1491961
WormBase: a multi-species resource for nematode biology and genomics
WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system.
6056437
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics
WormBase (http://www.wormbase.org), the model organism database for information about Caenorhabditis elegans and related nematodes, continues to expand in breadth and depth. Over the past year, WormBase has added multiple large-scale datasets including SAGE, interactome, 3D protein structure datasets and NCBI KOGs. To accommodate this growth, the International WormBase Consortium has improved the user interface by adding new features to aid in navigation, visualization of large-scale datasets, advanced searching and data mining. Internally, we have restructured the database models to rationalize the representation of genes and to prepare the system to accept the genome sequences of three additional Caenorhabditis species over the coming year.
2887282
Rat Genome Database (RGD): mapping disease onto the genome
The Rat Genome Database (RGD, http://rgd.mcw.edu) is an NIH-funded project whose stated mission is 'to collect, consolidate and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community'. In a collaboration between the Bioinformatics Research Center at the Medical College of Wisconsin, the Jackson Laboratory and the National Center for Biotechnology Information, RGD has been created to meet these stated aims. The rat is uniquely suited to its role as a model of human disease and the primary focus of RGD is to aid researchers in their study of the rat and in applying their results to studies in a wider context. In support of this we have integrated a large amount of rat genetic and genomic resources in RGD and these are constantly being expanded through ongoing literature and bulk dataset curation. RGD version 2.0, released in June 2001, includes curated data on rat genes, quantitative trait loci (QTL), microsatellite markers and rat strains used in genetic and genomic research. VCMap, a dynamic sequence-based homology tool was introduced, and allows researchers of rat, mouse and human to view mapped genes and sequences and their locations in the other two organisms, an essential tool for comparative genomics. In addition, RGD provides tools for gene prediction, radiation hybrid mapping, polymorphic marker selection and more. Future developments will include the introduction of disease-based curation expanding the curated information to cover popular disease systems studied in the rat. This will be integrated with the emerging rat genomic sequence and annotation pipelines to provide a high-quality disease-centric resource, applicable to human and mouse via comparative tools such as VCMap. RGD has a defined community outreach focus with a Visiting Scientist program and the Rat Community Forum, a web-based forum for rat researchers and others interested in using the rat as an experimental model. Thus, RGD is not only a valuable resource for those working with the rat but also for researchers in other model organisms wishing to harness the existing genetic and physiological data available in the rat to complement their own work.
28223559
Constructions of point-colour-symmetric graphs
Throuhout this paper, we shall restrict ourselves to finite graphs G which are undirected and line-coloured. For any points x, y in G, we shall write x y to mean that x and y are adjacent and by x w1 y to mean that x y and the colour of the line joining x and y is i. Also, we shall denote the line joining x and y by Xy; the colour of Xy by c(xy); and the set {c(Xy)l x y in Gl by C(G). Let G and H be (undirected, line-coloured) graphs. A one to one mapping ffrom G onto His called an isomorphism if the following two conditions are satisfied:
8408042
The Rat Genome Database (RGD): developments towards a phenome database
The Rat Genome Database (RGD) (http://rgd.mcw.edu) aims to meet the needs of its community by providing genetic and genomic infrastructure while also annotating the strengths of rat research: biochemistry, nutrition, pharmacology and physiology. Here, we report on RGD's development towards creating a phenome database. Recent developments can be categorized into three groups. (i) Improved data collection and integration to match increased volume and biological scope of research. (ii) Knowledge representation augmented by the implementation of a new ontology and annotation system. (iii) The addition of quantitative trait loci data, from rat, mouse and human to our advanced comparative genomics tools, as well as the creation of new, and enhancement of existing, tools to enable users to efficiently browse and survey research data. The emphasis is on helping researchers find genes responsible for disease through the use of rat models. These improvements, combined with the genomic sequence of the rat, have led to a successful year at RGD with over two million page accesses that represent an over 4-fold increase in a year. Future plans call for increased annotation of biological information on the rat elucidated through its use as a model for human pathobiology. The continued development of toolsets will facilitate integration of these data into the context of rat genomic sequence, as well as allow comparisons of biological and genomic data with the human genomic sequence and of an increasing number of organisms.
41020572
Cycle Partitions in Graphs
In this paper, we prove that every graph contains a cycle intersecting all maximum independent sets. Using this, we further prove that every graph with stability number α is spanned by α disjoint cycles. Here, the empty set, the graph of order 1 and the path of order 2 are all considered as degenerate cycles.
61209915
CiteSpace II: Detecting and visualizing emerging trends and transient patterns in scientific literature
This article describes the latest development of a generic approach to detecting and visualizing emerging trends and transient patterns in scientific literature. The work makes substantial theoretical and methodological contributions to progressive knowledge domain visualization. A specialty is conceptualized and visualized as a time-variant duality between two fundamental concepts in information science: research fronts and intellectual bases. A research front is defined as an emergent and transient grouping of concepts and underlying research issues. The intellectual base of a research front is its citation and co-citation footprint in scientific literature—an evolving network of scientific publications cited by research-front concepts. Kleinberg's (2002) burst-detection algorithm is adapted to identify emergent research-front concepts. Freeman's (1979) betweenness centrality metric is used to highlight potential pivotal points of paradigm shift over time. Two complementary visualization views are designed and implemented: cluster views and time-zone views. The contributions of the approach are that (a) the nature of an intellectual base is algorithmically and temporally identified by emergent research-front terms, (b) the value of a co-citation cluster is explicitly interpreted in terms of research-front concepts, and (c) visually prominent and algorithmically detected pivotal points substantially reduce the complexity of a visualized network. The modeling and visualization process is implemented in CiteSpace II, a Java application, and applied to the analysis of two research fields: mass extinction (1981–2004) and terrorism (1990–2003). Prominent trends and pivotal points in visualized networks were verified in collaboration with domain experts, who are the authors of pivotal-point articles. Practical implications of the work are discussed. A number of challenges and opportunities for future studies are identified. © 2006 Wiley Periodicals, Inc.