Biochemical network matching and composition

This paper looks at biochemical network matching and compositio

Composition of Biochemical Networks using Domain Knowledge

Graph composition has applications in a variety of practical applications. In drug development, for instance, in order to understand possible drug interactions, one has to merge known networks and examine topological variants arising from such composition. Similarly, the design of sensor nets may use existing network infrastructures, and the superposition of one network on another can help with network design and optimisation. The problem of network composition has not received much attention in algorithm and database research. Here, we work with biological networks encoded in Systems Biology Markup Language (SBML), based on XML syntax. We focus on XML merging and examine the algorithmic and performance challenges we encountered in our work and the possible solutions to the graph merge problem. We show that our XML graph merge solution performs well in practice and improves on the existing toolsets. This leads us into future work directions and the plan of research which will aim to implement graph merging primitives using domain knowledge to perform composition and decomposition on specific graphs in the biological domain

reSearch : enhancing information retrieval with images

Combining image and text search is an open research question. The main issues are what technologies to base this solution on, and what measures of relevance to employ. Our reSearch prototype mashes up papers indexed using information retrieval techniques (Terrier) with Google image search for faces and Google book search. The user can interactively employ query expansion with additional terms suggested by Terrier, and use those terms to expand both the text and image search. We test this solution with a selection of recent publications and queries concerning people engaged in research. We report on the effectiveness of this solution. It seems that the combination works to a large extent, as testified by our observations

Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

Background: TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory. Results: We report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL http://spira.zoology.gla.ac.uk/app/tbasewrapper.php The methodology we developed is scalable and can be applied to new data, as those become available in the future. Conclusion: Significantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection

VisGenome: visualization of single and comparative genome representations

Summary: VisGenome visualizes single and comparative representations for the rat, the mouse and the human chromosomes at different levels of detail. The tool offers smooth zooming and panning which is more flexible than seen in other browsers. It presents information available in Ensembl for single chromosomes, as well as homologies (orthologue predictions including ortholog one2one, apparent ortholog one2one, ortholog many2many) for any two chromosomes from different species. The application can query supporting data from Ensembl by invoking a link in a browser. Availability: http://www.dcs.gla.ac.uk/~asia/VisGenome Contact: [email protected]

Proposal for a Standard Representation of Two-Dimensional Gel Electrophoresis Data

The global analysis of proteins is now feasible due to improvements in techniques such as two-dimensional gel electrophoresis (2-DE), mass spectrometry, yeast two-hybrid systems and the development of bioinformatics applications. The experiments form the basis of proteomics, and present significant challenges in data analysis, storage and querying. We argue that a standard format for proteome data is required to enable the storage, exchange and subsequent re-analysis of large datasets. We describe the criteria that must be met for the development of a standard for proteomics. We have developed a model to represent data from 2-DE experiments, including difference gel electrophoresis along with image analysis and statistical analysis across multiple gels. This part of proteomics analysis is not represented in current proposals for proteomics standards. We are working with the Proteomics Standards Initiative to develop a model encompassing biological sample origin, experimental protocols, a number of separation techniques and mass spectrometry. The standard format will facilitate the development of central repositories of data, enabling results to be verified or re-analysed, and the correlation of results produced by different research groups using a variety of laboratory techniques

Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies

This paper summarises the lessons and experiences gained from a case study of the application of semantic web technologies to the integration of data from the bacterial species Francisella tularensis novicida (Fn). Fn data sources are disparate and heterogeneous, as multiple laboratories across the world, using multiple technologies, perform experiments to understand the mechanism of virulence. It is hard to integrate these data sources in a flexible manner that allows new experimental data to be added and compared when required

Associations de kystes de dinoflagellés des séries du Jurassique supérieur (Oxfordien–Tithonien) du Rif externe (Prérif interne et Mésorif, Maroc) et comparaisons régionales = Dinoflagellate cyst assemblages of the Upper Jurassic (Oxfordian–Tithonian) from the External Rif Chain (Internal Prerif and Mesorif, Morocco) and regional comparisons

A biostratigraphic study of dinoflagellate cysts of the Upper Jurassic series from the eastern External Rif Chain, has been achieved for the first time on four outcrop sections : the DM section (Douar Marticha), the TB section (the Tarhchenna “Sof”), the KSD section (the Kef Mallou “Sof”) and the Y section (Douar Lamriene) among which three sections (TB, KSD and Y) are well-dated by ammonites and calpionellids fauna. The DM and TB sections are complementary in terms of stratigraphy and correspond respectively to the upper part of the “Ferrysch” Formation, a thick shaly–silty and sandy sequence assigned to the Callovian-Oxfordian stages and to the El Gouzat limestones Formation (Kimmeridgian - Lower Tithonian age) and to the Tarhchenna marly limestones Formation (Upper Tithonian age) from the EL Gouzat area (Mesorif). The KSD and Y sections are also complementary and correspond to the Kimmeridgian-Lower Tithonian Msila limestones Formation and to the overlying marly limestones Massif Formation of Upper Tithonian age, outcropping in the Msila region (Internal Prerif). These four sections have shown many dinocysts rich levels, which had allowed characterizing the Middle? and Upper Oxfordian substages in the DM section. In the other sections, the dinoflagellate cyst assemblages are nearly similar to those of the Kimmeridgian–Tithonian of many sections from the Boreal, Sub-boreal and North tethyan realms, particularily from England, Russia and South-East France basin. The results of the present work confirm once again, the important value of dinoflagellate cysts, for age dating of ammonites-lacking Mesozoic sedimentary sequences and for biostratigraphic correlations

Strange Particle Production in pp Collisions at sqrt(s) = 0.9 and 7 TeV

Peer reviewe