 2005
    ..SNPs that result in amino acid residue changes (nsSNPs) are of critical importance in variation between individuals, including disease and drug sensitivity...
  95. pmc The Diamond STING server
    Goran Neshich
    Núcleo de Bioinformática Estrutural, Embrapa Informática Agropecuária Campinas, Brazil
    Nucleic Acids Res 33:W29-35. 2005
    ..This is the fundamental step toward a more interesting endeavor-the prediction of such residues. Diamond STING is freely accessible at http://sms.cbi.cnptia.embrapa.br and http://trantor.bioc.columbia.edu/SMS...
  96. pmc SOAP-based services provided by the European Bioinformatics Institute
    S Pillai
    European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:W25-8. 2005
    ..Harte, V. Silventoinen, E. Quevillon, S. Robinson, K. Kallio, X. Fustero, P. Patel, P. Jokinen and R. Lopez (2004) Nucleic Acids Res., 32, 3-9]. These services are available free to all users from http://www.ebi.ac.uk/Tools/webservices...
  97. ncbi O3-DPACS Open-Source Image-Data Manager/Archiver and HDW2 Image-Data Display: an IHE-compliant project pushing the e-health integration in the world
    Paolo Inchingolo
    Health Telematics Lab, Open Source Lab and Neuromodelling Lab, DEEI, University of Trieste, Italy
    Comput Med Imaging Graph 30:391-406. 2006
    ....
  98. pmc GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining
    Marco Masseroli
    Bioengineering Department, Politecnico di Milano, I 20133 Milano, Italy
    Nucleic Acids Res 32:W293-300. 2004
    ..GFINDer is available online at http://www.medinfopoli.polimi.it/GFINDer/...
  99. pmc Interactive analysis of systems biology molecular expression data
    Mingwu Zhang
    Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
    BMC Syst Biol 2:23. 2008
    ..The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations...
  100. ncbi A life scientist's gateway to distributed data management and computing: the PathPort/ToolBus framework
    J Dana Eckart
    Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
    OMICS 7:79-88. 2003
    ..On the server-side, we employ web-services. On the client-side, a Java application called ToolBus acts as a client-side "bus" for contacting data and tools and viewing results through a single, consistent user interface...
  101. pmc Update on XplorMed: A web server for exploring scientific literature
    Carolina Perez-Iratxeta
    European Molecular Biology Laboratory, Meyerhofstr 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 31:3866-8. 2003
    ..Here we describe new features added to XplorMed during the last 2 years (http://www.bork.embl-heidelberg.de/xplormed/)...

Research Grants19

  1. OpenLIS: The Development of a Clinical Laboratory Information System Using the Op
    ROGER ALLAN HUBBARD; Fiscal Year: 2010
    ..Such support may include hosting, training, systems integration and other services...
  2. Appalachian Regional Informatics Consortium (ARIC)Planning Project
    Brian Phillips; Fiscal Year: 2005
    ..for a regional electronic medical information system, identifying the required technical infrastructure and systems integration. The completion of specific Aim 1 will result in the establishment of a formal organization and management ..
  3. Automated Medication Transfer Between a Pharmacy Dispensing System and a Mobile D
    Daniel A Theobald; Fiscal Year: 2010
    ..Vecna), a market leader in hospital automation, systems integration, and robotics, sees a tremendous opportunity to extend the benefits of automated pharmacy dispensing ..
  4. Nanotechnology for Multiplexed and Intraoperative Cancer Detection
    Shuming Nie; Fiscal Year: 2010
    ..26, 83-90, 2008);(2) systems integration and implementation for intraoperative cancer detection and visualization, especially by using handheld "..
  5. Systems Engineering Focus on Clinical Informatics
    Ellen J Bass; Fiscal Year: 2012
    ..include human-automation interaction, computational statistics and simulation, risk and decision analysis, systems integration, and optimization and control...
  6. Information Systems Integration--Point-of-Care Delivery
    WYATT TELLIS; Fiscal Year: 2004
    ..Metrics for comparison will be gathered from existing clinical information systems as well as through the applications built for the project. ..
  7. NEW YORK UNIVERSITY MEDICAL CENTER IAIMS PLANNING
    Marc Triola; Fiscal Year: 2007
    ..level via standards-based information management concepts and tools, and consolidate the infrastructure and systems integration already achieved; 4) Develop a plan for a continuous assessment process that will ensure the ..
  8. Sensorimotor learning of facial expressions: A novel intervention for autism
    Marian Stewart Bartlett; Fiscal Year: 2010
    ..The project will also contribute to the understanding of the development and learning of motor skills essential to social functioning. ..
  9. Development of Distributed Electronic Clinical Trials
    NIGEL JOHN; Fiscal Year: 2002
    ..major components, the Clinical Trial Developer, Clinical Trial Administrator, Clinical Trial Database, and Systems Integration. The system utilizes the Internet and handheld mobile devices to provide easy coordination of clinical ..
  10. Holomua Project-Improving Patient Hand-Offs in Hawaii
    CHRISTINE SAKUDA; Fiscal Year: 2004
    ..the use of a Steering Committee, Advisory Committee, and several domain specific work groups, the Holomua Project will create an agreed upon implementation plan that should lead to successful systems integration in the following year.
  11. CENTER FOR THE STUDY OF ISSUES IN PUBLIC MENTAL HEALTH
    Carole Siegel; Fiscal Year: 2003
    ..Seeking Systems Integration studies integration between the mental health system and other health and social systems as well as among ..
  12. Cell Endoscopy with Nanowire Probe
    Peidong Yang; Fiscal Year: 2009
    ..This program will be built upon our extensive expertise in nanostructure synthesis/assembly, systems integration and nanowire based photonics...
  13. Systems integration and substance abuse service delivery
    Heather Larkin; Fiscal Year: 2004
    ..The ultimate impact of increased continuity within the system on the health of the population at large is likely to offer a significant cost-reduction to society. ..
  14. Linking Data Sources from the Autism Genetic Resource Exchange (AGRE) with NDAR
    Clara M Lajonchere; Fiscal Year: 2010
    ..enhance AGRE by bringing together the leaders in clinical phenotyping, data collection, data management, systems integration, and genetic analysis to provide a shared common platform that will facilitate data sharing and scientific ..
  15. OPTIMIZING PROTON THERAPY AT THE LBL MEDICAL ACCELERATOR
    Jose Alonso; Fiscal Year: 1990
    ....
  16. ASCB Summer Meeting: Coordinating the Events of Directed
    Clare Waterman Storer; Fiscal Year: 2005
    This meeting "Systems Integration in Directed Cell Motility" will be sponsored by the American Society of Cell Biology (ASCB)...
  17. Assessment and Referral Technologies in Juvenile Justice
    Faye Taxman; Fiscal Year: 2009
    ..g., placement, service use, retention, and completion) and systems integration (e.g., interagency communication, increase diversity of placements)...
  18. Microscale Instrument Development for Genomic Analysis
    Deirdre Meldrum; Fiscal Year: 2005
    ..module-to-module interconnect problem that is ubiquitous in all integrated microsystems, emphasize overall systems integration, and enable the production of comprehensive data sets...
  19. MAGNETO OPTICAL AMBULATORY EEG RECORDER
    Fernando Casas; Fiscal Year: 2000
    ..Successful porting of consumer technology to the Ambulatory EEG setting will be critical to the systems integration effort during Phase II...