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1 1 of 4 18/11/ HOME ABOUT LOG IN REGISTER SEARCH CURRENT ARCHIVES ANNOUNCEMENTS ARCHIVES (EMBNET.NEWS) CONTACT Home > Archives > Vol 18 Supplement B OPEN JOURNAL SYSTEMS Journal Help USER Username Password Remember me Log In NETTAB 2012 Table of Contents Entire issue EMBnet.journal 18 Suppl. B ARTICLES Editorial HTML p. 2 BITS Introduction HTML p. 3 Preface - NETTAB 2012 Workshop on Integrated HTML Bio-Search, Paolo Romano, Frédérique Lisacek pp. 4-7 Scientific Programme pp Keynote Lectures Integration and analysis of multi-type high-throughput data for biomolecular knowledge discovery Erik Bongcam-Rudloff p. 13 Semantics based biomedical knowledge search, integration and discovery Barend Mons p. 14 Clinical and genomic data integration in support of biomedical research and clinical practice Eric Neumann p. 15 Tutorials Multi-scale data integration and virtual exploration from promoters, through networks to drug targets Alexander Kel p. 17 The Taverna Workbench: Integrating and analysing biological and clinical data with computerised workflows Katy Wolstencroft p. 18 Oral Communications Rational design of organelle compartments in cells FONT SIZE JOURNAL CONTENT Search All Search Browse By Issue By Author By Title INFORMATION For Readers For Authors For Librarians KEYWORDS COST ChIP-seq EMBnet ISCB Italian Bioinformatics Society RIBio RNA-seq annual meeting bioinformatics services committee report data analysis education gene expression metagenomics next generation sequencing node report resequencing small RNA structural bioinformatics training CURRENT ISSUE

2 2 of 4 18/11/ Claudio Angione, Giovanni Carapezza, Jole Costanza, pp Pietro Lió, Giuseppe Nicosia Filtering with alignment free distances for high throughput DNA reads assembly Maria C De Cola, Giovanni Felici, Daniele Santoni, pp Emanuel Weitschek A semantic collaborative system for the management of translational research projects Matteo Gabetta, Giuseppe Milani, Cristiana Larizza, pp Valentina Favalli, Eloisa Arbustini, Riccardo Bellazzi Answering Gene Ontology terms to proteomics questions by supervised macro reading in Medline Julien Gobeill, Emilie Pasche, Douglas Teodoro, pp Anne-Lise Veuthey, Patrick Ruch Using graph theory to analyze gene network coherence Francisco Gómez-Vela, Norberto Díaz-Díaz, José A pp Lagares, José A Sánchez, Jesús S Aguilar-Ruiz The open source ISA software suite and its international user community: knowledge management of experimental data Alejandra González-Beltrán, Eamonn Maguire, pp Philippe Rocca-Serra, Susanna-Assunta Sansone Network-based gene-disease prioritization using PROPHNET Víctor Martínez, Carlos Cano, Armando Blanco pp QTreds: a flexible LIMS for omics laboratories Piergiorgio Palla, Gianfranco Frau, Laura Vargiu, pp Patricia Rodriguez-Tomé Development of a text search engine for medicinal chemistry patents Emilie Pasche, Julien Gobeill, Fatma Oezdemir-Zaech, pp Therese Vachon, Christian Lovis, Patrick Ruch The ontogene system: an advanced information extraction application for biological literature Fabio Rinaldi pp IntelliGenWiki: An Intelligent Semantic Wiki for Life Sciences Bahar Sateli, Marie-Jean Meurs, Greg Butler, Justin pp Powlowski, Adrian Tsang, René Witte ROCK: a resource for integrative breast cancer data analysis Saif Ur-Rehman, Costas Mitsopoulos, Marketa Zvelebil pp Technological Industrial Communications Extracting knowledge from biomedical data through Logic Learning Machines and Rulex Marco Muselli pp Data modeling: the key to biological data integration François Rechenmann pp Short Oral Communications BioQuery-ASP: querying biomedical databases and ontologies using answer set programming Esra Erdem, Umut Oztok pp A strategy to reduce technical variability and bias in RNA sequencing data Francesca Finotello, Enrico Lavezzo, Luisa Barzon, pp Paolo Mazzon, Paolo Fontana, Stefano Toppo, Barbara Di Camillo Applications of a generic model of genomic variations functional analysis Sarah Mapelli, Uberto Pozzoli pp Ranking-aware integration and explorative search of distributed bio-data, Matteo Picozzi, Giorgio Ghisalberti pp DiGSNP: a web tool for Disease-Gene-SNP hierarchical prioritization Carmen Navarro, Carlos Cano, Armando Blanco, pp Fernando García-Alcalde

3 3 of 4 18/11/ The BioVel Project: Robust phylogenetic workflows running on the GRID Saverio Vicario, Bachir Balech, Giacinto Donvito, Pasquale Notarangelo, Graziano Pesole pp Posters Empowering web portal users with personalized text mining services Fedor Bakalov, Marie-Jean Meurs, Birgitta König-Ries, pp Bahar Sateli, Rene Witte, Greg Butler, Adrian Tsang Ordering copy number alteration data to analyze colorectal cancer progression Iuliana M. Bocicor, Giulio Caravagna, Alex Graudenzi, pp Claudia Cava, Giancarlo Mauri, Marco Antoniotti Glycans, the forgotten biomolecular actors of the big picture Matthew P. Campbell, Julien A. Mariethoz, Catherine pp M. Hayes, Pauline G. Rudd, Niclas G. Karlsson, Nicki H. Packer, Frédérique Lisacek Genomic and proteomic data integration for comprehensive biodata search Arif Canakoglu, pp Generation of explicit rules predicting neuroblastoma patients outcome Davide Cangelosi, Fabiola Blengio, Rogier Versteeg, pp Angelika Eggert, Alberto Garaventa, Claudio Gambini, Massimo Conte, Alessandra Eva, Luigi Varesio Simulation of caspases apoptotic signalling pathway in a tuple space-based bioinformatics infrastructure Maura Cárdenas-García, Pedro P González-Pérez, Sara pp Montagna Chromosome instability for tumor progression inference Claudia Cava, Italo Zoppis, Manuela Gariboldi, James pp F. Reid, Marco Antoniotti, Giancarlo Mauri Distilling structure in scientific workflows Juiqiang Chen, Christine Froidevaux, Carole Goble, pp Alan R. Williams, Sarah Cohen-Boulakia CorrelaGenes: a new tool for the interpretation of the human transcriptome Paolo Cremaschi, Sergio Rovida, Lucia Sacchi, pp Antonella Lisa, Alessandra Montecucco, Giuseppe Biamonti, Silvia Bione, Gianni Sacchi Business intelligence for biopharmaceutical company Anass El Haddadi, Bernard Dousser pp Biomedical Text Mining for Disease Gene Discovery Sarah ElShal, Jesse Davis, Yves Moreau pp An ontological-based knowledge organization for bioinformatics workflow management system Antonino Fiannaca, Massimo La Rosa, Salvatore pp Gaglio, Riccardo Rizzo, Alfonso Urso A tool for the extraction of new disease biomarkers from ex vivo and in vivo data Francesca Gallivanone, Carla Canevari, Isabella Sassi, pp Alberto Marassi, Maria Picchio, Maria C Gilardi, Isabella Castiglioni Prediction and 3D visualization of biological networks using cytological disease mapping Björn Sommer, Vladimir Ivanisenko, Patrizio Arrigo, pp Ralf Hofestädt A Grid-enabled web platform for integrated digital biobanking in paediatrics Massimiliano Izzo, Andrea Schenone, Sara Barzaghi, pp Fabiola Blengio, Marco M Fato, Luigi Varesio MBLabDB: a social database for molecular biodiversity data Flavio Licciulli, Domenico Catalano, Domenica D'Elia, pp Giorgio De Caro, Giorgio Grillo, Pietro Leo, Giuseppina Mulè, Paolo Pannarale, Graziano Pappadà, Francesco Rubino, Antonella Susca, Saverio Vicario, Gaetano Scioscia

4 4 of 4 18/11/ A multivariate analysis of protein microarrays for signature selection profiles Saveria Mazzara, Antonella Sinisi, Angela Cardaci, pp Sergio Abrignani, Mauro Bombaci Extracting correspondences between terminologies for an easier access to biomedical information Adila Merabti, Lina F Soualmia, Stéfan J Darmoni pp Detection of allele-specific gene expression on Next Generation Sequencing data Vladan Mijatovic, Luciano Xumerle, Alberto Ferrarini, pp Ilaria Iacobucci, Chiara Pighi, Antonio Mori, Chiara Zusi, Paola Prandini, Elisabetta Trabetti, Massimo Delledonne, Giovanni Martinelli, Alberto Zamò, Pier F Pignatti, Giovanni Malerba Network-based analysis of stem cells differentiation Francesca Mulas, Lan Zagar, Blaz Zupan, Riccardo pp Bellazzi AnnotateGenomicRegions: a web application Heiko Muller, Luca Zammataro, Gabriele Bucci pp G-SNPM - A GPU-based SNP mapping tool Alessandro Orro, Andrea Manconi, Emanuele Manca, pp Giuliano Armano, Luciano Milanesi HARP: an automated platform for targeted resequencing data analysis Fernando Palluzzi pp The integration of microrna target data by biclustering techniques opens new roads for signaling networks analysis Gianvito Pio, Michelangelo Ceci, Corrado Loglisci, pp Donato Malerba, Domenica D'Elia ONCO-i2b2: improve patients selection through CBR techniques with heterogeneous distance functions Daniele Segagni, Matteo Gabetta, Valentina Tibollo, pp Arianna Dagliati, Alberto Zambelli, Cristiana Larizza, Silvia G Priori, Riccardo G Bellazzi Bioinformatics approach for data management about bone cells grown on substitute materials Federica Viti, Ivan Merelli, Silvia Scaglione, Luciano pp Milanesi A first RDF implementation of the COSMIC database on mutations in cancer Achille Zappa, Paolo Romano pp This work is licensed under a Creative Commons Attribution 3.0 License. ISSN:

5 4 EMBnet.journal Volume 18 Nr. B Preface NETTAB 2012 Workshop on Integrated Bio-Search 1, Paolo Romano 2, Frédérique Lisacek IRCCS San Martino IST, Genova, Italy 3 NETTAB Workshops are a series of International meetings on Network Tools and Applications in Biology held annually in Italy. They are aimed at introducing participants to the most promising among those innovative Information and Communication Technologies (ICTs) that are being applied to the biomedical application domain. Workshops include many focused sessions which are devoted to tools, systems, applications, and perspectives. Keynote lectures introduce the sessions topics, and are followed by presentations selected from among the submitted contributions after peer review by members of the Scientific Committee. Discussion is a key factor, both within sessions and in a special Panel Discussion. Tutorials and poster sessions complete the agenda of the NETTAB workshops. Each year, the workshop is focused on a different technology or domain. Since 2001, many different topics, often related to data integration issues, were discussed. These included, e.g., Standardization for data integration (Genoa, 2001), Multi agent systems (Bologna, 2002), Scientific workflows (Naples, 2005), Grid and Web Services (Santa Margherita di Pula, 2006), The Semantic Web (Pisa, 2007), Collaborative research and development (Catania, 2009), Biological wikis (Naples, 2010), and Clinical Bioinformatics (Pavia, 2011). The NETTAB 2012 workshop, the twelfth in the series, was held in Como, Italy, on November Its rationale is based on the consideration that the data deluge of the current post-genomic era is providing scientists with potentially very valuable information, but it makes difficult to find and extract from the increasing available highthroughput omics data those information that are most reliable, specific and most related to the biomedical questions to be answered. Such questions are increasingly complex and they often simultaneously regard many heterogeneous aspects of an organism, tissue, cell and the role of all biomolecular entities. Several of these questions can be addressed only by comprehensively searching different types of data, which generally are distributed in many heterogeneous sources. Usually, scientists explore these data by using the individual search services and tools available in Internet and they then struggle in combining the essential information in order to answers their global questions. In this context, moreover, quality and consistency checking is a central issue that should be brought up Searching and combining all open and linked data and algorithmic sources has the potential of reshaping the scenario of current bioinformatics applications, going beyond the capabilities of conventional tools, Web services and existing search engines. Yet, it also presents new technological challenges. Solving data integration and automatic extraction problems requires new solutions, including the use of universal URIs, efficient indexing, partial or approximate value matching, rank aggregation, continuous or push-based search, exploratory methods and context-aware paradigms, collaborative and social search, and building new efficient information retrieval approaches, based on automation of workflows too that may contribute to new good practices in data searching, retrieval, and integration, with the specific goal of ensuring quality of procedures, as well as their reproducibility coupled with efficiency and efficacy. On these premises, then, the NETTAB 2012 workshop has been focused on Integrated Bio- Search, which includes all aspects that relate to technologies, methods, architectures, systems and applications for searching, retrieving, integrating and analyzing data, information, knowledge, infrastructures, services and tools that are required to answer complex bio-medical-molecular questions. Workshop topics included four main areas. The first area relates to data integration. It in-

6 Volume 18.A EMBnet.journal 5 cludes syntactic and semantic methods and algorithms for biological and clinical data and knowledge integration, information and knowledge retrieval, data and knowledge query, data, information and knowledge extraction, and data and knowledge mining. The second area refers to new and optimized technologies for data management. It includes federated databases, data warehouses, and triple stores. It also includes topics as biomedical terminologies and ontologies, systems interoperability, natural language processing, and scientific workflow processing. Tools and platforms for molecular data management and storage, deep sequencing analysis, omics data computing, search computing, decision support, and clinical bioinformatics are the third topic area, while the fourth area includes examples of applications of these methods, technologies and tools in different biomedical domains, such as knowledge assessment, integration, discovery, and validation, drug design, diagnosis and prognosis support, and personalized medicine. The Call for abstracts was able to attract 34 submissions for oral communications. From Speakers Keynote Speakers Erik Bongcam-Rudloff Swedish University of Agricultural Sciences, and Uppsala University, Sweden Barend Mons Leiden University Medical Center, and Netherlands Bioinformatics Center, The Netherlands Eric Neumann PanGenX, and Clinical Semantics Technologies, USA Tutorials Alexander Kel GeneXplain GmbH, Wolfenbüttel, Germany, and Biosoft.ru, Skolkovo Center of Bioinformatics, Novosibirsk, Russian Federation Katy Wolstencroft School of Computer Science, University of Manchester, United Kingdom these submissions, the Scientific Committee of the workshop was able to select 12 oral communications, seven short oral communications, and three technological communications from industry. All submissions underwent peer review by at least two members of the Scientific Committee. At the workshop, 29 posters were also presented. Submissions for posters were also peer reviewed by one or two members of the Scientific Committee. This Supplement therefore includes about 50 abstracts, all revised according to reviews, which are grouped by submission type and ordered by first author name. The NETTAB 2012 workshop has been a great meeting for all researchers involved in data search and integration in biology and medicine. It was possible to discuss ideas, and doubts, with such scientists as Erik Bongcam-Rudloff, Barend Mons, Eric Neumann, Alexander Kel, Katy Wolstencroft, who accepted to give invited lectures and tutorials, and many others who enthusiastically joined the workshop. And, of course, the workshop has been a great occasion to enjoy Italian lifestyle... Oral presentations Claudio Angione Bachir Balech Esra Erdem Giovanni Felici Francesca Finotello Matteo Gabetta Francisco Gómez-Vela Alejandra Gonzalez-Beltran Claudia Gugenmus Víctor Martínez Marco Muselli Carmen Navarro Piergiorgio Palla Uberto Pozzoli François Rechenmann Fabio Rinaldi Patrick Ruch Bahar Sateli Saif Ur-Rehman

7 6 EMBnet.journal Volume 18 Nr. B Editors Paolo Romano Frédérique Lisacek Editorial Staff Davide Chicco Arif Canakoglu IRCCS San Martino IST, Genoa, Italy Chairs and Conference Committees Chairs Paolo Romano Frédérique Lisacek IRCCS San Martino IST, Genoa, Italy Scientific committee Francisco Azuaje Riccardo Bellazzi Olivier Bodenreider Mario Cannataro Bastien Chopard Marie-Dominique Devignes Christine Froidevaux Carole Goble Nicolas le Novère Ulf Leser Frédérique Lisacek Paolo Magni Roberto Marangoni Luciano Milanesi Paolo Missier Heiko Muller Norman Paton Horacio Pérez-Sánchez Paolo Romano Patrick Ruch Indra Neil Sarkar Organising Committee Arif Canakoglu Davide Chicco Centre de Recherche Public de la Santé, Luxemburg University of Pavia, Italy National Institutes of Health, USA University Magna Græcia of Catanzaro, Italy Swiss Institute of Bioinformatics, University of Geneva, Switzerland CNRS LORIA, France University Paris-Sud, France The University of Manchester, United Kingdom European Bioinformatics Institute, United Kingdom Humboldt University, Germany University of Pavia, Italy University of Pisa, Italy Biomedical Technologies Institute, CNR, Italy Newcaste University, United Kingdom Istituto Italiano di Tecnologia, Italy University of Manchester, United Kingdom University of Murcia, Spain IRCCS San Martino IST, Genoa, Italy University of Applied Sciences, Geneva, Switzerland University of Vermont, USA Organization Staff Centro Studi Scientifici Alessandro Volta, Como, Italy

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