Accepted Posters
Category 'N'- Databases'
Poster N01
MetaCyc and the BioCyc Collection of Pathway/Genome Databases
Peter Karp- SRI International
Ron Caspi (SRI International, Bioinformatics Research Group); Carol Fulcher (SRI International, Bioinformatics Research Group); Michelle Green (SRI International, Bioinformatics Research Group); Pallavi Kaipa (SRI International, Bioinformatics Research Group); Ingrid Keseler (SRI International, Bioinformatics Research Group); Markus Krummenacker (SRI International, Bioinformatics Research Group); Mario Latendresse (SRI International, Bioinformatics Research Group); Suzanne Paley (SRI International, Bioinformatics Research Group); Alexander Shearer (SRI International, Bioinformatics Research Group);
Short Abstract: MetaCyc is a universal database of experimentally determined metabolic
pathways and enzymes, focused primarily on microbial and plant
metabolism. BioCyc is a collection of 260 organism-specific
Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the
predicted metabolic network of one organism.
Long Abstract: Click Here

Poster N03
The Mammalian Protein Complex Database (MPCDB)
Andreas Ruepp- GSF
Andreas Ruepp (GSF, Institute for Bioinformatics/MIPS); Barbara Brauner (GSF, Institute for Bioinformatics); Irmtraud Dunger (GSF, Institute for Bioinformatics); Goar Frishman (GSF, Institute for Bioinformatics); Corinna Montrone (GSF, Institute for Bioinformatics); Octave Noubibou-Doudieu (GSF, Institute for Bioinformatics); Volker Stuempflen (GSF, Institute for Bioinformatics); Werner Mewes (GSF, Institute for Bioinformatics);
Short Abstract: Protein complexes occupy a pivotal position in cells since they are central players in various vital functions like protein synthesis and cell cycle. MPCDB is a manually annotated resource of mammalian protein complexes, providing not only the composition of protein complexes but also information like cellular localization and cellular function.
Long Abstract: Click Here

Poster N04
InSide4D: A cross species expression pattern database
Yannick Haudry- EMBL Heidelberg (European Molecular Biology Laboratory)
Thorsten Henrich (EMBL Heidelberg, Centre for Computational Biology);
Short Abstract: High-resolution gene expression data acquired by whole mount in situ- or antibody experiments is stored in model organism databases such as ZFIN (zebrafish), BDGP (drosophila), MEPD (medaka). We have set up InSide4D to allow scientists to query, compare and analyse gene expression data across species.
InSide4D is available at ani.embl.de/inside
Long Abstract: Click Here

Poster N05
The Identifier Mapping Service: cross-referencing protein identifiers across multiple reference databases
Richard Cote- EMBL - EBI
Richard C?t? (EMBL-EBI, Proteomic Services); Philip Jones (EMBL-EBI, Proteomic Services); Lennart Martens (EMBL-EBI, Proteomic Services); Quan Lin (EMBL-EBI, Sequence Database Group); Rolf Apweiler (EMBL-EBI, Sequence Database Group); Henning Hermjakob (EMBL-EBI, Proteomic Services);
Short Abstract: Mapping protein identifiers across various databases is a considerable challenge that is exacerbated by unstable and deleted identifiers. The Identifier Mapping Service (IMS) presented here solves this problem by mapping lists of identifiers or sequences to any combination of protein databases via an interactive interface or a SOAP webservice.
Long Abstract: Click Here

Poster N06
CoryneRegNet ? An Integrative Online Database for the Analysis of Transcriptional Regulatory Networks of Corynebacteria and E. coli
Jan Baumbach- Bielefeld University
Tobias Wittkop (Bielefeld University, Center for Biotechnology); Jan Baumbach (Bielefeld University, Center for Biotechnology); Andreas Tauch (Bielefeld University, Center for Biotechnology); Sven Rahmann (Bielefeld University, Center for Biotechnology);
Short Abstract: CoryneRegNet (http://www.coryneregnet.de) is an online database designed to facilitate the reconstruction of transcriptional regulatory networks of bacteria. It integrates TFBS matching, network visualization and comparison, and Microarray based network analysis. CoryneRegNet 3.1 now also provides (publicly available) SOAP based Web Service interfaces to GenDB (genome annotations) and EMMA (Microarray data).
Long Abstract: Click Here

Poster N07
UniProtJAPI - A Remote API For Accessing UniProt
Samuel Patient- EBI - European Bioinformatics Institute
Nataliya Sklyar (EBI, Sequence Database); Michael Kleen (EBI, Sequence Database); Emilio Salazar (EBI, Sequence Database); Dani Wieser (EBI, Sequence Database); Samuel Patient (EBI, Sequence Database); Ernst Kretschmann (EBI, Sequence Database); Rolf Apweiler (EBI, Sequence Database);
Short Abstract: UniProtJAPI is part of the Universal Protein Resource (UniProt). It provides a minimum maintenance Java API that enables users to retrieve over 4 million distinct UniProtKB protein sequences, with their annotations in a fine-grain level of detail. UniProtJAPI is available at http://www.ebi.ac.uk/uniprot/remotingAPI/ .
Long Abstract: Click Here

Poster N08
PairsDB web server: hyperlinked atlas of protein sequence space
Andreas Heger- University of Oxford
Liisa Holm (University of Helsinki, Institute of Biotechnology); Taavi Hupponen (Center for Scientific Computing, CSC); Eija Korpelainen (Center for Scientific Computing, CSC); Kimmo Mattila (Center for Scientific Computing, CSC); Samuli Eldfors (Institute of Biotechnology, University of Helsinki);
Short Abstract: PairsDB (http://pairsdb.csc.fi) is a web server intended as a way to explore protein sequences and their similarity relationships quickly and easily. Instead of running BLAST or PSI-BLAST individually on each request, results are retrieved instantaneously from a database of pre-computed alignments. Matches can be filtered and viewed as stacked alignments.
Long Abstract: Click Here

Poster N09
MADIBA: An integrated web toolkit for the biological interpretation of Plasmodium and plant gene clusters.
Philip Law- University of Pretoria
Fourie Joubert (University of Pretoria, Bioinformatics and Computational Biology Unit); Dave Berger (University of Pretoria, Forestry and Agricultural Biotechnology Institute); Clotilde Claudel-Renard (Biogemma, Laboratoire de Biologie Cellulaire et Mol?culaire);
Short Abstract: Clusters of genes showing significant differential expression can be derived from microarray experiments. The MADIBA (MicroArray Data Interface for Biological Annotation) toolkit automatically assigns biological meaning to these gene expression clusters by identifying GO terms, metabolic pathways, transcriptional co-regulation and chromosomal localisations in clusters of Plasmodium, Arabidopsis or rice genes.
Long Abstract: Click Here

Poster N10
Viral encoded microRNAs predictions
Wen-chang Lin- Academia Sinica
Sung-Chou Li (Academia Sinica, Institute of Biomedical Sciences); Cheng-Kai Shiau (Academia Sinica, Institute of Biomedical Sciences);
Short Abstract: Using a previous established hairpin secondary structure and features selection filters, we have searched 2,266 published viral genome sequences from NCBI for putative miRNA hairpins and identified 33,691 viral miRNA candidates. A web user interface is established to query the predicted viral miRNA hairpins and to perform target gene predictions.
Long Abstract: Click Here

Poster N11
Gene Name Service
Kuan-Ting Lin- Academia Sinica, Taiwan
Kuan-Ting Lin (Academia Sinica, Taiwan, Institute of Information Science); Chia-Hung Liu (Academia Sinica, Taiwan, Institute of Information Science); Jen-Jie Chiou (Academia Sinica, Taiwan, Institute of Information Science); Wen-Hsien Tseng (Academia Sinica, Taiwan, Institute of Information Science); Chun-Nan Hsu (Academia Sinica, Taiwan, Institute of Information Science);
Short Abstract: Gene Name Service (GNS) retrieves and organizes data from HUGO, NCBI, and GeneCards to provide gene alias resolution services for 26 different types of gene identifiers of Homo sapiens genes via both Web server and Web Service interfaces with an automatic updating process. GNS is available at http://bioagent.iis.sinica.edu.tw/GeneAlias.
Long Abstract: Click Here

Poster N12
BiodiveR ? A Federated Query Engine
Oliver Karch- Merck KGaA
Thomas Grombacher (Merck KGaA, Bio- and Chemoinformatics); Anja von Heydebreck (Merck KGaA, Bio- and Chemoinformatics); Friedrich Rippmann (Merck KGaA, Bio- and Chemoinformatics);
Short Abstract: The BiodiveR federated query engine dynamically aggregates information from various biomedical data-sources in a flexible way by simultaneously querying disparate data repositories e.g. relational databases, ontologies, full-text, sequence indexes, web-services etc. Execution plans specifying a biomedical concept?s retrieval process are evaluated at runtime allowing dynamic search strategies to be realized.
Long Abstract: Click Here

Poster N13
A Data Resource on Splice-Mediated Changes in Isoform Protein Sequences.
Alphonse Thanaraj Thangavel- CRS4
Massimiliano Orsini (CRS4, Bioinformatics); Matteo Floris (CRS4, Bioinformatics); Anna Tramontano (CRS4, Bioinformatics);
Short Abstract: We have developed a computational pipeline that characterizes splice-mediated isoform protein sequences for functional & structural differences and involvement in disease processes. Classes of affected proteins include receptors, hydrolases, transferases, transport proteins, RNA/DNA associated proteins, cytokines and growth factors. The resultant value-added data is presented at CRS4 web pages.
Long Abstract: Click Here

Poster N14
BioMart ? a query oriented data management system
Damian Smedley- EBI
Richard Holland (EBI, Wellcome Trust Genome Campus); Syed Haider (EBI, Wellcome Trust Genome Campus); Benoit Ballester (EBI, Wellcome Trust Genome Campus); Lincoln Stein (Stein laboratory, Cold Spring Harbor Laboratory); Ewan Birney (EBI, Wellcome Trust Genome Campus); Peter Rice (EBI, Wellcome Trust Genome Campus); Arek Kasprzyk (EBI, Wellcome Trust Genome Campus);
Short Abstract: BioMart at www.biomart.org is an Open Source generic data management system consisting of:
(i) a selection of user interfaces including a website that can be standalone installed and customised according to requirements.
(ii) the administration tools to ?mart? configure your own data.
(iii) web-services, Perl and Java APIs for programmatic access.
Long Abstract: Click Here

Poster N15
The OverView systems biology platform
Martin Werber- Max Planck Institute for Molecular Genetics
Phillip Grote (Max Planck Institute for Molecular Genetics, Developmental Genetics); Bernhard G. Herrmann (Max Planck Institute for Molecular Genetics, Developmental Genetics);
Short Abstract: The OverView systems biology platform integrates the analysis of large scale experimental data such as ChIP-chip, expression profiling and massive parallel sequencing data. The analyzed data is presented to the user in the context of additional biological information serving as a tool for the elucidation of regulatory networks.
Long Abstract: Click Here

Poster N16
IGetDB ? Towards a Bioinformatics Online Analytical Processing Platform
Kai Runte- Bielefeld University
Tim Nattkemper (Bielefeld University, Department of Technology); Alexander Goesmann (Bielefeld University, BRF);
Short Abstract: IGetDB is an OLAP platform based on BioMart (http://www.biomart.org/). The current prototype offers a user-friendly web-interface for issuing queries. Data can be imported from GenDB, SAMS and EMMA. The results of a query can be first previewed, then be exported as Excel sheets, HTML, and other formats.
Long Abstract: Click Here

Poster N17
MyoBase: a multi organism database focusing on muscle development and muscular diseases.
David Salgado- Developmental Biology Institute of Marseille-Luminy, IBDML
David Salgado (Developmental Biology Institute of Marseille-Luminy, IBDML , UMR6216 CNRS ); Gregory Gimenez (Developmental Biology Institute of Marseille-Luminy, IBDML, UMR6216 CNRS); Christophe Marcelle (Developmental Biology Institute of Marseille-Luminy, IBDML, UMR6216 CNRS);
Short Abstract: MyoBase is a bioinformatics system where all information related to muscle and muscular diseases will be available in one place. Data from various sources are correlated to allow an user to easily retrieve and compare a large amount of muscle-relevant information across species.
Long Abstract: Click Here

Poster N18
sRNAMap: Genomics Maps for sRNA Genes and Their Targets in Escherichia coli
Hsi-Yuan Huang- National Chiao Tung University
Hsi-Yuan Huang (National Chiao Tung University, Institute of Bioinformatics); Chi-Dung Yang (National Chiao Tung University, Department of Biological Science and Technology); Hsien-Da Huang (National Chiao Tung University, Institute of Bioinformatics); Ching-Ping Tseng (National Chiao Tung University, Department of Biological Science and Technology);
Short Abstract: The regulated role of small RNAs on the synthesis of proteins and the activity of specific proteins is important. Therefore, this research will develop an integrated database, sRNAMap, to store the known and putative sRNA genes and targets and the relationships between the sRNAs genes and the sRNA targets.
Long Abstract: Click Here

Poster N19
g:Profiler -? a web-based toolset for functional profiling of gene lists from large-scale experiments
J?ri Reimand- University of Tartu
Meelis Kull (University of Tartu, Institute of Computer Science); Hedi Peterson (Estonian Biocentre, Department of Bioinformatics); Jaanus Hansen (University of Tartu, Institute of Computer Science); Jaak Vilo (University of Tartu, Institute of Computer Science);
Short Abstract: g:Profiler is a web toolkit for characterising high-throughput gene lists. It retrieves statistically significant Gene Ontology terms, biological pathways, and Transfac motifs to genes, proteins or microarray probes, allows ranked lists analysis, multiple testing corrections, interactive visualisation, etc. The toolkit also provides ID conversions, ortholog mappings and expression similarity search.
Long Abstract: Click Here

Poster N20
Tools and Services within Bioinformatics Research
Janet Copeland- EMBL-EBI
Janet Copeland (EMBL-EBI, Outreach and Training); Vicky Schneider (EMBL-EBI, Outreach and Training); Alison Barker (EMBL-EBI, Outreach and Training); Cath Brooksbank (EMBL-EBI, Outreach and Training);
Short Abstract: The European Bioinformatics Institute is a unique resource which gathers and builds not only databases but ad hoc tools for searching/retrieving and interpreting bioinformatics data. Advances in Systems Biology call for a multidisciplinary platform from which to explore and extract information which EBI can provide, as shown in this poster.
Long Abstract: Click Here

Poster N21
ProGMap - Protein Groups Mapping
Arnold Kuzniar- Wageningen University and Research Centre
Ying He (Wageningen University and Research Centre, Laboratory of Bioinformatics); Blaise Alako (Wageningen University and Research Centre, Laboratory of Bioinformatics); Ke Lin (Wageningen University and Research Centre, Laboratory of Bioinformatics); Harm Nijveen (Wageningen University and Research Centre, Laboratory of Bioinformatics); Sandor Pongor (International Centre for Genetic Engineering and Biotechnology, Protein Structure and Bioinformatics); Jack A.M. Leunissen (Wageningen University and Research Centre, Laboratory of Bioinformatics);
Short Abstract: Comparison of protein classification databases is a non-trivial task due to the large and heterogeneous source datasets, different classification models, inconsistent sequence identifiers and sequence redundancy. We created an integrated system, ProGMap, which provides a versatile gateway to map and compare the large number of protein groups from diverse resources.
Long Abstract: Click Here

Poster N22
The Human Proteome Initiative
Silvia Jimenez- Swiss Institute of Bioinformatics
No additional authors
Short Abstract: The Human Proteome Initiative (HPI) aims at annotating all known human protein sequences and their mammalian orthologs according to the quality standards of UniProtKB/Swiss-Prot knowledgebase. We strive to provide for each protein, an accurate sequence, a wealth of information including the description of its function, domain structure, subcellular location, etc
Long Abstract: Click Here

Poster N23
Integration of Animal Venoms and Medicinal Plant
Renato Puga- University of Sao Paulo
Saulo F Amui (University of Sao Paulo, Department of Genetics); Andreimar M Soares (University of Sao Paulo, Departamento de An?lises Cl?nicas, Toxicol?gicas e Bromatol?gicas); Silvana Giuliatti (University of Sao Paulo, Department of Genetics);
Short Abstract: This database makes the integration of medicinal plants and animal venoms data and for this system it was chosen a content management system that was used for implementation of the interface and integration data. The system is on-line and ready to receive information from the groups and collaborators.
Long Abstract: Click Here

Poster N24
BeeVenom: a Venom of Apoidea (Hymenoptera) and medicinal plants relationship.
Daniel Jorge- Universty of Sao Paulo
Reanto D. Puga (Universty of Sao Paulo, Department of Genetics); Andreimar M Soares (Universty of Sao Paulo, Faculty of Science of Pharmacy of Ribeirao Preto ); Silvana Giuliatti (Universty of Sao Paulo , Department of Genetics);
Short Abstract: Bees are one of the most important insect in the world. Therefore we developed BeeVenom system that analyzes and organizes aspects of bee venom and integrates information of bee and medicinal plants. System was developed in web interface. This system will be a valuable source for researchers in this field.
Long Abstract: Click Here

Poster N25
SISYPHUS and the proteins that do not obey our rules.
Antonina Andreeva- MRC-CPE
Antonina Andreeva (MRC, CPE); Alexey Murzin (MRC, CPE); Andreas Prlic (Wellcome Trust, Sanger Centre); Tim Hubbard (Wellcome Trust, Sanger Centre);
Short Abstract: SISYPHUS is a compendium to the SCOP database and contains a collection of manually curated multiple structural alignments for proteins with structural relationships that do not fit into the SCOP hierarchy. The database provides a framework for structural annotation of different types of non-trivial protein relationships.
Long Abstract: Click Here

Poster N26
Protein Interaction Pool (PIP) - A comprehensive database and interface to protein interaction data
Alexander Mehrle- DKFZ
J?rg Kunert (DKFZ, MGA); Tim Beissbarth (DKFZ, MGA); David Zhang (DKFZ, MGA); Annemarie Poustka (DKFZ, MGA); Stefan Wiemann (DKFZ, MGA); Alexander Mehrle (DKFZ, MGA);
Short Abstract: Protein Interaction Pool (PIP) combines and integrates publicly available data from six major protein-protein interaction databases. The data is made non-redundant and available via an easy to use web-interface, a Distributed Annotation System (DAS)-server and via SOAP-compliant web-services. The interface to the database is freely available at: http://www.dkfz.de/mga/PIP
Long Abstract: Click Here

Poster N27
TB Gateway - a comprehensive database on Tuberculosis
Amrapali Zaveri- Sikkim-Manipal University
Chaitanya Gokhale (Sikkim-Manipal University, Bioinformatics); Deepak Waghchaware (Sikkim-Manipal University, Bioinformatics); Deepak Toppinkatti (Sikkim-Manipal University, Bioinformatics); Tejasvi Mahendraker (Sikkim-Manipal University, Bioinformatics); Shweta Jog (Sikkim-Manipal University, Bioinformatics); Sameera Kari (Sikkim-Manipal University, Bioinformatics); Suvarna Joshi (Sikkim-Manipal University, Bioinformatics);
Short Abstract: TB Gateway is an effort to create widespread awareness about Tuberculosis. It includes four databases, namely, drugs, herbs, strains and treatment units. Information about the disease, symptoms, diagnostic methods, prevention, alternative medicine, MDR-TB is also provided thus creating a platform where all relevant information about Tuberculosis is available at once.
Long Abstract: Click Here

Poster N28
ConquestExplorer - a Database Application Tool not only for Potato Genotypic and Phenotypic Data
Rico Basekow- RZPD GmbH
Axel Nagel (RZPD GmbH, Bioinformatics); Christiane Gebhardt (Max-Planck-Institut Koeln, Plant Breeding Research); Birgit Kersten (RZPD GmbH, Bioinformatics);
Short Abstract: The ConquestExplorer handles genomic and phenotypic data in a structured and consistent form to provide an overview and an efficient and standardised analysis of these data.
It has been developed in the scope of GABI-Conquest2 project which is aiming at identifying and characterising genes controlling quantitative pathogen resistance in potato by a candidate gene approach.
Long Abstract: Click Here

Poster N29
The Bielefeld Bioinformatics platform: Data Management and Data Integration in the ?-omics? Sciences
virginie Mittard-Runte- Bioinformatics Resource Facility (BRF)
Thomas Bekel (1Bioinformatics Resource Facility (BRF), Center for Biotechnology (CeBiTec), Bielefeld University); Michael Dondrup (Bioinformatics Resource Facility (BRF), Center for Biotechnology (CeBiTec), Bielefeld University); Kolja Henckel (Bioinformatics Resource Facility (BRF), Center for Biotechnology (CeBiTec), Bielefeld University); Burkhard Linke (Bioinformatics Resource Facility (BRF), Center for Biotechnology (CeBiTec), Bielefeld University); Kai Runte (Bioinformatics Resource Facility (BRF), Center for Biotechnology (CeBiTec), Bielefeld University); Alexander Goesmann (Bioinformatics Resource Facility (BRF), Center for Biotechnology (CeBiTec), Bielefeld University);
Short Abstract: Systems Biology, an emerging research field of biology, is fostered by the availability of high-throughput technology in genome and post-genome research. Only semantic integration of heterogeneous data sets allows for comprehensive discovery of new knowledge on biological systems. The BRF provides a comprehensive bioinformatics platform for genome and post-genome projects.
Long Abstract: Click Here

Poster N30
The Mouse Phenotype Database Integration Consortium: Integration of Mouse Phenome Data Resources
Simon Greenaway- MRC Mammalian Genetics Unit
John Hancock (MRC Mammalian Genetics Unit, Bioinformatics Group); Simon Greenaway (MRC Mammalian Genetics Unit, Bioinformatics Group); The Mouse Phenotype Database Integration Consortium (International, N/A);
Short Abstract: We describe a colaborative project involving groups from Europe, the USA and Japan to achive harmonisation of computational resources holding data on mouse phenotypes. Our aim is to improve access to this data and facilitate data mining.
Long Abstract: Click Here

Poster N31
EuroPhenome - http://www.europhenome.eu
Ann-Marie Mallon- MRC Mammalian Genetics Unit
Ann-Marie Mallon (MRC Mammalian Genetics Unit, Bioinformatics Group); Andrew Blake (MRC Mammalian Genetics Unit, Bioinformatics Group); Christopher Duran (MRC Mammalian Genetics Unit, Bioinformatics Group); Simon Greenaway (MRC Mammalian Genetics Unit, Bioinformatics Group); John Hancock (MRC Mammalian Genetics Unit, Bioinformatics Group);
Short Abstract: EuroPhenome is an online mouse phenotyping resource which has been developed to store phenome data derived from mice using the standardised tests contained in EMPReSS. EuroPhenome is the repository for phenotype data generated by the EUMODIC project, which will phenotype up to 500 knock-out lines generated by the EUCOMM project.
Long Abstract: Click Here

Poster N32
SABIO-RK: Data Source for Systems Biology
Ulrike Wittig- EML Research
Renate Kania (EML Research, -); Martin Golebiewski (EML Research, -); Olga Krebs (EML Research, -); Saqib Mir (EML Research, -); Andreas Weidemann (EML Research, -); Henriette Engelken (EML Research, -); Isabel Rojas (EML Research, -);
Short Abstract: SABIO-RK (http://sabio.villa-bosch.de/SABIORK/) is a curated database for the systems biology community containing biochemical reactions and their kinetic properties manually extracted from literature. In SABIO-RK kinetic data are related to reactions, organisms, and biological locations. The kinetic mechanism and corresponding rate equations are presented together with their parameters and experimental conditions.
Long Abstract: Click Here

Poster N33
EMPReSS ? http://www.empress.har.mrc.ac.uk/
Andrew Blake- MRC Mammalian Genetics Unit
Andrew Blake (MRC Mammalian Genetics Unit, Bioinformatics Group); Ann-Marie Mallon (MRC Mammalian Genetics Unit, Bioinformatics Group); Eain Green (MRC Mammalian Genetics Unit, Bioinformatics Group); Georgios Gkoutos (University of Cambridge, Department of Genetics); Heena Lad (MRC Mammalian Genetics Unit, EUMORPHIA); Mandy Studley (MRC Mammalian Genetics Unit, PRIME); Joseph Weekes (MRC Mammalian Genetics Unit, Bioinformatics Group); Hilary Gates (MRC Mammalian Genetics Unit, EU Office); John Hancock (MRC Mammalian Genetics Unit, Bioinformatics Group);
Short Abstract: EMPReSS (European Mouse Phenotyping Resource for Standardized Screens) is a comprehensive database of validated Standard Operating Procedures (SOPs) for screens to determine the phenotype of a mouse. It incorporates more than 150 new SOPs which cover all of the main body systems.
Long Abstract: Click Here

Poster N34
UniProt: the Universal Protein Resource
Maria Martin- European Bioinformatics Institute
No additional authors
Short Abstract: UniProt is a comprehensive resource on protein sequences and functional annotation, produced by EBI, PIR and SIB. It provides an expertly curated database (UniProt Knowledgebase), a comprehensive sequence repository (UniProt Archive), and non redundant data sets (UniProt Reference Clusters). UniMes contains Metagenomic and Environmental sequences. It is freely accessible: http://www.uniprot.org
Long Abstract: Click Here

Poster N35
DESITE: a complete database of destabilising sites in proteins of known
structure; indicating the location of potential binding sites
Marc Lensink- Universit? Libre de Bruxelles
Marc Lensink (Universit? Libre de Bruxelles, Center for Structural Biology and Bioinformatics); Beno?t Dessailly (University College London, Biomolecular Structure and Modelling); Shoshana Wodak (Hospital for Sick Children, Structural Biology and Biochemistry);
Short Abstract: The database is calculated from individual residue contribution to free energy of folding and updated automatically with the release of new structures. It does not rely on sequence conservation and may play an important future role in automated function prediction. Both interactive and WSDL-based XML-SOAP access is provided.
Long Abstract: Click Here

Poster N36
Protein Information Management System for the Membrane Protein Structure Initiative
Petr Troshin- STFC Daresbury Laboratory
Petr Troshin (STFC Daresbury Laboratory, SRD); Miroslav Papiz (STFC Daresbury Laboratory, SRD); Steve Prince (University of Manchester, Faculty of Life Sciences); Bill Lin (STFC Daresbury Laboratory, CSE); Edward Daniel (STFC Daresbury Laboratory, CSE); Susy Griffiths (University of York, York Structural Biology Laboratory); Jon Diprose (University of Oxford, Oxford Protein Production Facility); Johan van Niekerk (University of Dundee, Scottish Structural Proteomics Facility); Anne Pajon (European Bioinformatics Institute, EMBL Outstation - Hinxton); Chris Morris (SFTC Daresbury Laboratory, CSE); Marc Savitsky (University of Oxford, Oxford Protein Production Facility);
Short Abstract: Establishing large inter-organization consortia introduces novel communications and data exchange problems, which, together with the widespread of high-throughput techniques, dictate a critical need for innovative Laboratory Information Management Systems.
Such a system has been developed and used within the ?14M Structural Proteomics of Rational Targets initiative for 2 years
Long Abstract: Click Here

Poster N37
A Development of a geographic information web system of USP_RP Germoplasm DataBase.
Milton Faria Jr- UNAERP
Silvana Giuliatti (Universtiry of Sao Paulo, Genetics); Gustavo Caminiti (University of Sao Paulo, Genetics); Ana Lilia Marin (University of Sao Paulo, Genetics); Moacyr Mestriner (University of Sao Paulo, Genetics);
Short Abstract: We present a Geographic Information Web System using Content Management System Drupal and database Mysql to store data and information about matrices trees and derived populations which are part of the germoplasm data base ?USP/SP. We used SSR markers and have done statistic analyses to identify similarity between different species.
Long Abstract: Click Here

Poster N38
The Ensembl Variation Database: A database solution for variation, dense genotyping and resequencing data
Daniel Rios- EMBL-EBI
Paul Flicek (EBI, Ensembl); Ewan Birney (EBI, Ensembl); Yuan Chen (EBI, Ensembl); Arne Stabenau (EBI, Ensembl);
Short Abstract: We have created a database solution and software library designed to support multi-species variation data, dense genotype data and large-scale resequencing projects and have tested its ability to support the requirements posed by these challenging data types. Our tools are primarily designed for integration into the Ensembl project.
Long Abstract: Click Here

Poster N39
Dasty2
Rafael Jimenez- EMBL-EBI
Rafael Jimenez (EMBL-EBI, Proteomics Services); Antony Quinn (EMBL-EBI, Proteomics Services); Henning Hermjakob (EMBL-EBI, Proteomics Services);
Short Abstract: Dasty2 is a web client implemented for visualizing protein sequence feature information using the DAS protocol. The client merges collected data from DAS servers in order to provide the user with a unified view of those sequence-annotated features. Dasty2 allows multiple asynchronous DAS requests, as well as an interactive graphic functionality on the client side.
Long Abstract: Click Here

Poster N40
The Genome Reviews Database
Manuela Pruess- European Molecular Biology Laboratory
Paul Kersey (European Molecular Biology Laboratory, European Bioinformatics Institute); Rajesh Radhakrishnan (European Molecular Biology Laboratory, European Bioinformatics Institute); Peter Sterk (European Molecular Biology Laboratory, European Bioinformatics Institute); Rolf Apweiler (European Molecular Biology Laboratory, European Bioinformatics Institute);
Short Abstract: The Genome Reviews database provides an up-to-date, standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes. Genome Reviews contains over 880 genomes of archaea, bacteria, bacteriophages and selected eukaryota. Genome Reviews is available as a MySQL relational database, or a flat file format (http://www.ebi.ac.uk/GenomeReviews/).
Long Abstract: Click Here

Poster N41
Modware: An Object Oriented Perl Interface to the Chado Schema
Eric Just- Northwestern University
Eric Just (Northwestern University, Center for Genetic Medicine); Sohel Merchant (Northwestern University, Center for Genetic Medicine); Warren Kibbe (Northwestern University, Center for Genetic Medicine); Rex Chisholm (Northwestern University, Center for Genetic Medicine);
Short Abstract: Modware is an object-oriented Perl API that facilitates agile development and integration for genomics resources based on the Chado relational schema. It maps data from the database to in-memory Perl objects which semantically resemble biological entities. The architecture, coding practices, and sample use-cases are presented.
Long Abstract: Click Here

Poster N42
BioVenom: Database of Brazilian Serpents Venom and a Computational Analysis of Phosfolipases A2 Primary Structures
Saulo Amui- University of Sao Paulo
Renato D Puga (University of Sao Paulo, Department of Genetics); Andreimar M Soares (University of Sao Paulo, FCFRP / DACTB); Silvana Giuliatti (University of Sao Paulo, Department of Genetics);
Short Abstract: BioVenom is a system that offers a laboratory database of Brazilian snake venoms and natural antipoisons, analysis of pharmacological and biochemical data, as well as a computer tool for analysis of Phospholipase A2 primary structures, available in the internet (www.biovenom.net).
Long Abstract: Click Here

Poster N43
EMBL-Align: Multiple Sequence Alignment submission and retrieval
Robert Vaughan- EMBL-EBI
Gaurab Mukherjee (EMBL-EBI, Sequence Database Group); Weimin Zhu (EMBL-EBI, Sequence Database Group); Rolf Apweiler (EMBL-EBI, Sequence Database Group);
Short Abstract: The EMBL-Align database provides archival storage of protein and nucleotide multiple sequence alignments. Our dedicated submission system, Webin-Align, has recently been improved to ease submission of both new sequence data, and alignments of new and/or existing sequences. We have also improved crosslinks between alignments and other data types.
Long Abstract: Click Here

Poster N44
Data Storage and Mining of Helicobacter pylori Proteome
Klaus-Peter Pleissner- Max Planck Institute for Infection Biology
Franziska Schiele (University of Applied Sciences, Proteome Analysis); Robert Stein (Informatics&Biology, none); Peter R. Jungblut (Max Planck Institute for Infection Biology, Protein Analysis);
Short Abstract: Comprehensive collection of data, including 2-DE gel images and mass spectra, for the Helicobacter pylori proteome was realized in a web-accessible proteome database system. Taking these data, various sets of proteins have been compared in detail as regard of their physicochemical properties and functional classifications to discover new methodical and biological insights
Long Abstract: Click Here

Poster N45
NMR Manager ? Metabolomics software for interpreting complex NMR
Adrian Charlton- Central Science Laboratory
Robert Stones (Central Science Laboratory, Statistics and Informatics); James Donarski (Central Science Laboratory, NMR and Profiling);
Short Abstract: NMR Manager is a searchable database for storing, retrieving and interactively viewing NMR spectra and peak information. The software is designed to aid comparison and interpretation of spectra to identify metabolites in complex mixtures using novel automated peak detection algorithms and statistical methods.
Long Abstract: Click Here

Poster N46
PIRSF protein family classification system and its use in annotating UniProtKB protein records
Raja Mazumder- Georgetown University
No additional authors
Short Abstract: The PIRSF protein classification system (http://pir.georgetown.edu/pirsf/) reflects evolutionary relationship of full-length proteins and domains. PIRSFs are manually curated in terms of membership, annotation of biological functions, and sequence features. Curated families are used to create rules for protein names and functional sites to assist in the propagation of protein annotation in the UniProt Knowledgebase.
Long Abstract: Click Here

Poster N47
SchistoDB ? An integrated Schistosoma mansoni database
Adhemar Zerlotini- FIOCRUZ - CPqRR
RLV Moraes (FIOCRUZ - CPqRR, ); M Heiges (UGA, ); H Wang (UGA, ); AO Stahl (UGA, ); JC Kissinger (UGA, ); GC Oliveira (FIOCRUZ - CPqRR, );
Short Abstract: SchistoDB is a genomic database for the parasitic organism Schistosoma mansoni, the causative agent of schistosomiasis worldwide. The database currently incorporates all available Schistosoma mansoni sequence data in a single user-friendly database.
Long Abstract: Click Here

Poster N48
New Features of the Genome Browser at UCSC
Rachel Harte- University of California, Santa Cruz
Rachel Harte (University of California, Santa Cruz, Center for Biomolecular Science and Engineering); Heather Trumbower (University of California, Santa Cruz, Center for Biomolecular Science and Engineering); Donna Karolchik (University of California, Santa Cruz, Center for Biomolecular Science and Engineering); David Haussler (University of California, Santa Cruz, Center for Biomolecular Science and Engineering); W. James Kent (University of California, Santa Cruz, Center for Biomolecular Science and Engineering);
Short Abstract: The UCSC Genome Browser brings together a wealth of genomic annotations and data allowing the researcher to view and retrieve pertinent data using powerful data mining tools. A focus on key features of the browser includes the new in situ hybridization image viewer, genome-wide data visualization and variation data.
Long Abstract: Click Here

Poster N49
Database Tools for Human Gene
Nomenclature and Orthology
Michael Lush- UCL
Mathew Wright (UCL, Biology); Sue Povey (UCL, Biology); Elspeth Bruford (UCL, Biology);
Short Abstract: The HUGO Gene Nomenclature Committee (HGNC) is tasked with giving a unique and meaningful name and symbol to every human gene. We review the 'power user' features of our public database and HGNC Comparison of Orthology Predictions (HCOP), a service that compares orthology assertions from 10 databases and 8 species.
Long Abstract: Click Here

Poster N50
GeneAssist Pathway Atlas
Lisa Ni- RNAi
Lisa Ni (RNAi, Ambion);
Short Abstract: GeneAssist Pathway Atlas is a collection of 355 signal transduction, metabolic and disease state pathway maps. All pathways contain extensive reviews and references. Protein/gene information in each pathway can be retrieved through an interactive interface. The application is an essential research tool for understanding the mechanism of cellular signaling.
Long Abstract: Click Here

Poster N51
ProteomeAnalyst: Database for Human Proteome Compare and Analysis Comprehensively
Seul-Ki Jeong- Yonsei Proteome Research Center
Min-Seok Kwon (Yonsei Proteome Research Center, Department of Biochemistry); Eun Sik Kim (Yonsei Proteome Research Center, Department of Physics); Eun-Young Lee (Yonsei Proteome Research Center, Department of Biochemistry); Sang Yun Cho (Yonsei Proteome Research Center, Department of Biochemistry); Young-Ki Paik (Yonsei Proteome Research Center, Department of Biochemistry);
Short Abstract: ProteomeAnalyst is database that can facilitates various processes including data repository, search and metadata-gathering functions, which can automatically integrate datasets obtained from PPI, the gene ontology, protein domain, OMIM and other information on proteins in the proteome database.
Long Abstract: Click Here

Poster N52
The integrated herb database : From molecular interaction to clinical application
Bang Gul Oh- Kyunghee University
Mi Kyung Lee (Kyunghee University, College of Oriental Medicine); MinKyu Shin (Kyunghee University, College of Oriental medicine); Moochang Hong (Kyunghee University, College of Oriental Medicine); YangSeok Kim (Kyunghee University, College of Oriental Medicine);
Short Abstract: Scientific research in medicinal herbs requires investigation of its'molecular mechanism.Therefore, we constructed a DB for collection of the existing information and classifying its' relationships with genes/proteins.Furthermore, we extended the contents of DB to predict the molecular action of herbs .MySQL was used for database engine, and web interface was implemented by Java
Long Abstract: Click Here

Poster N53
DPTF: Database of Poplar Transcription Factors
Qihui Zhu- Peking University
Qihui Zhu (Peking University, College of life Sciences); Anyuan Guo (Peking University-, College of life Sciences); Ge Gao (Peking University, College of life Sciences); Minren Huang (Nanjing Forest University, College of life Sciences); Jinchu Luo (Peking University, College of life Sciences);
Short Abstract: DPTF is a plant transcription factor (TF) database containing 2,576 putative poplar TFs distributed in 64 families. These TFs were identified from both computational prediction and manual curation. We have provided extensive annotations including sequence features, functional domains, GO assignment and expression evidence for all TFs.
Long Abstract: Click Here

Poster N54
NATsDB: Natural Antisense Transcripts DataBase
Ge Gao- Peking University
Yong Zhang (Peking University); Jiongtang Li (Peking University); Lei Kong (Peking University); Qing-Rong Liu (NIH/NIDA/IRP); Liping Wei (Peking University);
Short Abstract: Natural antisense transcripts (NATs) regulate sense genes at multiple levels and are implicated in various diseases. We developed NATsDB (Natural Antisense Transcripts DataBase, http://natsdb.cbi.pku.edu.cn/) to enable efficient browsing, searching and downloading of this currently most comprehensive collection of sense/antisense genes, grouped into six classes based on their overlapping patterns.
Long Abstract: Click Here

Poster N55
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences
Taishin Kin- AIST
Taishin Kin (National Institute of Advanced Industrial Science and Technology (AIST), Computational Biology Research Center (CBRC)); Kouichirou Yamada (Information and Mathematical Science Laboratory Inc., Bio/Life Science System); Goro Terai (Intec Web and Genome Informatics Corporation, Bioinformatics Group); Hiroaki Okida (Intec Web and Genome Informatics Corporation, Bioinformatics Group); Yasuhiko Yoshinari (Mitsubishi Research Institute Inc., Advanced Science Research Center); Yukiteru Ono (Information and Mathematical Science Laboratory Inc, Bio/Life Science System); Aya Kojim (Intec Web and Genome Informatics Corporation, Bioinformatics Group); Takashi Komori (Intec Web and Genome Informatics Corporation, Bioinformatics Group); Kiyoshi Asai (Graduate School of Frontier Sciences, University of Tokyo, Department of Computational Biology);
Short Abstract: We introduce fRNAdb: a novel database service that hosts a large collection of non-coding transcripts including annotated/non-annotated sequences from the H-inv database, NONCODE, and RNAdb. fRNAdb allows users to computationally mine candidate functional transcripts from a pool of uncharacterized transcripts.
Long Abstract: Click Here

Poster N56
IntelliMS : Proteomic Consensus Validation Platform for Biomarker Discovery
Min-Seok Kwon- YPRC
Eun Sik Kim (Yonsei Proteome Research Center, Biochemistry); Seul-Ki Jeong (Yonsei Proteome Research Center, Biochemistry); Hyoung Joo Lee (Yonsei Proteome Research Center, Biochemistry); Eun-Young Lee (Yonsei Proteome Research Center, Biochemistry); Sang Yun Cho (Yonsei Proteome Research Center, Biochemistry); Young-Ki Paik (Yonsei Proteome Research Center, Biochemistry);
Short Abstract: IntelliMS, a new analytical and storage system is based on consensus approach by which one can determine the area of mass spectrometry(MS or MS/MS) data with high confidence by testing the accuracy of unbiased indices.
Long Abstract: Click Here

Poster N57
maize transcription factor database
Xin Chen- Center of Bioinformatics
Anyuan Guo (center of bioinfromatics, college of life scineces, Peking University); Ge Gao (center of bioinfromatics, college of life scineces, Peking University); Qihui Zhu (center of bioinfromatics, college of life scineces, Peking University); Kun He (center of bioinfromatics, college of life scineces, Peking University); Xiaocheng Gu (center of bioinfromatics, college of life scineces, Peking University); Jingchu Luo (center of bioinfromatics, college of life scineces, Peking University);
Short Abstract: The maize transcription factor database (ZmTF) collected a total of 764 putative transcription factors from Zea mays, distributed in 55 families. ZmTF provided annotations of sequence features, functional domains, Gene Ontology assignments, EST expression information, as well as multiple sequence alignments of DNA-binding domains of each family.
Long Abstract: Click Here

Poster N58
Enhanced access to biomedical databases through Web Services
Paolo Romano- National Cancer Research Institute
Chiara Rasi (National Cancer Research Institute, Bioinformatics); Domenico Marra (National Cancer Research Institute, Bioinformatics);
Short Abstract: We implemented Web Services for querying SRS public sites (about 1,000 databanks and 180 analysis tools) and other databases without programmatic access. They can identify the best site to search and return flexible results. We used SoapLab, MySQL and perl. Software is open source and can be downloaded.
Long Abstract: Click Here

Poster N59
Kazusa API: a web service for sequence and annotation resoureces in Kazusa DNA Research Institute
Mitsuteru Nakao- Kazusa DNA Research Institute
Shinobu Okamoto (Kazusa DNA Research Institute, Plant Genome Informatics); Yasukazu Nakamura (Kazusa DNA Research Institute, Plant Genome Informatics);
Short Abstract: Kazusa API project aims to provide web services for sequence and
annotation resources Kazusa DNA Research Institute provides. Kazusa API uses various web interface technologies including SOAP, REST, JSON and XML for accessing data. Kazusa API is builded up with Ruby on Rails.
Long Abstract: Click Here

Poster N60
HotSprint: Database of Computational Hot Spots at Protein Interfaces
Emre Guney- Koc University
Emre Guney (Koc University, Center for Computaitional Biology and Bioinformatics and College of Engineering ); Nurcan Tuncbag (Koc University, Center for Computaitional Biology and Bioinformatics and College of Engineering ); Attila Gursoy (Koc University, Center for Computaitional Biology and Bioinformatics and College of Engineering ); Ozlem Keskin (Koc University, Center for Computaitional Biology and Bioinformatics and College of Engineering );
Short Abstract: HotSprint is a database of computational hot spots at protein interfaces extracted from the multi-chain structures in Protein Data Bank (PDB). Hot spots are predicted based on sequence conservation and solvent accessibility of interface residues. The predicted hot spots are observed to correlate with the experimental hot spots.
Long Abstract: Click Here

Poster N61
Mapping the Binding Sites of Frequent Ligands in the Protein Data Bank
Zoltan Szabadka- Eotvos University
Gabor Ivan (Eotvos University, Computer Science); Vince Grolmusz (Eotvos University, Computer Science);
Short Abstract: We collected the residue-composition of the binding sites of the most frequently appearing ligands in protein-ligand complexes in the whole Protein Data Bank, and found association rules in the most frequently appearing ligands in the data.
Long Abstract: Click Here

Poster N62
A clinical data warehouse to support translational research
Hai Hu- Windber Research Institute
Mick Correll (InforSense Ltd, ); Michelle Osmond (InforSense Ltd., ); Jun Gao (InforSense Ltd., ); Anton Oleynikov (InforSense Ltd., ); Jonathan Sheldon (InforSense Ltd., ); Leonid Kvecher (Windber Research Institute, Biomedical Informatics); Richard Mural (Windber Research Institute, ); Craig Shriver (Walter Reed Army Medical Center, ); Michael Liebman (Windber Research Institute, );
Short Abstract: A data warehouse has been developed for the Clinical Breast Care Project, a translational research project. It is composed of an EAV data model, a questionnaire-based middle-tier, and a relational-OLAP. Developed on the innovative workflow-based Knowledge Discovery Environment platform, this data warehouse has greatly aided this translational research effort.
Long Abstract: Click Here

Poster N63
BlotBase: A Northern blot database
Andreas Teufel- Johannes Gutenberg University Mainz
Kai Schlamp (Johannes Gutenberg University , Department of Medicine I); Arndt Weinmann (Johannes Gutenberg University, Department of Medicine I); Markus Krupp (Johannes Gutenberg University, Department of Medicine I ); Peter R Galle (Johannes Gutenberg University, Department of Medicine I); Andreas Teufel (Johannes Gutenberg University, Department of Medicine I);
Short Abstract: BlotBase is a publically available (http://www.medicalgenomics.org/Databases/BlotBase) and easily accessable Northern blot database, designed to close the gap between individual highly reliable gene expression reports by means of published northern blots and available high throughput, genome wide expression data based on microarray experiments.
Long Abstract: Click Here

Poster N64
A Comparative miRNA Sequence and Expression Database
Ozlen Konu- Bilkent University
Koray Kaya (Bilkent University, Department of Molecular Biology and Genetics); Gokhan Karakulah (Dokuz Eylul University, Department of Medical Informatics, Institute of Health Sciences); Cengiz Yakicier (Bilkent University, Department of Molecular Biology and Genetics); Ozlen Konu (Bilkent University, Department of Molecular Biology and Genetics);
Short Abstract: miRNA Sequence and Expression Database at Bilkent University integrates and analyzes species-specific miRNA sequence information together with associated public microarray data. This database also uses GO annotation data of human miRNA targets for determining enrichment of GO terms in a subset of miRNAs.
Long Abstract: Click Here

Poster N65
Development of TMDU Clinical Omics Database
Ayako Fujisaki- Hitachi Software Engineering Co., Ltd.
Ayako Fujisaki (Hitachi Software Engineering Co., Ltd., Bioinformatics Department); Eiichi Araki (Hitachi Software Engineering Co., Ltd., Bioinformatics Department); Hiroshi Mizushima (Tokyo Medical and Dental University, University Center for Information Medicine); Hiroshi Tanaka (Tokyo Medical and Dental University, University Center for Information Medicine);
Short Abstract: We have developed TMDU Clinical Omics Database to store and analyze clinical omics data, which facilitates the understandings of relations between omics data and clinical data. For each case, the relationship is visualized as a network with three layers, clinical, pathological and omics layer.
Long Abstract: Click Here

Poster N66
GnpSNP : a database for storing plant polymorphism data
Fabienne Granier- INRA
Fabienne Granier (INRA, Genetics and plant breeding); Nicolas Grimault (INRA, EPGV); Cyril Pommier (INRA, URGI); Erik Kimmel (INRA, URGI); Frederic Sapet (INRA, URGI); Farid Chetouani (INRA, URGI); Delphine Grando (INRA, URGI); Jean-Baptiste Guidier (INRA, URGI); Frederic Potier (INRA, URGI); François Artiguenave (INRA, URGI); Delphine Steinbach (INRA, URGI); Dominique Brunel (INRA, EPGV);
Short Abstract: SNPs have an increasing role in plant genomics. Their discovery is laborious, but high-throughput genotyping platforms facilitate this task. We have built a database, GnpSNP, dedicated to the storage and analysis of plant polymorphism (SNP, insertion, deletion). GnpSNP constitutes a module of a global information system dedicated to plant genomics.
Long Abstract: Click Here

Poster N67
Visually enabling the construction of ontology-based cross-database queries
Kieran O'Neill- National Bioinformatics Network (South Africa)
Alexander Garcia-Castro (National Bioinformatics Network (of South Africa)/Center for Tropical Agricultural Research (Colombia), -); Dan Jacobson (National Bioinformatics Network (South Africa) , Central Node);
Short Abstract: We present a system for visually enabling the construction of ontology-based cross-database queries. Our system aims to make use of principles from the studies of information visualisation, human computer interaction, and visual cognition to provide cognitive support to biologists constructing these queries.
Long Abstract: Click Here

Poster N68
A geometrical extension of the RSPDB
Rafael Ördög- Protein Information Technology Group, Eotvos University, Budapest
Rafael Ördög (Protein Information Technology Group, Eotvos University, Budapest, Computer Science); Vince Grolmusz (Protein Information Technology Group, Eotvos University, Budapest, Computer Science); Zoltán Szabadka (Protein Information Technology Group, Eotvos University, Budapest, Computer Science);
Short Abstract: The RS-PDB is a cleaned version of the PDB, created by Z.Szabadka, and V.Grolmusz. In our current research we aim to calculate additional information and extend the RSPDB, to further aid geometrical searches.
The presented work describes the notion of Delaunay Tessellations, and difficulties with applying it to proteins.
Long Abstract: Click Here

Poster N69
Explicit Domain Family Hierarchies in the Conserved Domain Database (CDD)
Gabriele Marchler- National Institutes of Health
Aron Marchler-Bauer (NIH, NCBI); John B. Anderson (NIH, NCBI); Myra Derbyshire (NIH, NCBI); Carol DeWeese-Scott (NIH, NCBI); Farideh Chitsaz (NIH, NCBI); Noreen Gonzales (NIH, NCBI); Marc Gwadz (NIH, NCBI); David I. Hurwitz (NIH, NCBI); John D. Jackson (NIH, NCBI); Zhaoxi Ke (NIH, NCBI); Dmitri Krylov (NIH, NCBI); Christopher J. Lanczycki (NIH, NCBI); Cynthia A. Liebert (NIH, NCBI); Chunlei Liu (NIH, NCBI); Fu Lu (NIH, NCBI); Michael Mullokandov (NIH, NCBI); James S. Song (NIH, NCBI); Paul A. Thiessen (NIH, NCBI); Roxanne A. Yamashita (NIH, NCBI); Jodie J. Yin (NIH, NCBI); Dachuan Zhang (NIH, NCBI); Steve H. Bryant (NIH, NCBI);
Short Abstract: CDD is a resource for the annotation of domain footprints on protein sequences, which provides structure-based alignments and database search reagents for ancient orthologous groups of domains. CDD is built by expert curators, and links homologous domain models into explicit hierarchies, to reflect evolutionary history and functional divergence.
Long Abstract: Click Here

Poster N70
INOH pathway database and BioPAX export
Ken Fukuda- AIST
Satoko Yamamoto (JST(Japan Science and Technology Agency), BIRD(Institute for Bioinformatics Research and Development)); Noriko Sakai (JST(Japan Science and Technology Agency), BIRD(Institute for Bioinformatics Research and Development)); Hiromi Nakamura (Information and Mathematical Science Laboratory, Inc, Tokyo); Toshihisa Takagi (University of Tokyo, Graduate School of Frontier Sciences);
Short Abstract: INOH is a manually curated biological database of signal transduction pathways. As a member of the BioPAX working group, INOH has exported the data into BioPAX level 2 and BioPAX next level format. The BioPAX level 2 export includes more than 1970 interaction instances, 7583 physicalEntityParticipant.
Long Abstract: Click Here

Poster N71
Gramene, A growing comparative genome resource for Grasses
Chengzhi Liang- Cold Spring Harbor Laboratory
Chengzhi Liang (Cold Spring Harbor Laboratory, ); Shuly Avraham (Cold Spring Harbor Laboratory, ); Ed Buckler (Cornell University, USDA-ARS); Payan Canaran (Cold Spring Harbor Laboratory, ); Terry Casstevens (Cornell University, ); Ben Faga (Cold Spring Harbor Laboratory, ); Claire Hebbard (Cornell University, ); Bonnie Hurwitz (Cold Spring Harbor Laboratory, ); Pankaj Jaiswal (Cornell University, ); Susan McCouch (Cornell University, ); Junjian Ni (Cornell University, ); Dean Ravenscroft (Cornell University, ); Liya Ren (Cold Spring Harbor Laboratory, ); Will Spooner (Cold Spring Harbor Laboratory, ); Isaak Tecle (Cornell University, ); Doreen Ware (Cold Spring Harbor Laboratory, USDA-ARS); Jim Thomason (Cold Spring Harbor Laboratory, ); Sharon Wei (Cold Spring Harbor Laboratory, ); Immanuel Yap (Cornell University, ); Chih-Wei Tung (Cold Spring Harbor Laboratory, ); Lincoln Stein (Cold Spring Harbor Laboratory, );
Short Abstract: Gramene (www.gramene.org) is a curated comparative genetic and genomic resource for plants with a focus on grass species (eg, rice). The data includes genomes, genes, proteins, pathways, genetic/physical maps, QTLs, and genetic variations. This presentation will focus on recent updates.
Long Abstract: Click Here

Poster N72
A Molecular Genetics Information System (MOLGENIS) for Genetical Genomics experiments
Morris Swertz- University of Groningen
Morris Swertz (University of Groningen, Groningen Bioinformatics Center); Bruno Tesson (University of Groningen, Groningen Bioinformatics Center); Richard Scheltema (University of Groningen, Groningen Bioinformatics Center); Gonzalo Vera Rodriguez (University of Groningen, Groningen Bioinformatics Center); Ritsert Jansen (University of Groningen, Groningen Bioinformatics Center);
Short Abstract: Genetical genomics experiments accumulate (molecular) phenotype data on a large scale. We report a software infrastructure to store, navigate and retrieve data via a user interface or connect R and Java programs using a programmatic interface. To suit their research, groups can generate their own infrastructure-variant using MOLGENIS’ tools.
Long Abstract: Click Here

Poster N73
BiG: An Integrated Warehouse System for Brassica Genetic Resources
Fady Mohareb- Cranfield University
Fady Mohareb (Cranfield University, Cranfield Health); Graham King (Rothamsted Research, Bioinformatics Department); Conrad Bessant (Cranfield University, Cranfield Health);
Short Abstract: This poster describes the development of Brassica.info Genetics (BiG), an integrated warehouse system for Brassica genetic and breeding data. We describe the different aspects of the system architecture, this includes the generation of transformation parsers that enabled querying of the data repository, and the association of data browsing, retrieval and genetic mapping visualisation tools.
Long Abstract: Click Here

Poster N74
Web services at the European Bioinformatics Institute
Alberto Labarga- European Bioinformatics Institute
Alberto Labarga (European Bioinformatics Institute, External Services); Frank valentin (European Bioinformatics Institute, External Services); Rodrigo Lopez (European Bioinformatics Institute, External Services);
Short Abstract: Web Services technology gives scientists access to remote data and analysis applications as if they were installed on their laboratory computers. We will present the range of services we are developing at the European Bioinformatics Institute and how they can be used to construct complex analysis workflows.
Long Abstract: Click Here

Poster N75
CiTOX-Classification and Identification of toxins
Venkatakrishnan A.J- VIT University
Rohit Reja (VIT University, School of Biotechnology,Chemical and Biomedical Engineering); Abhishek Pratap (VIT University, School of Biotechnology,Chemical and Biomedical Engineering); Febin Prabhudas (VIT University, School of Biotechnology,Chemical and Biomedical Engineering);
Short Abstract: CiTOX is a dual interface server. CiTOX-C: For providing information on protein toxins and CiTOX-I: For identification of a protein sequence as a potential toxin. Classification is done by constructing HMM database from the MSA profiles of the conserved domains of known protein toxins.
Long Abstract: Click Here

Poster N76
Integration and Reassessment of Public Protein-Protein Interaction Data
Wolfgang StraĂźer- Upper Austrian University of Applied Sciences
Thomas Kern (Upper Austrian University of Applied Sciences, Research Center Hagenberg); Christian Frech (Upper Austrian University of Applied Sciences, Research Center Hagenberg); Michael Kommenda (Upper Austrian University of Applied Sciences, Research Center Hagenberg); Johann Bauer (Paracelsus Private Medical University Salzburg, Department of Dermatology); Kamil Ă–nder (Paracelsus Private Medical University Salzburg, Department of Dermatology);
Short Abstract: Technical redundancy, caused by missing linking identifiers or multiple submissions of identical information, poses a major problem during biological data integration. Within the scope of the InSilico Proteomics (ISP) project, publicly available protein-protein interaction (PPI) data are integrated and conferred to generate a non-redundant, comprehensive PPI data pool.
See: http://biomis.fh-hagenberg.at/isp/primos.
Long Abstract: Click Here

Poster N77
SAALSA, a UniProtKB/Swiss-Prot curator assistant for structural data integration
Fabrice David- Swiss Institute of Bioinformatics
Fabrice P.A. David (Swiss Institute of Bioinformatics, Swiss-Prot group); Anne-Lise Veuthey (Swiss Institute of Bioinformatics, Swiss-Prot group); Yum Lina Yip (Swiss Institute of Bioinformatics, Swiss-Prot group);
Short Abstract: SAALSA (Semi-Automatic Annotation from Local Structural Analysis) is a web-based interface designed to help annotation of proteins in UniProtKB/Swiss-Prot using structural data. This application facilitates annotation by gathering and crosschecking the information available from different structures. Built-in annotation rules and sequence to structure mappings further enforce consistency in annotation.
Long Abstract: Click Here

Poster N78
Navigating microbial space using the StrainInfo.net bioportal
Peter Dawyndt- Ghent University
Bart Van Brabant (Ghent University, Laboratory of Microbiology); Bernard De Baets (Ghent University, Research Unit Knowledge-based Systems); Paul De Vos (Ghent University, Laboratory of Microbiology); Peter Dawyndt (Ghent University, Department of Applied Mathematics and Computer Science);
Short Abstract: The StrainInfo.net portal envisions to overcome some of the problems related to the integration of basic information on biological resources as disseminated by hundreds of BRCs worldwide with the dynamically growing amount of downstream information that is generated on these organisms.
Long Abstract: Click Here

Poster N79
Agile Development and MVC Framework for Public-Health Databases: Implementing Ruby on Rails in HepSEQ and HepSEQ-Research
Saravanamuttu Gnaneshan- Health Protection Agency
Saravanamuttu Gnaneshan (Health Protection Agency, Bioinformatics, SMB, CFI); Anthony Underwood (Health Protection Agency, Bioinformatics, SMB, CFI); Joanne Moran (Health Protection Agency, Bioinformatics, SMB, CFI); Samreen Ijaz (Health Protection Agency, VRD, CFI); Mary Ramsay (Health Protection Agency, CFI); Jonathan Green (Health Protection Agency, Bioinformatics, SMB, CFI);
Short Abstract: Agile software development principles together with Model-View-Controller framework can be used to develop database solutions for bioinformatic projects. Public-health web databases, HepSEQ and HepSEQ-Research have recently been migrated to Ruby-on-Rails following agile methodologies. The database web interfaces, functionalities and the lessons learnt during the processes are shown on this poster.
Long Abstract: Click Here

Poster N80
The Stanford Microarray Database
Janos Demeter- Stanford University
Janos Demeter (Stanford University, Biochemistry); Heng Jin (Stanford University, Biochemistry); Farrell wymore (Stanford University, Biochemistry); Donald Maier (Stanford University, Biochemistry); Catherine Beauheim (Stanford University, Genetics); Michael Nitzberg (Stanford University, Biochemistry); Zachariah Zachariah (Stanford University, Biochemistry); Catherine Ball (Stanford University, Biochemistry); Gavin Sherlock (Stanford University, Genetics);
Short Abstract: The Stanford Microarray Database (SMD; http://smd.stanford.edu /) is a research database with an integrated collection of web-based, open-source tools that is open to the public. SMD development focuses on more effective and powerful representation of biological sequences, improved experiment annotation using biological ontologies and the use of MAGE file formats.
Long Abstract: Click Here

Poster N81
The EMBL Nucleotide Sequence Database (EMBL-BANK)- A publicly available repository of nucleotide sequences
Gaurab Mukherjee- EMBl-European Bioinformatics Institute
Gaurab Mukherjee (EMBl-European Bioinformatics Institute, Sequence Database Group); Robert Vaughan (EMBl-European Bioinformatics Institute, Sequence Database Group); Guy Cochrane (EMBl-European Bioinformatics Institute, Sequence Database Group);
Short Abstract: EMBL Nucleotide Sequence Database (EMBL-BANK) is a public repository of nucleotide sequences. Sequences are submitted by a number of methods according to data type and the submitter’s experience and requirements. The different methods are discussed and recent innovations in data deposition are introduced.
Long Abstract: Click Here

Poster N82
The new Pfam proteins families database website
Robert Finn- Wellcome Trust Sanger Institute
John Tate (WTSI, Informatics); Jaina Mistry (WTSI, Informatics); Penny Coggill (WTSI, Informatics); Alex Bateman (WTSI, Informatics);
Short Abstract: The Pfam database is a large collection of manually curated protein domains, each represented by multiple sequence alignments and hidden Markov models (HMMs). We have recently implemented a new website, providing a rich interface to the Pfam data, a variety of search tools and several programmatic interfaces.
Long Abstract: Click Here

Poster N83
Identification and Analysis of new EST dataset: Lepidopteran Choristoneura fumiferana
Lan Li- GLFC, Natural Resources Canada
Dayu Zhang (GLFC, Natural Resources Canada, Biotech Group); Peter Krell (University of Guelph, Molecular and Cellular Biology); Basil Arif (GLFC, Natural Resources Canada, Biotech); Daniel Doucet (GLFC, Natural Resources Canada, Biotech);
Short Abstract: Second EST dataset of C. fumiferana has been generated and annotated from several cDNA libraries using RNA isolated from tissues, such as embryos, diapausing, adult head etc. The dynamic C. fumiferana annotated EST database provides an informative platform for the scientific community to conduct gene cloning and identification of this forest insect.
Long Abstract: Click Here

Poster N84
Data centralization, integration, dissemination and web interface of the Human Salivary Proteome Project
Weihong Yan- University of California, Los Angeles
Weihong Yan (University of California, Los Angeles, Bioinformatics User Facility); Weixia Yu (University of California, Los Angeles, School of Dentistry); Shawn Than (University of California, Los Angeles, School of Dentistry); Joe Loo (University of California, Los Angeles, Chemistry and Biochemistry); David Wong (University of California, Los Angeles, School of Dentistry);
Short Abstract: We describe here a data central repository, integration, standardization and dissemination system built for the Human Salivary Proteome Project (HSPP) and its web resource. The system and web resource can be valuable for other proteome projects and biomedical research.
Long Abstract: Click Here

Poster N85
Archiving and distribution of genomic databases using virtualization technology
Todd Harris- Cold Spring Harbor Laboratory
No additional authors
Short Abstract: Virtualization -- or the ability to run an operating system entirely within another -- offers an easy solution to the challenges of archiving and distributing large genomic databases.
Long Abstract: Click Here

Poster N86
HspDB
Aditya Jitta- VIT University
Venkatakrishnan A.J (VIT University, School of biotechnology,chemical and biomedical engineering); Viswateja Nelakuditi (VIT Univesity, School of biotechnology, chemical and biomedical engineering);
Short Abstract: HspDB is a web application conceived to provide a fast and easy access to information on heat shock protein. It is a suite of tools with applications of presenting ontology information, organ specific protein information,generation of phylogenetic trees and a novel search engine which adapts dynamically to their priorities
Long Abstract: Click Here

Poster N87
Database of known therapeutic targets and a druggability index for sequences in SwissProt and PDB database
Julio Lopes- UFMG
Eduardo C. Campos (UFMG, Chemistry);
Short Abstract: A database of known therapeutic targets sequences has been constructed and the data was used to calculate a druggability index for protein sequences deposited in SwissProt and PDB databases. This index could be used to predict whether a sequence is a therapeutic target or is related to any therapeutic target.
Long Abstract: Click Here

Poster N88
A Design of the Terms Dictionary for Data Modeling on
Eunjoo Yang- Korea Centers for Disease Control and Prevention
Jung-Eun Lee (Korea Centers for Disease Control and Prevention, Center for Genome Science); Keun-Joon Park (Center for Genome Science, Center for Genome Science); Ju-Young Lee (Korea Centers for Disease Control and Prevention, Center for Genome Science); Kyungsoo Oh (Korea Centers for Disease Control and Prevention, Center for Genome Science); Hyun-Woo Han (Korea Centers for Disease Control and Prevention, Center for Genome Science);
Short Abstract: We designed terms dictionary in DB design level for the standard about enti
ties and attribute names of KSNP, Association Genotype, kGene DB at Center
for Genome Science in KNIH.

261 attribute names, 171 column names from three DB were collected and 61 s
yllables used commonly and representatively were extracted.
Long Abstract: Click Here

Poster N89
ArrayExpress Warehouse--a database of gene expression profiles
Misha Kapushesky- EBI
Misha Kapushesky (EBI, Microarray Informatics Team); Ibrahim Emam (EBI, Microarray Informatics Team); Hugo Berube (EBI, Microarray Informatics Team); Ugis Sarkans (EBI, Microarray Informatics Team); Alvis Brazma (EBI, Microarray Informatics Team); Helen Parkinson (EBI, Microarray Informatics Team); Ele Holloway (EBI, Microarray Informatics Team); Richard Coulson (EBI, Microarray Informatics Team); Anna Farne (EBI, Microarray Informatics Team); Margus Lukk (EBI, Microarray Informatics Team); Tim Rayner (EBI, Microarray Informatics Team); Eleanor Williams (EBI, Microarray Informatics Team);
Short Abstract: ArrayExpress Warehouse is a new gene-centric database at the EBI. Populated with curated, normalized data from the ArrayExpress Repository, it allows to visualize, compare and rank genes in terms of strengh of differential expression across experiments. Fully re-annotated array designs enable queries across different platforms over gene and sample properties.
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Poster N90
ProteinSQL: A novel Database Library for derived structural information from PDB data
Kerstin Koch- Hasselt University & Transnational University of Limburg
Wouter Gelade (University of Hasselt and Transnational Univerisity of Limburg, WNI); Tom Kellens (University of Hasselt and Transnational University of Limburg, WNI); Dirk Leinders (University of Hasselt and Transnational University of Limburg, WNI); Jan Leynen (University of Hasselt and Transnational University of Limburg, WNI); Stephen Martens (University of Hasselt and Transnational University of Limburg, WNI); Jan Van den Bussche (University of Hasselt and Transnational University of Limburg, WNI);
Short Abstract: We present a new database library for PDB data that contains
SQL-based functions and procedures in addition to the structural
data. With these functions, similar chains can be searched and
angles and distances can be calculated. Rotation of residues
leads to an alternative structure which can than be investigated.
Long Abstract: Click Here

Poster N91
beta.uniprot.org - a preview of the new Web site of the UniProt consortium
Eric Jain- Swiss Institute of Bioinformatics
No additional authors
Short Abstract: This poster presents beta.uniprot.org, the new Web site of the UniProt consortium. Screenshots give a brief overview of the functionality this site, along with some tips for regular users.
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Poster N92
PhosphoSite: A knowledge base of post-translational modifications and their role in cell signaling
David Merberg- Cell Signaling Technology
Roland Carel (3rd Millennium, Software Engineering); Jon Kornhauser (Cell Signaling Technology, PSKB); Juan Munoz (3rd Millennium, Software Engineering); Beth Murray (Cell Signaling Technology, PSKB); Julie Nardone (Cell Signaling Technology, PSKB); Ousama Shamma (3rd Millennium, Software Engineering); Elzbieta Skrzypek (Cell Signaling Technology, PSKB); Bin Zhang (Cell Signaling Technology, PSKB); Peter Hornbeck (Cell Signaling Technology, PSKB);
Short Abstract: PhosphoSite is a comprehensive resource for information concerning protein modifications and their role in regulating cellular functions. PhosphoSite has been completely re-engineered to provide better access to the growing volume of post-translational modification data. New user interfaces enable the formulation of queries based on treatments, diseases, tissues, etc.
Long Abstract: Click Here

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