1. 2641-2664 of 2744 « 1 2 ... 108 109 110 111 112 113 114 115 »
    1. A fault model for ontology mapping, alignment, and linking systems.

      Related Articles A fault model for ontology mapping, alignment, and linking systems. Pac Symp Biocomput. 2007;:233-44 Authors: Johnson HL, Cohen KB, Hunter L There has been much work devoted to the mapping, alignment, and linking of ontologies (MALO), but little has been published about how to evaluate systems that do this. A fault model for conducting fine-grained evaluations of MALO systems is proposed, and its application to the system described in Johnson et al. [15] is illustrated. Two judges categorized errors according to the model, and inter-judge agreement was calculated by error category. Overall inter-judge agreement was 98% after ...
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    2. Discovery of protein interaction networks shared by diseases.

      Related Articles Discovery of protein interaction networks shared by diseases. Pac Symp Biocomput. 2007;:76-87 Authors: Sam L, Liu Y, Li J, Friedman C, Lussier YA The study of protein-protein interactions is essential to define the molecular networks that contribute to maintain homeostasis of an organism's body functions. Disruptions in protein interaction networks have been shown to result in diseases in both humans and animals. Monogenic diseases disrupting biochemical pathways such as hereditary coagulopathies (e.g. hemophilia), provided a deep insight in the biochemical pathways of acquired coagulopathies of complex diseases. Indeed, a variety of complex liver diseases can ...
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    3. Semi-automated XML markup of biosystematic legacy literature with the GoldenGATE editor.

      Related Articles Semi-automated XML markup of biosystematic legacy literature with the GoldenGATE editor. Pac Symp Biocomput. 2007;:391-402 Authors: Sautter G, Böhm K, Agosti D Today, digitization of legacy literature is a big issue. This also applies to the domain of biosystematics, where this process has just started. Digitized biosystematics literature requires a very precise and fine grained markup in order to be useful for detailed search, data linkage and mining. However, manual markup on sentence level and below is cumbersome and time consuming. In this paper, we present and evaluate the GoldenGATE editor, which is designed for the ...
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      Mentions: Germany
    4. Processing of inconsistent emotional information: an fMRI study.

      Processing of inconsistent emotional information: an fMRI study. Exp Brain Res. 2007 Dec 20; Authors: Rota G, Veit R, Nardo D, Weiskopf N, Birbaumer N, Dogil G Previous studies investigating the anterior cingulate cortex (ACC) have relied on a number of tasks which involved cognitive control and attentional demands. In this fMRI study, we tested the model that ACC functions as an attentional network in the processing of language. We employed a paradigm that requires the processing of concurrent linguistic information predicting that the cognitive costs imposed by competing trials would engender the activation of ACC. Subjects were confronted with ...
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    5. e-Science and biological pathway semantics.

      Related Articles e-Science and biological pathway semantics. BMC Bioinformatics. 2007;8 Suppl 3:S3 Authors: Luciano JS, Stevens RD BACKGROUND: The development of e-Science presents a major set of opportunities and challenges for the future progress of biological and life scientific research. Major new tools are required and corresponding demands are placed on the high-throughput data generated and used in these processes. Nowhere is the demand greater than in the semantic integration of these data. Semantic Web tools and technologies afford the chance to achieve this semantic integration. Since pathway knowledge is central to much of the scientific research today ...
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    6. AlzPharm: integration of neurodegeneration data using RDF.

      Related Articles AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics. 2007;8 Suppl 3:S4 Authors: Lam HY, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong GT, Liu N, Crasto C, Morse T, Stephens S, Cheung KH BACKGROUND: Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data ...
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    7. LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.

      Related Articles LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics. BMC Bioinformatics. 2007;8 Suppl 3:S5 Authors: Smith AK, Cheung KH, Yip KY, Schultz M, Gerstein MK BACKGROUND: A key abstraction in representing proteomics knowledge is the notion of unique identifiers for individual entities (e.g. proteins) and the massive graph of relationships among them. These relationships are sometimes simple (e.g. synonyms) but are often more complex (e.g. one-to-many relationships in protein family membership). RESULTS: We have built a software system called LinkHub using Semantic Web RDF that manages the graph ...
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    8. Towards Semantic e-Science for Traditional Chinese Medicine.

      Related Articles Towards Semantic e-Science for Traditional Chinese Medicine. BMC Bioinformatics. 2007;8 Suppl 3:S6 Authors: Chen H, Mao Y, Zheng X, Cui M, Feng Y, Deng S, Yin A, Zhou C, Tang J, Jiang X, Wu Z BACKGROUND: Recent advances in Web and information technologies with the increasing decentralization of organizational structures have resulted in massive amounts of information resources and domain-specific services in Traditional Chinese Medicine. The massive volume and diversity of information and services available have made it difficult to achieve seamless and interoperable e-Science for knowledge-intensive disciplines like TCM. Therefore, information integration and service coordination ...
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    9. Evaluation of high-throughput functional categorization of human disease genes.

      Related Articles Evaluation of high-throughput functional categorization of human disease genes. BMC Bioinformatics. 2007;8 Suppl 3:S7 Authors: Chen JL, Liu Y, Sam LT, Li J, Lussier YA BACKGROUND: Biological data that are well-organized by an ontology, such as Gene Ontology, enables high-throughput availability of the semantic web. It can also be used to facilitate high throughput classification of biomedical information. However, to our knowledge, no evaluation has been published on automating classifications of human diseases genes using Gene Ontology. In this study, we evaluate automated classifications of well-defined human disease genes using their Gene Ontology annotations and compared ...
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    10. Text mining and protein annotations: the construction and use of protein description sentences.

      Related Articles Text mining and protein annotations: the construction and use of protein description sentences. Genome Inform. 2006;17(2):121-30 Authors: Krallinger M, Malik R, Valencia A Existing biological knowledge stored as structured database records has been extracted manually by database curators analyzing the scientific literature. Most of this information was derived from sentences which describe biologically relevant aspects of genes and gene products. We introduce the Protein description sentence (Prodisen) corpus, a useful resource for the automatic identification and construction of text-based protein and gene description records using information extraction and text classification techniques. Basic guidelines and criteria ...
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      Mentions: Spain
    11. Style grammars for interactive visualization of architecture.

      Related Articles Style grammars for interactive visualization of architecture. IEEE Trans Vis Comput Graph. 2007 Jul-Aug;13(4):786-97 Authors: Aliaga DG, Rosen PA, Bekins DR Interactive visualization of architecture provides a way to quickly visualize existing or novel buildings and structures. Such applications require both fast rendering and an effortless input regimen for creating and changing architecture using high-level editing operations that automatically fill in the necessary details. Procedural modeling and synthesis is a powerful paradigm that yields high data amplification and can be coupled with fast-rendering techniques to quickly generate plausible details of a scene without much or ...
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    12. GoldMiner: a radiology image search engine.

      Related Articles GoldMiner: a radiology image search engine. AJR Am J Roentgenol. 2007 Jun;188(6):1475-8 Authors: Kahn CE, Thao C OBJECTIVE: We sought to create an Internet-based search engine to retrieve images from a large collection of figures published in peer-reviewed journals. CONCLUSION: The GoldMiner search engine provides easy, rapid access to a large library of images and their associated text, and it is freely available for use on the Internet. PMID: 17515364 [PubMed - indexed for MEDLINE]
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      Mentions: Milwaukee Wisconsin
    13. Medical informatics and bioinformatics: a bibliometric study.

      Related Articles Medical informatics and bioinformatics: a bibliometric study. IEEE Trans Inf Technol Biomed. 2007 May;11(3):237-43 Authors: Bansard JY, Rebholz-Schuhmann D, Cameron G, Clark D, van Mulligen E, Beltrame E, Barbolla E, Martin-Sanchez Fdel H, Milanesi L, Tollis I, van der Lei J, Coatrieux JL This paper reports on an analysis of the bioinformatics and medical informatics literature with the objective to identify upcoming trends that are shared among both research fields to derive benefits from potential collaborative initiatives for their future. Our results present the main characteristics of the two fields and show that these domains ...
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    14. A novel method of language modeling for automatic captioning in TC video teleconferencing.

      Related Articles A novel method of language modeling for automatic captioning in TC video teleconferencing. IEEE Trans Inf Technol Biomed. 2007 May;11(3):332-7 Authors: Zhang X, Zhao Y, Schopp L We are developing an automatic captioning system for teleconsultation video teleconferencing (TC-VTC) in telemedicine, based on large vocabulary conversational speech recognition. In TC-VTC, doctors' speech contains a large number of infrequently used medical terms in spontaneous styles. Due to insufficiency of data, we adopted mixture language modeling, with models trained from several datasets of medical and nonmedical domains. This paper proposes novel modeling and estimation methods for the ...
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      Mentions: Columbia
    15. Prediction of Gpcr-g protein coupling specificity using features of sequences and biological functions.

      Related Articles Prediction of GPCR-G protein coupling specificity using features of sequences and biological functions. Genomics Proteomics Bioinformatics. 2006 Nov;4(4):238-44 Authors: Ono T, Hishigaki H Understanding the coupling specificity between G protein-coupled receptors (GPCRs) and specific classes of G proteins is important for further elucidation of receptor functions within a cell. Increasing information on GPCR sequences and the G protein family would facilitate prediction of the coupling properties of GPCRs. In this study, we describe a novel approach for predicting the coupling specificity between GPCRs and G proteins. This method uses not only GPCR sequences but also ...
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    16. Clustering microarray-derived gene lists through implicit literature relationships.

      Related Articles Clustering microarray-derived gene lists through implicit literature relationships. Bioinformatics. 2007 Aug 1;23(15):1995-2003 Authors: Burkart MF, Wren JD, Herschkowitz JI, Perou CM, Garner HR MOTIVATION: Microarrays rapidly generate large quantities of gene expression information, but interpreting such data within a biological context is still relatively complex and laborious. New methods that can identify functionally related genes via shared literature concepts will be useful in addressing these needs. RESULTS: We have developed a novel method that uses implicit literature relationships (concepts related via shared, intermediate concepts) to cluster related genes. Genes are evaluated for implicit connections within ...
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    17. BioText Search Engine: beyond abstract search.

      Related Articles BioText Search Engine: beyond abstract search. Bioinformatics. 2007 Aug 15;23(16):2196-7 Authors: Hearst MA, Divoli A, Guturu H, Ksikes A, Nakov P, Wooldridge MA, Ye J The BioText Search Engine is a freely available Web-based application that provides biologists with new ways to access the scientific literature. One novel feature is the ability to search and browse article figures and their captions. A grid view juxtaposes many different figures associated with the same keywords, providing new insight into the literature. An abstract/title search and list view shows at a glance many of the figures associated ...
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    18. Interpretation of spatial language in a map navigation task.

      Related Articles Interpretation of spatial language in a map navigation task. IEEE Trans Syst Man Cybern B Cybern. 2007 Jun;37(3):667-79 Authors: Levit M, Roy D We have developed components of an automated system that understands and follows navigational instructions. The system has prior knowledge of the geometry and landmarks of specific maps. This knowledge is exploited to infer complex paths through maps based on natural language descriptions. The approach is based on an analysis of verbal commands in terms of elementary semantic units that are composed to generate a probability distribution over possible spatial paths in a ...
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    19. Electronic medical records for clinical research: application to the identification of heart failure.

      Related Articles Electronic medical records for clinical research: application to the identification of heart failure. Am J Manag Care. 2007 Jun;13(6 Part 1):281-8 Authors: Pakhomov S, Weston SA, Jacobsen SJ, Chute CG, Meverden R, Roger VL OBJECTIVE: To identify patients with heart failure (HF) by using language contained in the electronic medical record (EMR). METHODS: We validated 2 methods of identifying HF through the EMR, which offers transcription of clinical notes within 24 hours or less of the encounter. The first method was natural language processing (NLP) of the EMR text. The second method was predictive modeling ...
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    20. Identification of trauma patients at a level 1 trauma center utilizing natural language processing.

      Related Articles Identification of trauma patients at a level 1 trauma center utilizing natural language processing. J Trauma Nurs. 2007 Apr-Jun;14(2):79-83 Authors: Day S, Christensen LM, Dalto J, Haug P Trauma centers use trauma registries to collect information on injured patients they receive. The information is used for evaluation of care rendered, research, system and process improvement, and evaluation of injury prevention programs. Identification of patients qualifying for inclusion in registries can be problematic. Searching for those who meet inclusion criteria is often time consuming and inefficient. This has changed at a Salt Lake City trauma center ...
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      Mentions: Salt Lake City
    21. Building co-operative bibliographic databases in European bioethics: a contribution from EU New Member States.

      Related Articles Building co-operative bibliographic databases in European bioethics: a contribution from EU New Member States. Comput Methods Programs Biomed. 2007 Aug;87(2):123-31 Authors: Dimec J, Leskosek B The paper presents a web-based application, developed as a part of the Eurethnet database network, which is being used by project partners from EU New Member States to collect bibliographic records from bioethics domains. The application development was focused mainly on records compatibility with other Eurethnet databases, support for all European character sets, minimalisation of network traffic, and security issues. The time window available for the system development was very ...
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    22. ChemDB update--full-text search and virtual chemical space.

      Related Articles ChemDB update--full-text search and virtual chemical space. Bioinformatics. 2007 Sep 1;23(17):2348-51 Authors: Chen JH, Linstead E, Swamidass SJ, Wang D, Baldi P ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. The data is publicly available over the web for download and for targeted searches using a variety of powerful methods. The chemical data includes predicted or experimentally determined physicochemical properties, such as 3D structure, melting temperature and solubility ...
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    23. State-of-the-art anonymisation of medical records using an iterative machine learning framework.

      Related Articles State-of-the-art anonymisation of medical records using an iterative machine learning framework. J Am Med Inform Assoc. 2007 Jun 28; Authors: Szarvas G, Farkas R, Busa-Fekete R OBJECTIVE The anonymisation of medical records is of great importance in the human life sciences because a de-identified text can be made publicly available for non-hospital researchers as well, to facilitate research on human diseases. Here the authors have developed a de-identification model that can successfully remove personal health information (PHI) from discharge records to make them conform to the guidelines of the Health Information Portability and Accountability Act. DESIGN We introduce ...
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    2641-2664 of 2744 « 1 2 ... 108 109 110 111 112 113 114 115 »
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