1. 2617-2640 of 2805 « 1 2 ... 107 108 109 110 111 112 113 ... 115 116 117 »
    1. Comparative analysis of five protein-protein interaction corpora.

      Comparative analysis of five protein-protein interaction corpora. BMC Bioinformatics. 2008;9 Suppl 3:S6 Authors: Pyysalo S, Airola A, Heimonen J, Björne J, Ginter F, Salakoski T BACKGROUND: Growing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting protein-protein interaction (PPI) extraction. However, there is no general consensus regarding PPI annotation and consequently resources are largely incompatible and methods are difficult to evaluate. RESULTS: We present the first comparative evaluation of the diverse PPI corpora, performing quantitative evaluation using two separate information extraction methods as well ...
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    2. Extracting Protein-Protein Interactions from Medline using the Hidden Vector State model.

      Related Articles Extracting Protein-Protein Interactions from MEDLINE using the Hidden Vector State model. Int J Bioinform Res Appl. 2008;4(1):64-80 Authors: Zhou D, He Y, Kwoh CK A major challenge in text mining for biomedicine is automatically extracting protein-protein interactions from the vast amount of biomedical literature. We have constructed an information extraction system based on the Hidden Vector State (HVS) model for protein-protein interactions. The HVS model can be trained using only lightly annotated data whilst simultaneously retaining sufficient ability to capture the hierarchical structure. When applied in extracting protein-protein interactions, we found that it performed better ...
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    3. Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols.

      Related Articles Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols. BMC Bioinformatics. 2008;9:132 Authors: Campagne F BACKGROUND: The evaluation of information retrieval techniques has traditionally relied on human judges to determine which documents are relevant to a query and which are not. This protocol is used in the Text Retrieval Evaluation Conference (TREC), organized annually for the past 15 years, to support the unbiased evaluation of novel information retrieval approaches. The TREC Genomics Track has recently been introduced to measure the performance of information retrieval for biomedical applications. RESULTS: We ...
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    4. Mining phenotypes for gene function prediction.

      Related Articles Mining phenotypes for gene function prediction. BMC Bioinformatics. 2008;9:136 Authors: Groth P, Weiss B, Pohlenz HD, Leser U BACKGROUND: Health and disease of organisms are reflected in their phenotypes. Often, a genetic component to a disease is discovered only after clearly defining its phenotype. In the past years, many technologies to systematically generate phenotypes in a high-throughput manner, such as RNA interference or gene knock-out, have been developed and used to decipher functions for genes. However, there have been relatively few efforts to make use of phenotype data beyond the single genotype-phenotype relationships. RESULTS: We present ...
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    5. A collective decision model involving vague concepts and linguistic expressions.

      Related Articles A collective decision model involving vague concepts and linguistic expressions. IEEE Trans Syst Man Cybern B Cybern. 2008 Apr;38(2):421-8 Authors: Tang Y In linguistic collective decision, the main objective is to select the best alternatives using linguistic evaluations provided by multiple experts. This paper presents a collective decision model, which is able to deal with complex linguistic evaluations. In this decision model, the linguistic evaluations are represented by linguistic expressions which are the logic formulas obtained by applying logic connectives to the set of basic linguistic labels. The vagueness of each linguistic expression is implicitly ...
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    6. Temporal representation for gene networks: towards a qualitative temporal data mining.

      Related Articles Temporal representation for gene networks: towards a qualitative temporal data mining. Int J Data Min Bioinform. 2008;2(1):36-53 Authors: Turenne N, Schwer SR Processing literature (i.e., text corpora) to capture gene regulation events is not easy and can be driven by the final data representation. We propose to build, manually, an example of temporal representation (whole gene networks for coat formation in Bacillus Subtilis). Our temporal representation is based on a generalised formal language theory (S-languages). We propose an algorithm to link bags of relations with representation, by ordering interactions. In this paper, starting from ...
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      Mentions: France
    7. An analysis of the abstracts presented at the annual meetings of the society for neuroscience from 2001 to 2006.

      An analysis of the abstracts presented at the annual meetings of the society for neuroscience from 2001 to 2006. PLoS ONE. 2008;3(4):e2052 Authors: Lin JM, Bohland JW, Andrews P, Burns GA, Allen CB, Mitra PP Annual meeting abstracts published by scientific societies often contain rich arrays of information that can be computationally mined and distilled to elucidate the state and dynamics of the subject field. We extracted and processed abstract data from the Society for Neuroscience (SFN) annual meeting abstracts during the period 2001-2006 in order to gain an objective view of contemporary neuroscience. An important first ...
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      Mentions: New York
    8. Literature-based compound profiling: application to toxicogenomics.

      Related Articles Literature-based compound profiling: application to toxicogenomics. Pharmacogenomics. 2007 Nov;8(11):1521-34 Authors: Frijters R, Verhoeven S, Alkema W, van Schaik R, Polman J INTRODUCTION: To reduce continuously increasing costs in drug development, adverse effects of drugs need to be detected as early as possible in the process. In recent years, compound-induced gene expression profiling methodologies have been developed to assess compound toxicity, including Gene Ontology term and pathway over-representation analyses. The objective of this study was to introduce an additional approach, in which literature information is used for compound profiling to evaluate compound toxicity and mode of ...
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    9. A salient problem in informatics?

      A salient problem in informatics? J Am Med Inform Assoc. 2008 Apr 24; Authors: Schleyer T The Jan/Feb issue of JAMIA contained an interesting series of articles about the automated identification of smoking status from medical discharge records. It profiled the comparative performance of 11 different systems for the classification of patient records into five general categories for smoking status. The various classification approaches used, such as Bayesian classifiers, natural language processing, support vector machines and neural networks, illustrated the rich and diverse set of algorithms used in automated text processing and classification today. Even more impressive was the ...
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    10. OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression.

      Related Articles OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinformatics. 2008;9:78 Authors: Hunter L, Lu Z, Firby J, Baumgartner WA, Johnson HL, Ogren PV, Cohen KB BACKGROUND: Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a diverse literature. Here we report on the design, implementation and several evaluations of OpenDMAP, an ontology-driven, integrated concept analysis system. It significantly advances the state of ...
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    11. OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature.

      Related Articles OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature. BMC Bioinformatics. 2008;9:84 Authors: Furlong LI, Dach H, Hofmann-Apitius M, Sanz F BACKGROUND: Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature ...
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    12. Statistical search on the Semantic Web.

      Related Articles Statistical search on the Semantic Web. Bioinformatics. 2008 Apr 1;24(7):1002-10 Authors: Kobayashi N, Toyoda T MOTIVATION: Statistical analysis of links on the Semantic Web is important for various evaluation purposes such as quantifying an individual's scientific research output based on citation links. SPARQL has been proposed as a standardized query language for the Semantic Web and is intuitively understandable; however, it does not adequately support statistical evaluation of semantic links. RESULTS: We have extended SPARQL to a novel Resource Description Framework (RDF) query language termed General and Rapid Association Study Query Language (GRASQL) to ...
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    13. Taxonomy-based partitioning of the Gene Ontology.

      Related Articles Taxonomy-based partitioning of the Gene Ontology. J Biomed Inform. 2008 Apr;41(2):282-92 Authors: Kuśnierczyk W The Gene Ontology (GO) project is a collaborative effort to construct ontologies which facilitate biologically meaningful annotation of gene products. In some situations, only a generic or a species-specific subset of all GO terms is required to annotate and analyze the results of a particular biomedical experiment. We show that by defining explicit links between terms in the GO and terms in the Taxonomy of Species (TS) it is possible to automatically create partitions of the GO according to various taxonomic ...
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    14. Extracting interactions between proteins from the literature.

      Related Articles Extracting interactions between proteins from the literature. J Biomed Inform. 2008 Apr;41(2):393-407 Authors: Zhou D, He Y During the last decade, biomedicine has witnessed a tremendous development. Large amounts of experimental and computational biomedical data have been generated along with new discoveries, which are accompanied by an exponential increase in the number of biomedical publications describing these discoveries. In the meantime, there has been a great interest with scientific communities in text mining tools to find knowledge such as protein-protein interactions, which is most relevant and useful for specific analysis tasks. This paper provides a ...
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    15. Comparing and consolidating two heuristic metaschemas.

      Related Articles Comparing and consolidating two heuristic metaschemas. J Biomed Inform. 2008 Apr;41(2):293-317 Authors: Chen Y, Perl Y, Geller J, Hripcsak G, Zhang L A metaschema is an Abstraction Network of the UMLS's Semantic Network (SN) obtained from a connected partition into its collections of semantic types. A metaschema can support comprehension, visualization and navigation of the SN. In this paper, a methodology is presented to evaluate and compare two given metaschemas, based on their structural properties. This methodology was applied to the top-down metaschema and the bottom-up metaschema, derived from two studies involving two groups ...
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    16. Using statistical smoothing to estimate the psycholinguistic acceptability of novel phrases.

      Related Articles Using statistical smoothing to estimate the psycholinguistic acceptability of novel phrases. Behav Res Methods. 2008 Feb;40(1):84-93 Authors: Roberts MA, Chater N Native speakers of languages perceive differences in the acceptability of phrases even when those phrases are both grammatical and novel (previously unseen). We suggest that smoothing, a statistical technique used by natural language processing engineers, provides several candidate mechanisms for investigating this phenomenon. We describe the creation of a large data set of predictions from several smoothing algorithms about the acceptability of unseen grammatical phrases and a novel experimental method for the pairwise comparison ...
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    17. Natural Language Processing in aid of FlyBase curators.

      Related Articles Natural Language Processing in aid of FlyBase curators. BMC Bioinformatics. 2008 Apr 14;9(1):193 Authors: Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T ABSTRACT: BACKGROUND: Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear. RESULTS: PaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design ...
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    18. Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles.

      Related Articles Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles. BMC Bioinformatics. 2008;9 Suppl 1:S3 Authors: Tsai RT, Hung HC, Dai HJ, Lin YW, Hsu WL BACKGROUND: Experimentally verified protein-protein interactions (PPI) cannot be easily retrieved by researchers unless they are stored in PPI databases. The curation of such databases can be made faster by ranking newly-published articles' relevance to PPI, a task which we approach here by designing a machine-learning-based PPI classifier. All classifiers require labeled data, and the more labeled data available, the more reliable they become. Although many PPI databases ...
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    19. Efficient bibliographic searches on allergology using PubMed.

      Related Articles Efficient bibliographic searches on allergology using PubMed. Allergol Immunopathol (Madr). 2007 Nov-Dec;35(6):264-75 Authors: Sáez Gómez JM, Aguinaga Ontoso E, Negro Alvarez JM, Guillén-Grima F, Ivancevich JC, Bozzola CM INTRODUCTION: PubMed is the most important of the non-specialized databases on biomedical literature. International and quickly updated is elaborated by the American Government and contains only information about papers published in scientific journal/s. Although it can be used as an unique Data Base, as a matter of fact is the addition of several subgroups (among them MEDLINE) that can be searched simultaneously. OBJECTIVES: To present the ...
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      Mentions: Spain PubMed
    20. GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations.

      Related Articles GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations. BMC Bioinformatics. 2008;9 Suppl 1:S6 Authors: Xu Q, Shi Y, Lu Q, Zhang G, Luo Q, Li Y BACKGROUND: The most renowned biological ontology, Gene Ontology (GO) is widely used for annotations of genes and gene products of different organisms. However, there are shortcomings in the Resource Description Framework (RDF) data file provided by the GO consortium: 1) Lack of sufficient semantic relationships between pairs of terms coming from the three independent GO sub-ontologies, that limit the power to ...
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    21. Personal mobility and manipulation using robotics, artificial intelligence and advanced control.

      Related Articles Personal mobility and manipulation using robotics, artificial intelligence and advanced control. Conf Proc IEEE Eng Med Biol Soc. 2007;2007:4368-71 Authors: Cooper RA, Ding D, Grindle GG, Wang H Recent advancements of technologies, including computation, robotics, machine learning, communication, and miniaturization technologies, bring us closer to futuristic visions of compassionate intelligent devices. The missing element is a basic understanding of how to relate human functions (physiological, physical, and cognitive) to the design of intelligent devices and systems that aid and interact with people. Our stakeholder and clinician consultants identified a number of mobility barriers that have been ...
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    22. an API for supporting the development and analysis of bio-ontologies.

      Related Articles ONTO-PERL: an API for supporting the development and analysis of bio-ontologies. Bioinformatics. 2008 Mar 15;24(6):885-7 Authors: Antezana E, Egaña M, De Baets B, Kuiper M, Mironov V MOTIVATION: Many biomedical ontologies use OBO or OWL as knowledge representation language. The rapid increase of such ontologies calls for adequate tools to facilitate their use. In particular, there is a pressing need to programmatically deal with such ontologies in many applications, including data integration, text mining, as well as semantic applications supporting translational research. RESULTS: We present an Application Programming Interface (API) called ONTO-PERL. This API ...
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