1. 2593-2616 of 2664 « 1 2 ... 106 107 108 109 110 111 »
    1. Learning to extract relations for protein annotation.

      Related Articles Learning to extract relations for protein annotation. Bioinformatics. 2007 Jul 1;23(13):i256-63 Authors: Kim JH, Mitchell A, Attwood TK, Hilario M MOTIVATION: Protein annotation is a task that describes protein X in terms of topic Y. Usually, this is constructed using information from the biomedical literature. Until now, most of literature-based protein annotation work has been done manually by human annotators. However, as the number of biomedical papers grows ever more rapidly, manual annotation becomes more difficult, and there is increasing need to automate the process. Recently, information extraction (IE) has been used to address this ...
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    2. Negation of protein-protein interactions: analysis and extraction.

      Related Articles Negation of protein-protein interactions: analysis and extraction. Bioinformatics. 2007 Jul 1;23(13):i424-32 Authors: Sanchez-Graillet O, Poesio M MOTIVATION: Negative information about protein-protein interactions--from uncertainty about the occurrence of an interaction to knowledge that it did not occur--is often of great use to biologists and could lead to important discoveries. Yet, to our knowledge, no proposals focusing on extracting such information have been proposed in the text mining literature. RESULTS: In this work, we present an analysis of the types of negative information that is reported, and a heuristic-based system using a full dependency parser to extract ...
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    3. Identification of new drug classification terms in textual resources.

      Related Articles Identification of new drug classification terms in textual resources. Bioinformatics. 2007 Jul 1;23(13):i264-72 Authors: Kolárik C, Hofmann-Apitius M, Zimmermann M, Fluck J Knowledge about biological effects of small molecules helps in the understanding of biological processes and supports the development of new therapeutic agents. DrugBank is a high quality database providing such information about drugs that contains annotation of drug effects and classification of therapeutic effects. However, to broaden the scope of such a database in classifying and annotating drugs, systems for automatic extraction of classification terms and the corresponding annotation of drugs are ...
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    4. Annotating gene function by combining expression data with a modular gene network.

      Related Articles Annotating gene function by combining expression data with a modular gene network. Bioinformatics. 2007 Jul 1;23(13):i468-78 Authors: Shiga M, Takigawa I, Mamitsuka H MOTIVATION: A promising and reliable approach to annotate gene function is clustering genes not only by using gene expression data but also literature information, especially gene networks. RESULTS: We present a systematic method for gene clustering by combining these totally different two types of data, particularly focusing on network modularity, a global feature of gene networks. Our method is based on learning a probabilistic model, which we call a hidden modular random ...
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    5. Using contextual and lexical features to restructure and validate the classification of biomedical concepts.

      Related Articles Using contextual and lexical features to restructure and validate the classification of biomedical concepts. BMC Bioinformatics. 2007;8:264 Authors: Fan JW, Xu H, Friedman C BACKGROUND: Biomedical ontologies are critical for integration of data from diverse sources and for use by knowledge-based biomedical applications, especially natural language processing as well as associated mining and reasoning systems. The effectiveness of these systems is heavily dependent on the quality of the ontological terms and their classifications. To assist in developing and maintaining the ontologies objectively, we propose automatic approaches to classify and/or validate their semantic categories. In previous ...
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      Mentions: New York Xu H
    6. Semantic integration to identify overlapping functional modules in protein interaction networks.

      Related Articles Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics. 2007;8:265 Authors: Cho YR, Hwang W, Ramanathan M, Zhang A BACKGROUND: The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module ...
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    7. Automating document classification for the Immune Epitope Database.

      Related Articles Automating document classification for the Immune Epitope Database. BMC Bioinformatics. 2007;8:269 Authors: Wang P, Morgan AA, Zhang Q, Sette A, Peters B BACKGROUND: The Immune Epitope Database contains information on immune epitopes curated manually from the scientific literature. Like similar projects in other knowledge domains, significant effort is spent on identifying which articles are relevant for this purpose. RESULTS: We here report our experience in automating this process using Naïve Bayes classifiers trained on 20,910 abstracts classified by domain experts. Improvements on the basic classifier performance were made by a) utilizing information stored in ...
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    8. Compression of annotated nucleotide sequences.

      Related Articles Compression of annotated nucleotide sequences. IEEE/ACM Trans Comput Biol Bioinform. 2007 Jul-Sep;4(3):447-57 Authors: Korodi G, Tabus I This article introduces an algorithm for the lossless compression of DNA files, which contain annotation text besides the nucleotide sequence. First a grammar is specifically designed to capture the regularities of the annotation text. A revertible transformation uses the grammar rules in order to equivalently represent the original file as a collection of parsed segments and a sequence of decisions made by the grammar parser. This decomposition enables the efficient use of state-of-the-art encoders for processing the ...
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      Mentions: Finland Tampere
    9. A field theoretical approach to medical natural language processing.

      Related Articles A field theoretical approach to medical natural language processing. IEEE Trans Inf Technol Biomed. 2007 Jul;11(4):364-75 Authors: Taira RK, Bashyam V, Kangarloo H A parser for medical free text reports has been developed that is based on a chemistry/physics inspired "field theory" for word-word sentence-level dependencies. The transition from the linguistic world to the world of interacting particles with potential energies is guided by a psycholinguistics thought experiment related to the amount of "work" required to bring a reference word into an anchored configuration of words. Calibration experiments involving four and five grams were ...
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    10. Management and analysis of genomic functional and phenotypic controlled annotations to support biomedical investigation and practice.

      Related Articles Management and analysis of genomic functional and phenotypic controlled annotations to support biomedical investigation and practice. IEEE Trans Inf Technol Biomed. 2007 Jul;11(4):376-85 Authors: Masseroli M The growing available genomic information provides new opportunities for novel research approaches and original biomedical applications that can provide effective data management and analysis support. In fact, integration and comprehensive evaluation of available controlled data can highlight information patterns leading to unveil new biomedical knowledge. Here, we describe Genome Function INtegrated Discover (GFINDer), a Web-accessible three-tier multidatabase system we developed to automatically enrich lists of user-classified genes with several ...
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    11. Modeling drug mechanism knowledge using evidence and truth maintenance.

      Related Articles Modeling drug mechanism knowledge using evidence and truth maintenance. IEEE Trans Inf Technol Biomed. 2007 Jul;11(4):386-97 Authors: Boyce RD, Collins C, Horn J, Kalet I To protect the safety of patients, it is vital that researchers find methods for representing drug mechanism knowledge that support making clinically relevant drug-drug interaction (DDI) predictions. Our research aims to identify the challenges of representing and reasoning with drug mechanism knowledge and to evaluate potential informatics solutions to these challenges through the process of developing a knowledge-based system capable of predicting clinically relevant DDIs that occur via metabolic mechanisms ...
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    12. Psychiatric consultation record retrieval using scenario-based representation and multilevel mixture model.

      Related Articles Psychiatric consultation record retrieval using scenario-based representation and multilevel mixture model. IEEE Trans Inf Technol Biomed. 2007 Jul;11(4):415-27 Authors: Yu LC, Wu CH, Jang FL Psychiatric consultation record retrieval attempts to help people to efficiently and effectively locate the consultation records relevant to their depressive problems. Consultation records can also make people aware that they are not alone, because many individuals have suffered from the same or similar problems. Additionally, people can understand how to alleviate their depressive symptoms according to recommendations from health professionals. To achieve this goal, this paper proposes the use of ...
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    13. An Infrastructure For Application Integration And Knowledge Discovery In Bioinformatics.

      Related Articles BAAQ: an infrastructure for application integration and knowledge discovery in bioinformatics. IEEE Trans Inf Technol Biomed. 2007 Jul;11(4):428-34 Authors: Gong X, Nakamura K, Yu H, Yura K, Go N The emerging grid computing technologies enable bioinformatics scientists to conduct their researches in a virtual laboratory, in which they share public databases, computational tools as well as their analysis workflows. However, the development of grid applications is still a nightmare for general bioinformatics scientists, due to the lack of grid programming environments, standards and high-level services. Here, we present a system, which we named Bioinformatics: Ask ...
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    14. PepBank--a database of peptides based on sequence text mining and public peptide data sources.

      Related Articles PepBank--a database of peptides based on sequence text mining and public peptide data sources. BMC Bioinformatics. 2007;8:280 Authors: Shtatland T, Guettler D, Kossodo M, Pivovarov M, Weissleder R BACKGROUND: Peptides are important molecules with diverse biological functions and biomedical uses. To date, there does not exist a single, searchable archive for peptide sequences or associated biological data. Rather, peptide sequences still have to be mined from abstracts and full-length articles, and/or obtained from the fragmented public sources. DESCRIPTION: We have constructed a new database (PepBank), which at the time of writing contains a total of ...
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    15. Automatic reconstruction of a bacterial regulatory network using Natural Language Processing.

      Related Articles Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinformatics. 2007;8:293 Authors: Rodríguez-Penagos C, Salgado H, Martínez-Flores I, Collado-Vides J BACKGROUND: Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data. In this paper we report the implementation of a state-of-the-art Natural Language Processing system that creates computer-readable networks of regulatory interactions directly from different collections of abstracts and full-text papers. Our major aim is to understand how automatic annotation using Text-Mining techniques can complement manual curation of biological databases. We implemented a rule-based ...
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    16. Text extraction and document image segmentation using matched wavelets and MRF model.

      Related Articles Text extraction and document image segmentation using matched wavelets and MRF model. IEEE Trans Image Process. 2007 Aug;16(8):2117-28 Authors: Kumar S, Gupta R, Khanna N, Chaudhury S, Joshi SD In this paper, we have proposed a novel scheme for the extraction of textual areas of an image using globally matched wavelet filters. A clustering-based technique has been devised for estim ating globally matched wavelet filters using a collection of groundtruth images. We have extended our text extraction scheme for the segmentation of document images into text, background, and picture components (which include graphics and continuous ...
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    17. Using temporal cohesion to predict temporal coherence in narrative and expository texts.

      Related Articles Using temporal cohesion to predict temporal coherence in narrative and expository texts. Behav Res Methods. 2007 May;39(2):212-23 Authors: Duran ND, McCarthy PM, Graesser AC, McNamara DS We investigated the linguistic features of temporal cohesion that distinguish variations in temporal coherence. In an analysis of 150 texts, experts rated temporal coherence on three continuous scale measures designed to capture unique representations of time. Coh-Metrix, a computational tool that assesses textual cohesion, correctly predicted the human ratings with five features of temporal cohesion. The correlations between predicted and actual scores were all statistically significant. In a complementary ...
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    18. A multiagent system for retrieving bioinformatics publications from web sources.

      Related Articles A multiagent system for retrieving bioinformatics publications from web sources. IEEE Trans Nanobioscience. 2007 Jun;6(2):104-9 Authors: Armano G, Manconi A, Vargiu E Due to the enormous amount of information available on the Internet, extracting and classifying it has become one of the most important tasks. This principle is valid also while searching for scientific publications. This paper describes a system able to retrieve scientific publications from the Web throughout a text categorization process. To this end, a generic multiagent architecture has been customized according to the requirements imposed by the specific task. Experiments have been ...
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    19. Learning string similarity measures for gene/protein name dictionary look-up using logistic regression.

      Related Articles Learning string similarity measures for gene/protein name dictionary look-up using logistic regression. Bioinformatics. 2007 Oct 15;23(20):2768-74 Authors: Tsuruoka Y, McNaught J, Tsujii J, Ananiadou S MOTIVATION: One of the bottlenecks of biomedical data integration is variation of terms. Exact string matching often fails to associate a name with its biological concept, i.e. ID or accession number in the database, due to seemingly small differences of names. Soft string matching potentially enables us to find the relevant ID by considering the similarity between the names. However, the accuracy of soft matching highly depends on ...
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    20. High-dimensional unsupervised selection and estimation of a finite generalized Dirichlet mixture model based on minimum message length.

      Related Articles High-dimensional unsupervised selection and estimation of a finite generalized Dirichlet mixture model based on minimum message length. IEEE Trans Pattern Anal Mach Intell. 2007 Oct;29(10):1716-31 Authors: Bouguila N, Ziou D We consider the problem of determining the structure of high-dimensional data, without prior knowledge of the number of clusters. Data are represented by a finite mixture model based on the generalized Dirichlet distribution. The generalized Dirichlet distribution has a more general covariance structure than the Dirichlet distribution and offers high flexibility and ease of use for the approximation of both symmetric and asymmetric distributions. This ...
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    21. Internet surveillance: content analysis and monitoring of product-specific internet prescription opioid abuse-related postings.

      Related Articles Internet surveillance: content analysis and monitoring of product-specific internet prescription opioid abuse-related postings. Clin J Pain. 2007 Sep;23(7):619-28 Authors: Butler SF, Venuti SW, Benoit C, Beaulaurier RL, Houle B, Katz N OBJECTIVES: This study describes the development of a systematic approach to the analysis of Internet chatter as a means of monitoring potentially abusable opioid analgesics. METHODS: Message boards dedicated to drug abuse were selected using specific inclusion criteria. Threaded discussions containing 48,293 posts were captured. A coding system was created to compare content of posts related to 3 opioid analgesics: Kadian, Vicodin, and ...
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      Mentions: Newton
    22. Neural basis of syntactic processing of simple sentences in Japanese.

      Related Articles Neural basis of syntactic processing of simple sentences in Japanese. Neuroreport. 2007 Sep 17;18(14):1437-41 Authors: Ogawa K, Ohba M, Inui T This study used event-related functional magnetic resonance imaging to investigate the neural basis underlying the sequential involvement of syntactic processing in the course of sentence comprehension. In experiments, a noun, case particle, and verb were presented one by one, constituting simple sentences in Japanese. Participants judged whether the sentence was syntactically correct (syntactic judgment) or whether the particle and verb had the same vowel (phonological judgment). During particle presentation, greater activation in the left ...
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    23. A Semantic Role Labeling System For Biomedical Verbs Using A Maximum-Entropy Model With Automatically Generated Template Features.

      Related Articles BIOSMILE: a semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features. BMC Bioinformatics. 2007;8:325 Authors: Tsai RT, Chou WC, Su YS, Lin YC, Sung CL, Dai HJ, Yeh IT, Ku W, Sung TY, Hsu WL BACKGROUND: Bioinformatics tools for automatic processing of biomedical literature are invaluable for both the design and interpretation of large-scale experiments. Many information extraction (IE) systems that incorporate natural language processing (NLP) techniques have thus been developed for use in the biomedical field. A key IE task in this field is the extraction of biomedical ...
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    24. State-of-the-art anonymization of medical records using an iterative machine learning framework.

      Related Articles State-of-the-art anonymization of medical records using an iterative machine learning framework. J Am Med Inform Assoc. 2007 Sep-Oct;14(5):574-80 Authors: Szarvas G, Farkas R, Busa-Fekete R OBJECTIVE: The anonymization 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 ...
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      Discourse, Entailment, Machine Translation, NER, Parsing, Segmentation, Semantic, Sentiment, Summarization, WSD