Summary: Computerized compilations of information units (text, sound, graphics, and/or video) interconnected by logical nonlinear linkages that enable users to follow optimal paths through the material and also the systems used to create and display this information. (From Thesaurus of ERIC Descriptors, 1994)

Top Publications

  1. Wren J. 404 not found: the stability and persistence of URLs published in MEDLINE. Bioinformatics. 2004;20:668-72 pubmed
    ..Out of the 306 journals with a URL published in an abstract, Bioinformatics published the most (12% of total). URL database and program available by request. ..
  2. Bearman M, Kidd M, Cesnik B. Methodology for developing educational hypermedia systems. Stud Health Technol Inform. 1998;52 Pt 2:720-6 pubmed
    b>Hypermedia has the potential to greatly enhance teaching. It can, however, be difficult to develop hyperdocuments which provide medical students with the full benefit of the technology...
  3. Hucka M, Finney A, Sauro H, Bolouri H, Doyle J, Kitano H, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003;19:524-31 pubmed
    ..The specification of SBML Level 1 is freely available from http://www.sbml.org/ ..
  4. Taylor C, Paton N, Garwood K, Kirby P, Stead D, Yin Z, et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol. 2003;21:247-54 pubmed
    ..These make explicit what data might be most usefully captured about proteomics experiments and provide complementary routes toward the implementation of a proteome repository. ..
  5. Li F, Li M, Xiao Z, Zhang P, Li J, Chen Z. Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice. BMC Bioinformatics. 2006;7:13 pubmed
    ..The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/. ..
  6. Carver T, Bleasby A. The design of Jemboss: a graphical user interface to EMBOSS. Bioinformatics. 2003;19:1837-43 pubmed
    ..uk.embnet.org/Software/EMBOSS/, ftp://ftp.uk.embnet.org/pub/EMBOSS/. Registered HGMP-RC users can access an installed server from: http://www.uk.embnet.org/Software/EMBOSS/Jemboss/ ..
  7. Saeed A, Sharov V, White J, Li J, Liang W, Bhagabati N, et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003;34:374-8 pubmed
  8. DiCarlo J, Pastor X, Markovitz B. The shadow uniform resource locator: standardizing citations of electronically published materials. J Am Med Inform Assoc. 2000;7:149-51 pubmed
    ..Utilization of the "shadow" URL would bring us one step closer to truly universal resource locators. ..
  9. Carter K, Bellgard M. MASV--Multiple (BLAST) Annotation System Viewer. Bioinformatics. 2003;19:2313-5 pubmed
    ..This provides a unique capability for the user to conduct further bioinformatics analysis from the information obtained. http://cbbc.murdoch.edu.au/projects/masv/ ..

More Information


  1. Johnson J, Stromvik M, Silverstein K, Crow J, Shoop E, Retzel E. TableView: portable genomic data visualization. Bioinformatics. 2003;19:1292-3 pubmed
    ..umn.edu/software/java/apps/TableView/. ..
  2. Jamison D. Open bioinformatics. Bioinformatics. 2003;19:679-80 pubmed
  3. Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, Tomita M. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics. 2003;19:305-6 pubmed
    ..Both Windows and Linux versions are available. From http://www.g-language.org/ under GNU General Public License. CD-ROMs are distributed freely in major conferences. ..
  4. de Beer R, Coron A, Graveron Demilly D, Lethmate R, Nastase S, van Ormondt D, et al. MR image reconstruction algorithms for sparse k-space data: a Java-based integration. MAGMA. 2002;15:18-26 pubmed
  5. Shiffman R, Agrawal A, Deshpande A, Gershkovich P. An approach to guideline implementation with GEM. Stud Health Technol Inform. 2001;84:271-5 pubmed
    ..goal is to devise a system that can be applied by local clinical domain experts, quality assurance experts, and information systems programmers without requiring trained informaticians and knowledge engineers to serve as intermediaries ..
  6. Yang C, Granite S, Van Eyk J, Winslow R. MASCOT HTML and XML parser: an implementation of a novel object model for protein identification data. Proteomics. 2006;6:5688-93 pubmed
    ..The source code is freely available at http://www.ccbm.jhu.edu and the program uses only free and open-source Java libraries. ..
  7. Shimayoshi T, Amano A, Matsuda T. A generic representation format of physiological experimental protocols for computer simulation using ontology. Conf Proc IEEE Eng Med Biol Soc. 2007;2007:382-5 pubmed
    ..This feature facilitates the efficient simulation for verifications, comparisons and utilizations of physiological models. ..
  8. Dao T, Marin F, Ho Ba Tho M. Ontology of the musculo-skeletal system of the lower limbs. Conf Proc IEEE Eng Med Biol Soc. 2007;2007:386-9 pubmed
    ..Firstly, the context of research is presented, then the methods used to create our ontology. Preliminary results of modeling and applications will be addressed. ..
  9. Schleyer T, Forrest J. Methods for the design and administration of web-based surveys. J Am Med Inform Assoc. 2000;7:416-25 pubmed
    ..Web-based surveys can significantly reduce turnaround time and cost compared with mail surveys and may enhance survey item completion rates. ..
  10. Kim K, Yang J, Choi J, Yang K, Ha Y. A semantic inheritance/inverse-inheritance mechanism for systematic bio-ontology construction. Conf Proc IEEE Eng Med Biol Soc. 2007;2007:398-401 pubmed
    ..In the system, the mechanism is seamlessly applied to the ontology by well defined graphic notations based on OWL. OWL is adopted to fully express the subtle semantics inherently buried in the bio-ontology. ..
  11. Maier D, Wymore F, Sherlock G, Ball C. The XBabelPhish MAGE-ML and XML translator. BMC Bioinformatics. 2008;9:28 pubmed publisher
    ..More generally, it can be used to transform most XML files, including very large ones that exceed the capacity of most XML tools. ..
  12. Retrouvey J, Finkelstein A. Blended learning in orthodontic diagnosis: an interactive approach. J Can Dent Assoc. 2008;74:645-9 pubmed
    ..The goal is to bridge the gap between theoretical knowledge and the practical skills needed to be a successful dentist. ..
  13. Naumann A, Wechsung I, Krems J. How to support learning from multiple hypertext sources. Behav Res Methods. 2009;41:639-46 pubmed publisher
    ..No effect was shown for the type of texts available. ..
  14. Gouze A, Antonini M, Barlaud M, Macq B. Design of signal-adapted multidimensional lifting scheme for lossy coding. IEEE Trans Image Process. 2004;13:1589-603 pubmed
    ..The prediction step is designed in order to minimize the variance of the signal, and the update step is designed in order to minimize a reconstruction error. Application for lossy compression shows the performances of the method. ..
  15. Dameron O, Gibaud B, Morandi X. Numeric and symbolic knowledge representation of cerebral cortex anatomy: methods and preliminary results. Surg Radiol Anat. 2004;26:191-7 pubmed
    ..Demonstration software performs a mapping between the numeric and the symbolic aspects for browsing the knowledge base. ..
  16. Huang L, Chu H, Lien C, Hsiao C, Kao T. Embedding a hiding function in a portable electronic health record for privacy preservation. J Med Syst. 2010;34:313-20 pubmed
    ..The effects of executing the hiding function would be the same as through de-identification or anonymization process. ..
  17. Eminaga O, Hinkelammert R, Semjonow A, Neumann J, Abbas M, Koepke T, et al. Clinical map document based on XML (cMDX): document architecture with mapping feature for reporting and analysing prostate cancer in radical prostatectomy specimens. BMC Med Inform Decis Mak. 2010;10:71 pubmed publisher
    ..54% of PCa showed a multifocal growth pattern. cMDX can be used for routine histopathological reporting of radical prostatectomy specimens and provide data for scientific analysis. ..
  18. Spitzer M, Fuellen G, Cullen P, Lorkowski S. VisCoSe: visualization and comparison of consensus sequences. Bioinformatics. 2004;20:433-5 pubmed
    ..Furthermore, VisCoSe allows visualization of chemical properties of amino acids. ..
  19. Schatz B. Information retrieval in digital libraries: bringing search to the net. Science. 1997;275:327-34 pubmed
    ..By 2010, the visions will be realized, with concept search enabling semantic retrieval across large collections. ..
  20. Tjandra D, Wong S, Shen W, Pulliam B, Yu E, Esserman L. An XML message broker framework for exchange and integration of microarray data. Bioinformatics. 2003;19:1844-5 pubmed
    ..Open source software will be available from SourceForge (http://sourceforge.net/projects/microsoap/). ..
  21. Wiesman F, Hasman A, van den Herik H. Information retrieval: an overview of system characteristics. Int J Med Inform. 1997;47:5-26 pubmed
    ..Finally, the relevance of IR systems for the World Wide Web is established. ..
  22. Bental D, Cawsey A, Jones R. Patient information systems that tailor to the individual. Patient Educ Couns. 1999;36:171-80 pubmed
    ..We review some of the techniques used in developing tailored systems, and consider the evidence to date as to their efficacy. ..
  23. Frankewitsch T, Prokosch U. Navigation in medical Internet image databases. Med Inform Internet Med. 2001;26:1-15 pubmed
  24. Douglass J, Becker S, Subhani S, Mitri W. A web-based cleft lip and palate registry. Am J Orthod Dentofacial Orthop. 2002;121:424-5 pubmed
  25. Chiang S, Chen C. Effects of picture amount on preference, balance, and dynamic feel of Web pages. Percept Mot Skills. 2012;114:378-90 pubmed
    ..The research findings can serve as the basis for the application of design guidelines for future web page interface design. ..
  26. Philippi S. Light-weight integration of molecular biological databases. Bioinformatics. 2004;20:51-7 pubmed
    ..Additional files and modified components are available upon request from the author. ..
  27. Firriolo F, Levy B. Computer expert system for the histopathologic diagnosis of salivary gland neoplasms. Oral Surg Oral Med Oral Pathol Oral Radiol Endod. 1996;82:179-86 pubmed
    ..The knowledge and experience gained in the development and testing of the expert system described in this study have demonstrated the validity of histopathologic diagnostic expert systems in a selected area of oral pathology. ..
  28. Eysenbach G, Bauer J, Sager A, Bittorf A, Simon M, Diepgen T. An international dermatological image atlas on the WWW: practical use for undergraduate and continuing medical education, patient education and epidemiological research. Stud Health Technol Inform. 1998;52 Pt 2:788-92 pubmed
    ..We conclude that an online image atlas has multiple educational, clinical and research applications. ..
  29. Spallek H, Schleyer T. Internet basics. J Am Coll Dent. 1999;66:6-15 pubmed
    ..The World Wide Web and information about finding material are also presented. Emphasis is placed on defining basic terms and providing addresses, resources, and help. ..
  30. Shiffman R, Karras B, Agrawal A, Chen R, Marenco L, Nath S. GEM: a proposal for a more comprehensive guideline document model using XML. J Am Med Inform Assoc. 2000;7:488-98 pubmed
    ..Use of XML contributes to a flexible, comprehensible, shareable, and reusable knowledge representation that is both readable by human beings and processible by computers. ..
  31. Ruminski J. Representation of thermal infrared imaging data in the DICOM using XML configuration files. Conf Proc IEEE Eng Med Biol Soc. 2007;2007:258-62 pubmed
    ..The proposed solution works fast and requires minimal number of user interactions. The XML configuration file enables to compose a set of attributes for any source file format of thermal imaging camera. ..
  32. Thollesson M. LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences. Bioinformatics. 2004;20:416-8 pubmed
    ..The assignment to rate categories in lieu of a phylogeny can be done using Shannon-Wiener index as a crude token for relative rate. ..
  33. Shattuck D, Rapela J, Asma E, Chatzioannou A, Qi J, Leahy R. Internet2-based 3D PET image reconstruction using a PC cluster. Phys Med Biol. 2002;47:2785-95 pubmed
    ..We report on the speed-up factors using the Beowulf approach and the impacts of communication latencies in the local cluster network and the network connection between the user's machine and our PC cluster. ..
  34. Tsimhoni O, Smith D, Green P. Address entry while driving: speech recognition versus a touch-screen keyboard. Hum Factors. 2004;46:600-10 pubmed
    ..Applications of this research include the design of in-vehicle navigation systems as well as other systems requiring significant driver input, such as E-mail, the Internet, and text messaging. ..
  35. Li P, Allebach J. Tone-dependent error diffusion. IEEE Trans Image Process. 2004;13:201-15 pubmed
    ..We also propose an error diffusion system with parallel scan that uses variable weight locations to reduce worms. ..
  36. Salmerón L, Kintsch W, Cañas J. Reading strategies and prior knowledge in learning from hypertext. Mem Cognit. 2006;34:1157-71 pubmed
    ..Discussion focuses on resolving inconsistencies in the literature concerning whether or not hypertext supports better comprehension than does traditional linear texts. ..
  37. Ducla Soares L, Pereira F. Adaptive shape and texture intra refreshment schemes for improved error resilience in object-based video coding. IEEE Trans Image Process. 2004;13:662-76 pubmed
    ..These schemes allow to adaptively determine when the shape and texture of the various video objects in a scene should be refreshed in order to maximize the decoded video quality for a certain total bit rate. ..
  38. Lovis C, Baud R, Scherrer J. Internet integrated in the daily medical practice within an electronic patient record. Comput Biol Med. 1998;28:567-79 pubmed
  39. Wagner C, Gebremichael M, Taylor M, Soltys M. Disappearing act: decay of uniform resource locators in health care management journals. J Med Libr Assoc. 2009;97:122-30 pubmed publisher
    ..In addition to using website archiving tools like WebCite, publishers should require authors to both keep copies of Internet-based information they used and deposit copies of data with the publishers. ..
  40. Robinson P, Wollstein A, Böhme U, Beattie B. Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology. Bioinformatics. 2004;20:979-81 pubmed
    ..The application generates one HTML page with listings of the frequencies of explicit and implicit Gene Ontology annotations for each cluster, and separate, linked pages with listings of explicit annotations for each gene in a cluster. ..
  41. Frantsve Hawley J, Jeske A. The American Dental Association's Center for Evidence-Based Dentistry: a critical resource for 21st century dental practice. Tex Dent J. 2011;128:201-5 pubmed
  42. Toddenroth D, Dugas M, Frankewitsch T. Integrating personalized medical test contents with XML and XSL-FO. BMC Med Educ. 2011;11:8 pubmed publisher
    ..The automatic generation of personalized MCQ test sheets is feasible using freely available open source software libraries, and can be efficiently deployed on a faculty-wide scale. ..
  43. Lahaie U. Is nursing ready for WebQuests?. J Nurs Educ. 2008;47:567-70 pubmed
    ..They are based on solid theoretical foundations and promote critical thinking, inquiry, and problem solving. There is a role for WebQuests in nursing education. A WebQuest example is described in this article. ..
  44. Sun H, Li M, Xu Y. MOLVIE: an interactive visualization environment for molecular structures. Comput Methods Programs Biomed. 2003;71:85-90 pubmed
    ..Being developed in JAVA, MOLVIE is platform-independent. Moreover, it may run on a webpage as an applet for remote users. MOLVIE is available at http://www.cs.ucsb.edu/~mli/Bioinf/software/index.html. ..
  45. Spallek H. Adaptive hypermedia: a new paradigm for educational software. Adv Dent Res. 2003;17:38-42 pubmed
    ..Adaptive hypermedia (AH) is an emerging field in education research which investigates how computer systems can overcome this ..
  46. Wang Z, Bovik A, Sheikh H, Simoncelli E. Image quality assessment: from error visibility to structural similarity. IEEE Trans Image Process. 2004;13:600-12 pubmed
  47. Basu M. SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services. Bioinformatics. 2001;17:577-8 pubmed
    ..It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. ..
  48. Politou E, Pavlidis G, Chamzas C. JPEG2000 and dissemination of cultural heritage over the Internet. IEEE Trans Image Process. 2004;13:293-301 pubmed
  49. Whitbeck C. Desirable attributes of public educational websites. Sci Eng Ethics. 2005;11:463-76 pubmed
    ..as provision of annotation for all links and the use of annotated links to give the user alternate ways of ordering and organizing content, are important for making full use of the educational possibilities of hypermedia for websites.
  50. Ghedira C, Maret P, Fayn J, Rubel P. Adaptive user interface customization through browsing knowledge capitalization. Int J Med Inform. 2002;68:219-28 pubmed
    b>Hypermedia data browsing is a mean for improving information access...
  51. Nguyen T, Liu C, Gershon E, McMahon F. Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers. Bioinformatics. 2004;20:439-43 pubmed
    ..While limited to public databases that provide web-based access to allele frequencies, Frequency Finder provides a single, user-friendly interface for retrieving allele frequencies for large batches of SNPs from multiple data sources. ..
  52. Lewis P, Martinez K, Abas F, Fauzi M, Chan S, Addis M, et al. An integrated content and metadata based retrieval system for art. IEEE Trans Image Process. 2004;13:302-13 pubmed
    ..We show how effective retrieval results can be achieved by real end-users consisting of major museums and galleries, accessing the distributed but integrated digital collections. ..
  53. Sandars J, Homer M, Walsh K, Rutherford A. Don't forget the learner: an essential aspect for developing effective hypermedia online learning in continuing medical education. Educ Prim Care. 2012;23:90-4 pubmed
    There is increasing use of hypermedia online learning in continuing medical education (CME) that presents the learner with a wide range of different learning resources, requiring the learner to use self-regulated learning (SRL) skills...