Thu, 07 Aug 2008 21:25:11 BST CiteULike: Tag data http://www.citeulike.org/tag/data CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/zemeigo/article/265305 <i>Lecture Notes in Computer Science, Vol. 2800 (January 2003), pp. 185-207.</i><br /><br />This paper tackles two main disparities between conceptual data schemes and ontologies, which should be taken into account when (re)using conceptual data modeling techniques for building ontologies. Firstly, conceptual schemes are intended to be used during design phases and not at the run-time of applications, while ontologies are typically used and accessed at run-time. To handle this first difference, we define a conceptual markup language (ORM-ML) that allows to represent ORM conceptual diagrams in an open, textual syntax, so that ORM schemes can be shared, exchanged, and processed at the run-time of autonomous applications. Secondly, unlike ontologies that are supposed to hold application-independent domain knowledge, conceptual schemes were developed only for the use of an enterprise application(s), i.e. ldquoin-houserdquo usage. Hence, we present an ontology engineering-framework that enables reusing conceptual modeling approaches in modeling and representing ontologies. In this approach we prevent application-specific knowledge to enter or to be mixed with domain knowledge. To end, we present DogmaModeler: an ontology-engineering tool that implements the ideas presented in the paper. Keywords: Ontology, Conceptual data modeling, Context, Ontology tools, Reusability, DOGMA, DogmaModeler, ORM, ORM-ML. On Using Conceptual Data Modeling for Ontology Engineering Mustafa Jarrar Jan Demey Robert Meersman Lecture Notes in Computer Science, Vol. 2800 (January 2003), pp. 185-207. 2005-07-26T14:30:47-00:00 2003 Lecture Notes in Computer Science 2800 185 207 Springer conceptual data model ontology http://www.citeulike.org/user/zairah/article/2318610 <i>BMJ, Vol. 328, No. 7452. (5 June 2004), pp. 1372-1375.</i><br /><br />10.1136/bmj.328.7452.1372 Administering, analysing, and reporting your questionnaire Petra Boynton doi:10.1136/bmj.328.7452.1372 BMJ, Vol. 328, No. 7452. (5 June 2004), pp. 1372-1375. 2008-02-01T09:38:17-00:00 2004 BMJ 328 7452 1372 1375 analysing collection data questionnaire http://www.citeulike.org/user/yuval/article/79882 <i>Genome Res, Vol. 13, No. 4. (April 2003), pp. 703-716.</i><br /><br />Global analyses of RNA expression levels are useful for classifying genes and overall phenotypes. Often these classification problems are linked, and one wants to find "marker genes" that are differentially expressed in particular sets of "conditions." We have developed a method that simultaneously clusters genes and conditions, finding distinctive "checkerboard" patterns in matrices of gene expression data, if they exist. In a cancer context, these checkerboards correspond to genes that are markedly up- or downregulated in patients with particular types of tumors. Our method, spectral biclustering, is based on the observation that checkerboard structures in matrices of expression data can be found in eigenvectors corresponding to characteristic expression patterns across genes or conditions. In addition, these eigenvectors can be readily identified by commonly used linear algebra approaches, in particular the singular value decomposition (SVD), coupled with closely integrated normalization steps. We present a number of variants of the approach, depending on whether the normalization over genes and conditions is done independently or in a coupled fashion. We then apply spectral biclustering to a selection of publicly available cancer expression data sets, and examine the degree to which the approach is able to identify checkerboard structures. Furthermore, we compare the performance of our biclustering methods against a number of reasonable benchmarks (e.g., direct application of SVD or normalized cuts to raw data). Spectral biclustering of microarray data: coclustering genes and conditions. Y Kluger R Basri JT Chang M Gerstein doi:10.1101/gr.648603 Genome Res, Vol. 13, No. 4. (April 2003), pp. 703-716. 2005-01-18T23:58:47-00:00 2003 Genome Res 1088-9051 13 4 703 716 biclustering data microarray of spectral http://www.citeulike.org/user/yuntaotian/article/3065359 <i>Journal of Geophysical Research, Vol. 111 (8 July 2006), F03002.</i> Use of a regional, relict landscape to measure vertical deformation of the eastern Tibetan Plateau MK Clark LH Royden KX Whipple BC Burchfiel X Zhang W Tang doi:10.1029/2005JF000294 Journal of Geophysical Research, Vol. 111 (8 July 2006), F03002. 2008-07-31T11:32:31-00:00 2006 Journal of Geophysical Research 111 F03002 building channel data dem flow mountain plateau relic surface tibetan uplift http://www.citeulike.org/user/Yumyai/article/1218509 <i>Bioinformatics, Vol. 23, No. 6. (15 March 2007), pp. 664-672.</i> Deleterious SNP prediction: be mindful of your training data! Care A Matthew Needham J Chris Bulpitt J Andrew Westhead R David doi:10.1093/bioinformatics/btl649 Bioinformatics, Vol. 23, No. 6. (15 March 2007), pp. 664-672. 2007-04-09T23:47:22-00:00 2007 Bioinformatics 1367-4803 23 6 664 672 Oxford University Press data mining snp http://www.citeulike.org/user/yuju/article/2387468 <i>IEEE Transactions on Knowledge and Data Engineering, Vol. 17, No. 11. (November 2005), pp. 1505-1517.</i><br /><br />Senior Member-P. S. Sastry Discovering Frequent Episodes and Learning Hidden Markov Models: A Formal Connection Srivatsan Laxman KP Unnikrishnan doi:10.1109/TKDE.2005.181 IEEE Transactions on Knowledge and Data Engineering, Vol. 17, No. 11. (November 2005), pp. 1505-1517. 2008-02-15T22:22:31-00:00 2005 IEEE Transactions on Knowledge and Data Engineering 1041-4347 17 11 1505 1517 IEEE Educational Activities Department data mining temporal http://www.citeulike.org/user/yongchul/article/2322421 <i>(2006), pp. 29-44.</i> Stasis: flexible transactional storage Russell Sears Eric Brewer (2006), pp. 29-44. 2008-02-02T07:41:36-00:00 2006 29 44 USENIX Association data library storage structure http://www.citeulike.org/user/yodha/article/1401052 <i>ACM Trans. Graph., Vol. 25, No. 1. (January 2006), pp. 60-99.</i> Glift: Generic, efficient, random-access GPU data structures Aaron Lefohn Shubhabrata Sengupta Joe Kniss Robert Strzodka John Owens doi:10.1145/1122501.1122505 ACM Trans. Graph., Vol. 25, No. 1. (January 2006), pp. 60-99. 2007-06-20T13:20:21-00:00 2006 ACM Trans. Graph. 0730-0301 25 1 60 99 ACM Press data gpu structures http://www.citeulike.org/user/yodha/article/1445558 <i>(1987), pp. 86-99.</i> Primitives for the manipulation of three-dimensional subdivisions DP Dobkin MJ Laszlo doi:10.1145/41958.41967 (1987), pp. 86-99. 2007-07-10T06:42:39-00:00 1987 86 99 ACM Press data geometry structure http://www.citeulike.org/user/yodha/article/1445417 <i>(1998), pp. 146-154.</i> Designing a data structure for polyhedral surfaces Lutz Kettner doi:10.1145/276884.276901 (1998), pp. 146-154. 2007-07-10T06:08:42-00:00 1998 146 154 ACM Press data geometry structure http://www.citeulike.org/user/yijunyu/article/611041 <i>(2005), pp. 143-156.</i> Efficient Techniques for Advanced Data Dependence Analysis Konstantinos Kyriakopoulos Kleanthis Psarris doi:10.1109/PACT.2005.19 (2005), pp. 143-156. 2006-05-02T01:09:23-00:00 2005 143 156 IEEE Computer Society analysis data dependence http://www.citeulike.org/user/yggdrasil/article/557314 <i>Comput Biol Med (3 September 2005)</i><br /><br />ONTOFUSION is an ontology-based system designed for biomedical database integration. It is based on two processes: mapping and unification. Mapping is a semi-automated process that uses ontologies to link a database schema with a conceptual framework-named virtual schema. There are three methodologies for creating virtual schemas, according to the origin of the domain ontology used: (1) top-down-e.g. using an existing ontology, such as the UMLS or Gene Ontology-, (2) bottom-up-building a new domain ontology- and (3) a hybrid combination. Unification is an automated process for integrating ontologies and hence the database to which they are linked. Using these methods, we employed ONTOFUSION to integrate a large number of public genomic and clinical databases, as well as biomedical ontologies. ONTOFUSION: Ontology-based integration of genomic and clinical databases. D Pérez-Rey V Maojo M García-Remesal R Alonso-Calvo H Billhardt F Martin-Sánchez A Sousa doi:10.1016/j.compbiomed.2005.02.004 Comput Biol Med (3 September 2005) 2006-03-20T21:58:46-00:00 2005 Comput Biol Med 0010-4825 data integration ontology http://www.citeulike.org/user/yggdrasil/article/2695529 <i>Omics : a journal of integrative biology, Vol. 10, No. 2. (2006), pp. 138-144.</i><br /><br />The Microarray Gene Expression Data (MGED) society is an international organization established in 1999 for facilitating sharing of functional genomics and proteomics array data. To facilitate microarray data sharing, the MGED society has been working in establishing the relevant data standards. The three main components (which will be described in more detail later) of MGED standards are Minimum Information About a Microarray Experiment (MIAME), a document that outlines the minimum information that should be reported about a microarray experiment to enable its unambiguous interpretation and reproduction; MAGE, which consists of three parts, The Microarray Gene Expression Object Model (MAGE-OM), an XML-based document exchange format (MAGE-ML), which is derived directly from the object model, and the supporting tool kit MAGEstk; and MO, or MGED Ontology, which defines sets of common terms and annotation rules for microarray experiments, enabling unambiguous annotation and efficient queries, data analysis and data exchange without loss of meaning. We discuss here how these standards have been established, how they have evolved, and how they are used. MGED standards: work in progress. CA Ball A Brazma doi:10.1089/omi.2006.10.138 Omics : a journal of integrative biology, Vol. 10, No. 2. (2006), pp. 138-144. 2008-04-21T09:50:33-00:00 2006 Omics : a journal of integrative biology 1536-2310 10 2 138 144 data interchange http://www.citeulike.org/user/ygarb/article/778023 <i>Science, Vol. 313, No. 5786. (28 July 2006), pp. 504-507.</i><br /><br />High-dimensional data can be converted to low-dimensional codes by training a multilayer neural network with a small central layer to reconstruct high-dimensional input vectors. Gradient descent can be used for fine-tuning the weights in such "autoencoder" networks, but this works well only if the initial weights are close to a good solution. We describe an effective way of initializing the weights that allows deep autoencoder networks to learn low-dimensional codes that work much better than principal components analysis as a tool to reduce the dimensionality of data. 10.1126/science.1127647 Reducing the Dimensionality of Data with Neural Networks GE Hinton RR Salakhutdinov doi:10.1126/science.1127647 Science, Vol. 313, No. 5786. (28 July 2006), pp. 504-507. 2006-07-28T15:16:42-00:00 2006 Science 313 5786 504 507 data mining networks neural http://www.citeulike.org/user/yangxian/article/611884 <i>Data Knowledge Engineering, Vol. 10 (1993), pp. 65-100.</i><br /><br />Conceptual data modelling techniques aim at the representation of data at a high level of abstraction. The Conceptualisation Principle states that only those aspects are to be represented that deal with the meaning of the Universe of Discourse. Conventional conceptual data modelling techniques, as e.g. ER or NIAM, have to violate the Conceptualisation Principle when dealing with objects with a complex structure. In order to represent these objects conceptually irrelevant choices have to made.... Expressiveness in Conceptual Data Modelling Arthur Theo van der Weide Data Knowledge Engineering, Vol. 10 (1993), pp. 65-100. 2006-05-02T19:36:50-00:00 1993 Data Knowledge Engineering 10 65 100 data http://www.citeulike.org/user/yangxian/article/71495 <i></i><br /><br />We study the fundamental limitations of relational algebra (RA) and SQL in supporting sequence and stream queries, and present effective query language and data model enrichments to deal with them. We begin by observing the well-known limitations of SQL in application domains which are important for data streams, such as sequence queries and data mining. Then we present a formal proof that, for continuous queries on data streams, SQL su#ers from additional expressive power problems.... Query Languages and Data Models for Database Sequences Data 2004-12-30T23:14:25-00:00 data http://www.citeulike.org/user/xiangzhangchina/article/2369145 <i>(2002), pp. 759-775.</i><br /><br />We present a framework for representing and matching multiscale, qualitative feature hierarchies. The coarse shape of an object is captured by a set of blobs and ridges, representing compact and elongated parts of an object. These parts, in turn, map to nodes in a directed acyclic graph, in which parent/child edges represent feature overlap, sibling edges join nodes with shared parents, and all edges encode geometric relations between the features. Given two feature hierarchies,... On the Representation and Matching of Qualitative Shape at Multiple Scales Ali Shokoufandeh Sven Dickinson Clas Jonsson Lars Bretzner Tony Lindeberg (2002), pp. 759-775. 2008-02-13T10:01:22-00:00 2002 759 775 data matching multiple representation http://www.citeulike.org/user/xapc2/article/3055011 <i>International Journal for Numerical and Analytical methods in Geomechanics, Vol. 11, No. 1. (1987), pp. 79-102.</i><br /><br />A rational approach for dealing with uncertainties in geotechnical performance predictions is presented. First, sources of uncertainty are identified and treated stochastically. Then, the relative importance of each source is analysed and its influence in the decision-making process is evaluated. Strong inferences concerning the spatial structure of soils are drawn from field or laboratory measurements, while maintaining consistency with engineering knowledge and experimenal findings. Optimal estimates of soil properties are derived by a stochastic method which is mathematically meaningful and portrays adequately the real behaviour of the data. The method is powerful when the data exhibit homogeneous or non-homogeneous characteristics, and works well with any kind of data support. Its applicability is illustrated in a case study involving field vane data. Furthermore, contributions and benefits of the results obtained to the geotechnical decisions and design are discussed. A stochastic approach in modelling and estimating geotechnical data George Christakos doi:10.1002/nag.1610110107 International Journal for Numerical and Analytical methods in Geomechanics, Vol. 11, No. 1. (1987), pp. 79-102. 2008-07-29T01:42:56-00:00 1987 International Journal for Numerical and Analytical methods in Geomechanics 11 1 79 102 data geotechnical model stochastic http://www.citeulike.org/user/wwlsung/article/166211 <i>Bioinformatics, Vol. 18, No. 11. (November 2002), pp. 1540-1541.</i><br /><br />SNOMAD is a collection of algorithms for the normalization and standardization of gene expression datasets derived from diverse biological and technological sources. In addition to conventional transformations and visualization tools, SNOMAD includes two non-linear transformations which correct for bias and variance which are non-uniformly distributed across the range of microarray element signal intensities: (1). Local mean normalization; and (2). Local variance correction (Z-score generation using a locally calculated standard deviation). SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis. C Colantuoni G Henry S Zeger J Pevsner Bioinformatics, Vol. 18, No. 11. (November 2002), pp. 1540-1541. 2005-04-21T13:32:29-00:00 2002 Bioinformatics 1367-4803 18 11 1540 1541 analysis data microarray http://www.citeulike.org/user/wwlsung/article/888793 <i>J Mol Diagn, Vol. 5, No. 2. (1 May 2003), pp. 73-81.</i><br /><br />High-throughput cDNA microarray technology allows for the simultaneous analysis of gene expression levels for thousands of genes and as such, rapid, relatively simple methods are needed to store, analyze, and cross-compare basic microarray data. The application of a classical method of data normalization, Z score transformation, provides a way of standardizing data across a wide range of experiments and allows the comparison of microarray data independent of the original hybridization intensities. Data normalized by Z score transformation can be used directly in the calculation of significant changes in gene expression between different samples and conditions. We used Z scores to compare several different methods for predicting significant changes in gene expression including fold changes, Z ratios, Z and t statistical tests. We conclude that the Z score transformation normalization method accompanied by either Z ratios or Z tests for significance estimates offers a useful method for the basic analysis of microarray data. The results provided by these methods can be as rigorous and are no more arbitrary than other test methods, and, in addition, they have the advantage that they can be easily adapted to standard spreadsheet programs. Analysis of Microarray Data Using Z Score Transformation Chris Cheadle Marquis Vawter William Freed Kevin Becker J Mol Diagn, Vol. 5, No. 2. (1 May 2003), pp. 73-81. 2006-10-08T00:39:01-00:00 2003 J Mol Diagn 5 2 73 81 analysis data microarray http://www.citeulike.org/user/wormik/article/101908 <i>Web Information Systems Engineering Workshops, 2003. Proceedings. Fourth International Conference on (2003), pp. 45-53.</i><br /><br />One of the main challenges in today's world of vastly distributed sources of information is to re-combine information sources to provide uniform access. We propose a distributed data management system that should provide the "glue" for combining data sources. This system advocates services as a means to access data. New services are defined on demand and their creation is supported by a behaviorist approach that incorporates new service ideas provided by the user. Services can be based on data and/or on the output of existing services. To increase the usability of services in the system we utilize two ontologies to denote relevant metadata. Service ontology structures existing services and helps in discovering new ones. Parameter ontology structures the parameters used in services and supports the creation of new services. Our proposal of a services-based data management system exhibits similarities to the newsgroup approach in that both "systems" are examples of semantic search engines based on user interaction. By exploring these similarities and by looking at some statistics of newsgroup user/posting behavior, we validate our services-based approach. Services-based data management in a global computing environment D Pfoser N Tryfona V Verykios Web Information Systems Engineering Workshops, 2003. Proceedings. Fourth International Conference on (2003), pp. 45-53. 2005-02-23T14:27:14-00:00 2003 Web Information Systems Engineering Workshops, 2003. Proceedings. Fourth International Conference on 45 53 computing data database distributed environment global information internet management mobile ontology processing service services-based sources structures system systems web http://www.citeulike.org/user/wormik/article/463044 <i></i><br /><br />In the last decade, the Web has become a primary source of information for many people. Due to its ease and ubiquity, many people first look up pages on the Web whenever they need to look up certain information. The popularity of the Web, however, has brought many interesting challenges. In particular, the ever-expanding size of the Web makes it increasingly di#cult to discover, store, organize and retrieve the information on the Web to help users to identify what they are looking for. In... Frontiers in Web Data Management Junghoo Cho 2006-01-12T14:00:06-00:00 data management web http://www.citeulike.org/user/wnpx/article/572874 <i>Nat Genet, Vol. 34, No. 2. (June 2003), pp. 166-176.</i><br /><br />Much of a cell's activity is organized as a network of interacting modules: sets of genes coregulated to respond to different conditions. We present a probabilistic method for identifying regulatory modules from gene expression data. Our procedure identifies modules of coregulated genes, their regulators and the conditions under which regulation occurs, generating testable hypotheses in the form 'regulator X regulates module Y under conditions W'. We applied the method to a Saccharomyces cerevisiae expression data set, showing its ability to identify functionally coherent modules and their correct regulators. We present microarray experiments supporting three novel predictions, suggesting regulatory roles for previously uncharacterized proteins. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. E Segal M Shapira A Regev D Pe'er D Botstein D Koller N Friedman doi:10.1038/ng1165 Nat Genet, Vol. 34, No. 2. (June 2003), pp. 166-176. 2006-04-02T02:35:31-00:00 2003 Nat Genet 1061-4036 34 2 166 176 data expression gene module networks http://www.citeulike.org/user/wnpx/article/1781899 <i>Science, Vol. 262, No. 5133. (22 October 1993), pp. 502-503.</i> Managing the genome data deluge. Peter Aldhous Science, Vol. 262, No. 5133. (22 October 1993), pp. 502-503. 2007-10-18T00:16:12-00:00 1993 Science 0036-8075 262 5133 502 503 data datadeluge dt http://www.citeulike.org/user/wnpx/article/435359 <i>Bioinformatics, Vol. 21, No. 24. (15 December 2005), pp. 4401-4407.</i><br /><br />MOTIVATION: Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed. RESULTS: In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data. Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX Lena Strömbäck Patrick Lambrix doi:10.1093/bioinformatics/bti718 Bioinformatics, Vol. 21, No. 24. (15 December 2005), pp. 4401-4407. 2005-12-12T00:25:42-00:00 2005 Bioinformatics 1367-4803 21 24 4401 4407 Oxford University Press biopax data dt format pathway psi-mi representation sbml http://www.citeulike.org/user/wnpx/article/484884 <i></i><br /><br />In this paper, we introduce a dynamic multidimensional model, which is suitable for building text warehouses. The dimensions are atomic semantic categories embedded in a familiar taxonomy. This approach to text warehouses requires a large number of dimensions, some of which may be not known in advance. Central to the dynamic multi-dimensional model is the meta-snowflake schema, which is a snowflake schema with an index table. The index table contains metadata on dimensions consisting of... Dynamic Multi-Dimensional Models for Text Warehouses Maria Bleyberg 2006-01-29T19:43:37-00:00 data database multidimensional natlang warehouse http://www.citeulike.org/user/wnpx/article/484883 <i></i><br /><br />Database design for data warehouses is based on the notion of the snowflake schema and its important special case, the star schema. The snowflake schema represents a dimensional model which is composed of a central fact table and a set of constituent dimension tables which can be further broken up into subdimension tables. We formalise the concept of a snowflake schema in terms of an acyclic database schema whose join tree satisfies certain structural properties. We then define a normal form... Why is the Star Schema a Good Data Warehouse Design? Mark Levene George Loizou 2006-01-29T19:43:05-00:00 data database multidimensional schema star http://www.citeulike.org/user/wnpx/article/484879 <i></i><br /><br />Database design for data warehouses is based on the notion of the snowflake schema and its important special case, the star schema. The snowflake schema represents a dimensional model which is composed of a central fact table and a set of constituent dimension tables which can be further broken up into subdimension tables. We formalise the concept of a snowflake schema in terms of an acyclic database schema whose join tree satisfies certain structural properties. We then define a normal form... Why is the snowflake schema a good data warehouse design M Levene G Loizou 2006-01-29T19:37:06-00:00 data schema snowflake warehouse http://www.citeulike.org/user/wnpx/article/483206 <i>Drug Discov Today, Vol. 10, No. 13. (1 July 2005), pp. 937-942.</i><br /><br />Scientists seeking to understand the inner workings of cells have access to a multitude of pathway data resources. However, the representations of pathway data within these resources are not consistent or interchangeable. To facilitate easy information retrieval from a wide variety of pathway resources, such as signal transduction, gene regulation, molecular interaction and metabolic pathway databases, a broad effort in the biopathways community called BioPAX was formed. New biological pathway software applications built using the BioPAX standard will be able to integrate knowledge from multiple sources in a coherent and reliable way. This article reports the progress that the BioPAX work-group has made towards building and deploying the BioPAX data-exchange format for biological pathway data. PAX of mind for pathway researchers. JS Luciano doi:10.1016/S1359-6446(05)03501-4 Drug Discov Today, Vol. 10, No. 13. (1 July 2005), pp. 937-942. 2006-01-27T23:53:25-00:00 2005 Drug Discov Today 1359-6446 10 13 937 942 biopax data dt format pathway representation http://www.citeulike.org/user/winterschlaefer/article/2587350 <i>J Biomed Inform (5 February 2008)</i><br /><br />Data integration is a perennial issue in bioinformatics, with many systems being developed and many technologies offered as a panacea for its resolution. The fact that it is still a problem indicates a persistence of underlying issues. Progress has been made, but we should ask "what lessons have been learnt?", and "what still needs to be done?" Semantic Web and Web 2.0 technologies are the latest to find traction within bioinformatics data integration. Now we can ask whether the Semantic Web, mashups, or their combination, have the potential to help. This paper is based on the opening invited talk by Carole Goble given at the Health Care and Life Sciences Data Integration for the Semantic Web Workshop collocated with WWW2007. 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. State of the nation in data integration for bioinformatics. Carole Goble Robert Stevens doi:10.1016/j.jbi.2008.01.008 J Biomed Inform (5 February 2008) 2008-03-25T18:13:44-00:00 2008 J Biomed Inform 1532-0480 data integration http://www.citeulike.org/user/wilmegape/article/1211926 <i>SIGKDD Explor. Newsl., Vol. 5, No. 1. (July 2003), pp. 1-16.</i> Multi-relational data mining: an introduction Sa&\#353;o D&\#382;eroski doi:10.1145/959242.959245 SIGKDD Explor. Newsl., Vol. 5, No. 1. (July 2003), pp. 1-16. 2007-04-06T13:37:08-00:00 2003 SIGKDD Explor. Newsl. 1931-0145 5 1 1 16 ACM Press data ilp mining multi-relational relational http://www.citeulike.org/user/wilmegape/article/1202379 <i>No. INS-R9908. (MarchJanuary, 1999)</i><br /><br />An important aspect of data mining algorithms and systems is that they should scale well to large databases. A consequence of this is that most data mining tools are based on machine learning algorithms that work on data in attribute-value format. Experience has proven that such 'single-table' mining algorithms indeed scale well. The downside of this format is, however, that more complex patterns are simply not expressible in this format and, thus, cannot be discovered. One way to enlarge the... Multi-relational data mining Arno Knobbe Hendrik Blockeel Arno Siebes DMG van der Wallen No. INS-R9908. (MarchJanuary, 1999) 2007-04-02T04:05:01-00:00 1999 INS-R9908 data mining relational http://www.citeulike.org/user/wilmegape/article/222956 <i>Nature, Vol. 435, No. 7043., pp. 814-818.</i> Uncovering the overlapping community structure of complex networks in nature and society Gergely Palla Imre Derényi Illés Farkas Tamás Vicsek doi:10.1038/nature03607 Nature, Vol. 435, No. 7043., pp. 814-818. 2005-06-08T20:26:31-00:00 Nature 0028-0836 435 7043 814 818 Nature Publishing Group community data mining networks overlap structure webmining http://www.citeulike.org/user/wilmegape/article/1580199 <i>(2007), pp. 76-85.</i> Extracting semantic relations from query logs Ricardo Baeza-Yates Alessandro Tiberi doi:10.1145/1281192.1281204 (2007), pp. 76-85. 2007-08-21T13:20:37-00:00 2007 76 85 ACM Press data databases logs mining query relations semantic http://www.citeulike.org/user/wilmegape/article/1580198 <i>(2007), pp. 390-399.</i> Correlation search in graph databases Yiping Ke James Cheng Wilfred Ng doi:10.1145/1281192.1281236 (2007), pp. 390-399. 2007-08-21T13:19:17-00:00 2007 390 399 ACM Press data databases graph mining webmining http://www.citeulike.org/user/wilmegape/article/1580173 <i>(2007), pp. 163-172.</i> Structural and temporal analysis of the blogosphere through community factorization Yun Chi Shenghuo Zhu Xiaodan Song Junichi Tatemura Belle Tseng doi:10.1145/1281192.1281213 (2007), pp. 163-172. 2007-08-21T13:16:30-00:00 2007 163 172 ACM Press data databases mining webmining http://www.citeulike.org/user/wilmegape/article/1202762 <i>: Database Theory - ICDT'99: 7th International Conference, Jerusalem, Israel, January 1999. Proceedings (1998), 398.</i> Discovering Frequent Closed Itemsets for Association Rules Nicolas Pasquier Yves Bastide Rafik Taouil Lotfi Lakhal : Database Theory - ICDT'99: 7th International Conference, Jerusalem, Israel, January 1999. Proceedings (1998), 398. 2007-04-02T11:55:20-00:00 1998 : Database Theory - ICDT'99: 7th International Conference, Jerusalem, Israel, January 1999. Proceedings 398 closed data itemsets mining http://www.citeulike.org/user/wilmegape/article/142200 <i>(2004), pp. 683-688.</i> Dense itemsets Jouni Sepp&\#228;nen Heikki Mannila doi:10.1145/1014052.1014140 (2004), pp. 683-688. 2005-03-28T17:52:06-00:00 2004 683 688 ACM Press data dense itemsets mining http://www.citeulike.org/user/wigmapoole/article/2863510 <i>The Journal of Financial and Quantitative Analysis, Vol. 33, No. 3. (1998), pp. 383-408.</i><br /><br />This paper studies the high frequency reaction of the DEM/USD exchange rate to publicly announced macroeconomic information emanating from Germany and the U.S. By using data sampled at a five-minute frequency, we are able to identify significant impacts of most announcements on the exchange rate change in the 15 minutes post-announcement, although the significance of these effects decreases rapidly as the interval over which the post-announcement change in exchange rates is increased. The direction of the exchange rate response conforms, in general, with a reaction function interpretation whereby reactions to macroeconomic news are driven by the likely operations of monetary authorities in domestic money markets. Further, we detect influences of German monetary policy decisions on the reaction of the exchange rate, and also differences between U.S. and German announcements in the exchange rate reaction time pattern. The Effects of Macroeconomic News on High Frequency Exchange Rate Behavior Alvaro Almeida Charles Goodhart Richard Payne doi:10.2307/2331101 The Journal of Financial and Quantitative Analysis, Vol. 33, No. 3. (1998), pp. 383-408. 2008-06-05T06:19:54-00:00 1998 The Journal of Financial and Quantitative Analysis 33 3 383 408 University of Washington School of Business Administration data frequency high surprise usddem http://www.citeulike.org/user/wig/article/235727 <i>(2001)</i><br /><br />Currently, Grid resear h as well as distributed database resear h deals with data repli ation but both ta kle the problem from different points of view. The aim of this paper is to outline both approa hes and try to find ommonalities between the two worlds in order to have a most effi ient Data Grid that manages data stored in obje toriented databases. Our target obje t-oriented database management system is Obje tivity/DB whi h is urrently the database of hoi e in some existing High Energy... Distributed Database Management Systems and the Data Grid H Stockinger (2001) 2005-06-23T19:02:19-00:00 2001 data databases grid no-tag http://www.citeulike.org/user/whirldpixc/article/576264 <i>Anthropology News, Vol. 46, No. 9. (2005), pp. 12-14.</i> AnthroSourceActually Useful? Alex Golub doi:10.1525/an.2005.46.9.12 Anthropology News, Vol. 46, No. 9. (2005), pp. 12-14. 2006-04-04T19:12:33-00:00 2005 Anthropology News 46 9 12 14 anthropology anthrosource data interent mining news technology http://www.citeulike.org/user/wandall/article/1445073 <i>Hum Exp Toxicol, Vol. 22, No. 10. (October 2003), pp. 541-549.</i><br /><br />Results obtained in long-term carcinogenicity studies with animals should be evaluated, first and foremost, by statistical comparisons of the data obtained from the treated group with that from the concurrent control group. Often the results are compared with data from so-called historical control groups in order to take variations in the incidences of spontaneous tumours into account. Because historical control data change in the course of time and for a variety of reasons, certain requirements must be met before they may be used in the evaluation of the results of long-term studies. The present paper discusses potential sources of variability of tumour incidences in untreated animals, presents databanks for historical control data, mentions the factors that affect tumour incidences in untreated animals and describes biostatistical data evaluation. Finally, details are given of the criteria used by the DFG Commission for the Investigation of Health Hazards of Chemical Compounds in the Work Area to decide whether historical control data may be applied. These include the requirement that the historical control data were obtained with animals of the same species and strain and from the same breeder. The data were obtained in the same laboratory, the study design, experimental methods and assessment criteria were the same, and the studies used for the comparison were carried out within a limited time window. Historical control data that have not been published may be used provided they fulfil the above criteria and have been made available in sufficient detail to be comprehensible. Evaluation of historical control data in carcinogenicity studies. H Greim HP Gelbke U Reuter HW Thielmann L Edler Hum Exp Toxicol, Vol. 22, No. 10. (October 2003), pp. 541-549. 2007-07-09T23:40:15-00:00 2003 Hum Exp Toxicol 0960-3271 22 10 541 549 animal_studies carcinogen data expert_judgment histrorical_control http://www.citeulike.org/user/wandall/article/1697166 <i>Futures, Vol. 39, No. 9. (November 2007), pp. 1117-1130.</i><br /><br />A central subcategory of futures research is technology foresight. There is a concern that today's technology foresight processes do not serve technology-political decision-making and strategy processes of companies well enough. The regional level needs to be emphasized, too, and the inclusion of a wide variety of actors and organizations. There is a danger that results of foresight processes are not absorbed into regional strategy-making processes, leading to a "black hole of interpretation and implementation of foresight knowledge". Particularly knowledge, but also data and information are crucial concepts in foresight processes. An important issue is how to transform foresight information into future-oriented innovation knowledge. Concrete tools and institutional settings to enhance data, information and knowledge quality in foresight processes and strategy work are needed. This article investigates limitations of established foresight processes and planning approaches, limitations in practical utilization of results of foresight processes, and quality of data, information and knowledge as concrete tools and as a systematic response to limitations. The article is partly based on empirical results from a technology foresight survey undertaken in Finland in 2005. The research responds to societal and academic interest by combining the fields of (i) futures research and (ii) data, information and knowledge quality. Future-oriented considerations are not routine tasks, which makes it especially challenging and important to ensure that these processes benefit from data, information and knowledge of good quality. Quality of data, information and knowledge in regional foresight processes Tuomo Uotila Helina Melkas doi:10.1016/j.futures.2007.03.019 Futures, Vol. 39, No. 9. (November 2007), pp. 1117-1130. 2007-09-26T12:42:02-00:00 2007 Futures 39 9 1117 1130 data uncertainty http://www.citeulike.org/user/wandall/article/39378 <i>Journal for General Philosophy of Science, Vol. 35, No. 1., 13.</i> Wofur sprechen die Daten? Thomas Bartelborth doi:10.1023/B:JGPS.0000035150.90850.c1 Journal for General Philosophy of Science, Vol. 35, No. 1., 13. 2004-12-28T17:10:43-00:00 Journal for General Philosophy of Science 0925-4560 35 1 13 Kluwer Academic Publishers abduction bayesian data induction scientific_method scientific_practice statistics http://www.citeulike.org/user/wandall/article/2844506 <i>Psychological reports, Vol. 99, No. 3. (December 2006), pp. 675-680.</i><br /><br />Results are described for a survey assessing prevalence of missing data and reporting practices in studies with missing data in a random sample of empirical research journal articles from the PsychINFO database for the year 1999, two years prior to the publication of a special section on missing data in Psychological Methods. Analysis indicates missing data problems were found in about one-third of the studies. Further, analytical methods and reporting practices varied widely for studies with missing data. One may consider these results as baseline data to assess progress as reporting standards evolve for studies with missing data. Some potential reporting standards are discussed. Missing data: prevalence and reporting practices. TE Bodner Psychological reports, Vol. 99, No. 3. (December 2006), pp. 675-680. 2008-05-29T14:02:46-00:00 2006 Psychological reports 0033-2941 99 3 675 680 bias bias_ra data data_manipulation http://www.citeulike.org/user/waffle168/article/765090 <i>Health Serv Res, Vol. 38, No. 6 Pt 1. (December 2003), pp. 1529-1545.</i><br /><br />OBJECTIVES: Health care organizations often measure processes of care using only administrative data. We assessed whether measuring processes of diabetes care using administrative data without medical record data is likely to underdetect compliance with accepted standards for certain groups of patients. DATA SOURCES/STUDY SETTING: Assessment of quality indicators during 1998 using administrative and medical records data for a cohort of 1,335 diabetic patients enrolled in three Minnesota health plans. STUDY DESIGN: Cross-sectional retrospective study assessing hemoglobin A1c testing, LDL cholesterol testing, and retinopathy screening from the two data sources. Analyses examined whether patient or clinic characteristics were associated with underdetection of quality indicators when administrative data were not supplemented with medical record data. DATA COLLECTION/EXTRACTION METHODS: The health plans provided administrative data, and trained abstractors collected medical records data. PRINCIPAL FINDINGS: Quality indicators that would be identified if administrative data were supplemented with medical records data are often not identified using administrative data alone. In adjusted analyses, older patients were more likely to have hemoglobin A1c testing underdetected in administrative data (compared to patients <45 years, OR 2.95, 95 percent CI 1.09 to 7.96 for patients 65 to 74 years, and OR 4.20, 95 percent CI 1.81 to 9.77 for patients 75 years and older). Black patients were more likely than white patients to have retinopathy screening underdetected using administrative data (2.57, 95 percent CI 1.16 to 5.70). Patients in different health plans also differed in the likelihood of having quality indicators underdetected. CONCLUSIONS: Diabetes quality indicators may be underdetected more frequently for elderly and black patients and the physicians, clinics, and plans who care for such patients when quality measurement is based on administrative data alone. This suggests that providers who care for such patients may be disproportionately affected by public release of such data or by its use in determining the magnitude of financial incentives. Measuring the quality of diabetes care using administrative data: is there bias? NL Keating MB Landrum BE Landon JZ Ayanian C Borbas E Guadagnoli Health Serv Res, Vol. 38, No. 6 Pt 1. (December 2003), pp. 1529-1545. 2006-07-19T19:38:19-00:00 2003 Health Serv Res 0017-9124 38 6 Pt 1 1529 1545 data diabetes http://www.citeulike.org/user/waffle168/article/1094452 <i>Womens Health Issues, Vol. 13, No. 4. (g 2003), pp. 150-157.</i><br /><br />Despite growing recognition of significant morbidity and mortality among women from cardiovascular disease, management of primary and secondary cardiac risk factors continues to be suboptimal for many women. Although there is a good deal of room to improve the care for cardiovascular disease and diabetes in men, existing gender differences in performance suggest much can be gained by specifically assessing and monitoring quality of care for these conditions in women. In this paper, we describe recent work showing gender differences in quality of ambulatory care in managed care plans with some plans having substantial gender differences on widely used measures of the quality of primary and secondary prevention of cardiac disease. We then discuss potential benefits of and barriers to routine reporting of objective measures of the quality of care, such as Health Plan Employer Data and Information Set (HEDIS) measures, by health plans. Improving women's quality of care for cardiovascular disease and diabetes: the feasibility and desirability of stratified reporting of objective performance measures. CE Bird A Fremont S Wickstrom AS Bierman E McGlynn Womens Health Issues, Vol. 13, No. 4. (g 2003), pp. 150-157. 2007-02-08T09:25:16-00:00 2003 Womens Health Issues 1049-3867 13 4 150 157 cardiovascular data diabetes quality reporting http://www.citeulike.org/user/waffle168/article/1094407 <i>Jt Comm J Qual Patient Saf, Vol. 31, No. 1. (January 2005)</i><br /><br />The heart of the Card Response Project, a six-step data collection strategy, is the clinician, armed with a pocket-sized card for rapid completion during clinic visits. It's in the cards: a practice-friendly, real-time data collection strategy for quality improvement. JL Wofford JR Kimberly WP Moran DP Miller JL Hopping CE Pedley CH Messick PR Lichstein R Velez Jt Comm J Qual Patient Saf, Vol. 31, No. 1. (January 2005) 2007-02-08T08:42:09-00:00 2005 Jt Comm J Qual Patient Saf 1553-7250 31 1 data improvement quality real-time http://www.citeulike.org/user/vpschulz/article/447015 <i>Nature Reviews Genetics, Vol. 7, No. 1., pp. 55-65.</i> Microarray data analysis: from disarray to consolidation and consensus David Allison Xiangqin Cui Grier Page Mahyar Sabripour doi:10.1038/nrg1749 Nature Reviews Genetics, Vol. 7, No. 1., pp. 55-65. 2005-12-21T22:57:48-00:00 Nature Reviews Genetics 1471-0056 7 1 55 65 Nature Publishing Group analysis data microarray review http://www.citeulike.org/user/vpschulz/article/239528 <i>Biostatistics, Vol. 4, No. 2. (April 2003), pp. 249-264.</i><br /><br />In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting of five MGU74A mouse GeneChip arrays, part of the data from an extensive spike-in study conducted by Gene Logic and Wyeth's Genetics Institute involving 95 HG-U95A human GeneChip arrays; and part of a dilution study conducted by Gene Logic involving 75 HG-U95A GeneChip arrays. We display some familiar features of the perfect match and mismatch probe (PM and MM) values of these data, and examine the variance-mean relationship with probe-level data from probes believed to be defective, and so delivering noise only. We explain why we need to normalize the arrays to one another using probe level intensities. We then examine the behavior of the PM and MM using spike-in data and assess three commonly used summary measures: Affymetrix's (i) average difference (AvDiff) and (ii) MAS 5.0 signal, and (iii) the Li and Wong multiplicative model-based expression index (MBEI). The exploratory data analyses of the probe level data motivate a new summary measure that is a robust multi-array average (RMA) of background-adjusted, normalized, and log-transformed PM values. We evaluate the four expression summary measures using the dilution study data, assessing their behavior in terms of bias, variance and (for MBEI and RMA) model fit. Finally, we evaluate the algorithms in terms of their ability to detect known levels of differential expression using the spike-in data. We conclude that there is no obvious downside to using RMA and attaching a standard error (SE) to this quantity using a linear model which removes probe-specific affinities. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. RA Irizarry B Hobbs F Collin YD Beazer-Barclay KJ Antonellis U Scherf TP Speed doi:10.1093/biostatistics/4.2.249 Biostatistics, Vol. 4, No. 2. (April 2003), pp. 249-264. 2005-06-28T15:56:12-00:00 2003 Biostatistics 1465-4644 4 2 249 264 analysis data expression gene microarray normalization rma