Exposing The Cancer Genome Atlas (TCGA) as a SPARQL endpoint

Automated discovery of candidate biomarkers from multiple databases has been the central challenge in the Life Sciences in general and in the study of systemic processes such as those documented by The Cancer Genome Atlas (TCGA) in particular. 

The maturation of Semantic Web technologies offers solutions to those problems by allowing the query to be defined by navigating a normally represented domains of discourse instantiated by the data. 

We address the systems challenge of The Cancer 
Genome Atlas initiative (http://cancergenome.nih.gov/), which generates a large scale repository of high throughput molecular biology data generated and processed at 5 academic facilities across the USA

A Linked Data Approach to Help Identify Therapeutic Targets for Cancer

Cancer is still one of the leading causes of death in the developed world. To address this problem, the US National Institutes of Health (NIH) has launched The Cancer Genome Atlas (TCGA), a large scale systematic approach to characterize tumor samples from 20 cancer types and approximately 10,000 donor patients by using multiple high-throughput approaches. 

Multidisciplinary projects such as TCGA and related projects across Europe aim at identifying cancer “driver” mutations to be used as therapeutic targets or diagnostic tests. Extracting and aggregating the knowledge necessary to identify such mutations remains a challenge primarily due to the need to reliably integrate the experimental datasets with heterogeneous, distributed biomedical data sources, including public databases, biomedical literature and controlled access clinical information. 

Linked Data is a set of best practices to integrate and link data with those characteristics. We present here a method to easily integrate and enrich high-throughput experiment results such as those generated by TCGA, with public biomedical data sources such as Diseasome, DrugBank or KEGG, available in Linked Data formats

Evolution of particle density in high-energy pp collisions

We study the evolution of the particle density, dn/d\eta at fixed \eta with the beam rapidity Y in the framework of string percolation model. Our main results are: (i) The width of the "plateau" increases proportionally to Y, (ii) limiting fragmentation is violated, and (iii) the particle density, reduces to a step function.Comment: 8 pages, 2 figures, to appear in Nuclear Physics A. Minor changes are don

Absorption and J/psi Suppression in Heavy Ion Collisions

We discuss the J/psi suppression in the framework of multiple collision models. From the analysis of the Pb-Pb NA50 data we conclude that the strength of the absorption has increased, but we find no clear evidence for the formation of the quark-gluon plasma.Comment: 8 pages, 4 figure

String Percolation and the Glasma

We compare string percolation phenomenology to Glasma results on particle rapidity densities, effective string or flux tube intrinsic correlations, the ridge phenomena and long range forward-backward correlations. Effective strings may be a tool to extend the Glasma to the low density QCD regime. A good example is given by the minimum of the negative binomial distribution parameter k expected to occur at low energy/centrality.Comment: Submitted to Phys. Lett

String and Parton Percolation

A brief review to string and parton percolation is presented. After a short introduction, the main consequences of percolation of color sources on the following observables in A-A collisions: $J/\psi$ suppression, saturation of the multiplicity, dependence on the centrality of the transverse momentum fluctuations, Cronin effect and transverse momentum distributions, strength of the two and three body Bose-Einstein correlations and forward-backward multiplicity correlations, are presented. The behaviour of all of them can be naturally explained by the clustering of color sources and the dependence of the fluctuations of the number of these clusters on the density.Comment: 7 pages, 6 figures. Plenary talk given at Hard Probes 2004, Ericeira, Portuga

Energy conservation and scaling violations in particle production

We use a simple Colour Glass Condensate/String Percolation Model argument to show the existence, due to energy conservation, of bounds to the violation of Feynman scaling and limiting fragmentation.Comment: 5 pages, 1 figure. Final versio

Density saturation and the decrease of the normalised width of the multiplicity distribution in high energy pp collisions

It is experimentally observed that the width of the KNO multiplicity distribution --or the negative binomial parameter 1/k-- for pp collisions, in the energy region 10 to 1800 GeV, is an increasing function of the energy. We argue that in models with parton or string saturation such trend will necessary change: at some energy the distribution will start to become narrower. In the framework of percolating strings, we have estimated the change to occur at an energy of the order of 5--10 TeV.Comment: 10 pages, 4 figures, uses elsart and amsmath; comparison with some other models was added; version accepted by PL

Cumulative particle production as a rare event

The generalization of the Glauber formula for cumulative production events is derived. On its basis the multiplicity distribution in such events is related to the one in the minimum bias events. As compared to the rare events of type $C$, the formula involves a shift in the arguments determined by the multiplicity from a collision with a cluster of several nucleons.Comment: 11 pages, LaTe