| Accepted Posters |
| Category 'E'- Databases' |
| Poster E01 |
| Integrative storage and retrieval of computational biochemical models |
| Ron Henkel- Universität Rostock |
| Dagmar Köhn (Universität Rostock, Database- and Information systems); Carsten Maus (Universität Rostock, Modeling and Simulation); |
| Short Abstract: Increasing numbers and complexity of biochemical models make model reusemore imperative. This work introduces an integrative storage approach for models from different formalisms and their meta-information given as annotations.It provides retrieval techniques, enables model comparison regarding model similarity, and suggests the generation of simulation experiments. |
| Long Abstract: Click Here |
| Poster E02 |
| TparvaDB: a database to support Theileria parva vaccine development |
| Etienne de Villiers- International Livestock Research Institute |
| Paul Visendi (University of Nairobi, Center for Biotechnology and Bioinformatics ); Wallace Bulimo (US Army Medical Research Unit , Nairobi); Wanjiku Ng’ang’a (University of Nairobi, School of Computing and Informatics); Richard Bishop (International Livestock Research Institute, Biotechnology); |
| Short Abstract: We have developed TparvaDB, an integrated database for Theileria parva based on GMOD. TparvaDB houses full genome sequences, Expressed Sequence Tags (ESTs), Massivelly Parallel Signature Sequencing (MPSS) data, vaccine candidate gene and other related data. |
| Long Abstract: Click Here |
| Poster E03 |
| GabiPD: The Gabi Primary Database - a plant integrative ‘omics’ database |
| Diego Mauricio Riaño-Pachón- Max Planck Institute for Molecular Plant Physiology |
| Axel Nagel (Max Planck Institute for Molecular Plant Physiology, Bioinformatics); Robert Wagner (Max Planck Institute for Molecular Plant Physiology, Bioinformatics); Rico Basekow (Max Planck Institute for Molecular Plant Physiology, Bioinformatics); Jost Neigenfind (Max Planck Institute for Molecular Plant Physiology, Bioinformatics); Elke Weber (Max Planck Institute for Molecular Plant Physiology, Bioinformatics); Sabrina Kleessen (Max Planck Institute for Molecular Plant Physiology, Bioinformatics); Birgit Kersten (Max Planck Institute for Molecular Plant Physiology, Bioinformatics); |
| Short Abstract: The GabiPD – Gabi Primary Database, constitutes a repository for ‘omics’ data in the plant field. Integrated data is available to the scientific community via http://www.gabipd.org/. The main goal of GabiPD is to collect, integrate, visualize and link primary information from `omics` data of various plant species. |
| Long Abstract: Click Here |
| Poster E04 |
| The Universal Protein Resource (UniProt) |
| Manuela Pruess- European Bioinformatics Institute |
| The UniProt Consortium (Swiss Institute of Bioinformatics, Centre Medical Universitaire); The UniProt Consortium (Protein Information Resource, Georgetown University Medical Center); |
| Short Abstract: UniProt (http://www.uniprot.org) is a high-quality, freely accessible resource of protein sequence and functional information, highly cross-referenced to other databases. UniProt is comprised of an Archive, a Knowledgebase, Reference Clusters, and a Metagenomic and Environmental Sequence Database. Recently the first draft of the complete human proteome in UniProtKB/Swiss-Prot has been completed. |
| Long Abstract: Click Here |
| Poster E05 |
| CHDWiki : An online collaborative and interactive data repository dedicated to congenital heart defects. |
| Sylvain Brohée- Katholieke Universiteit Leuven |
| Roland Barriot (Katholieke Universiteit Leuven, ESAT - SCD); Jeroen Breckpot (Katholieke Universiteit Leuven, Center for Human Genetics); Bernard Thienpont (Katholieke Universiteit Leuven, Center for Human Genetics); Steven Van Vooren (Katholieke Universiteit Leuven, ESAT - SCD); Bert Coessens (Katholieke Universiteit Leuven, ESAT - SCD); Léon-Charles Tranchevent (Katholieke Universiteit Leuven, ESAT - SCD); Peter Van Loo (Katholieke Universiteit Leuven, ESAT - SCD); Marc Gewellig (Katholieke Universiteit Leuven, Department of Pediatric Cardiology); Koen Devriendt (Katholieke Universiteit Leuven, Center for Human Genetics); Yves Moreau (Katholieke Universiteit Leuven, ESAT - SCD); |
| Short Abstract: We present a user-friendly resource and gene prioritization portal aimed at mapping genes involved in congenital heart defects and untangling their relations with corresponding human phenotypes. It combines both the facilities of Wiki databases and the strictness of specialized databases. This model could be applied to any other specialized fields. |
| Long Abstract: Click Here |
| Poster E06 |
| PRIDE, the PRoteomics IDEntifications database |
| Florian Reisinger- EMBL-EBI |
| Lennart Martens (EMBL-EBI, Proteomics Services ); Richard Côté (EMBL-EBI, Proteomics Services ); Juan A. Vizcaino (EMBL-EBI, Proteomics Services ); Henning Hermjakob (EMBL-EBI, Proteomics Services ); |
| Short Abstract: PRIDE, the PRoteomics IDEntifications database, is a public data repository for proteomics data consisting of proteins, peptides and spectral evidence. It provides the scientific community with a common data exchange format that implements HUPO PSI standards along with a stable repository to support proteomics literature publications and the peer-review process. |
| Long Abstract: Click Here |
| Poster E07 |
| Arabidopsis Reactome: A Pathway Database for Plant Systems Biology |
| Janet Higgins- John Innes Centre |
| Matthew Couchman (John Innes Centre, Computational and Systems Biology); Sean Walsh (John Innes Centre, Computational and Systems Biology); Michael Bevan (John Innes Centre, Cell and Developmental Biology); |
| Short Abstract: Arabidopsis Reactome is an online knowledgebase of plant metabolic, genetic and signalling pathways available at www.arabidopsisreactome.org. Pathways can be exported in BioPAX and SBML and visualised using Cytoscape. The SkyPainter tool allows visualisation of high-throughput data. Arabidopsis Reactome pathways are electronically projected onto plants and available as protein-protein interaction datasets. |
| Long Abstract: Click Here |
| Poster E08 |
| BioRPC: A Server-side Bioinformatics Platform Proposal |
| Paulo Paiva- Federal University of São Paulo |
| Jackson Lima (Federal University of São Paulo, Health Informatics Department); Cleber Magnagnagno (Federal University of São Paulo, Health Informatics Department); |
| Short Abstract: A server-side bioinformatics platform is proposed in order to allow applications based on the new paradigms of Web technology to make use of well established biological databases and tools.This is accomplished by using the Remote Procedure Call protocol and is intended to work under a Service Oriented Architecture. |
| Long Abstract: Click Here |
| Poster E09 |
| The Protein Structure Initiative Structural Genomics Knowledgebase |
| Andrei Kouranov- Protein Data Bank |
| Margaret Gabanyi (Rutgers, The State University of New Jersey, Chemistry and Chemical Biology); John Westbrook (Rutgers, The State University of New Jersey, Chemistry and Chemical Biology); Wendy Tao (Rutgers, The State University of New Jersey, Chemistry and Chemical Biology); RAship Shah (Rutgers, The State University of New Jersey, Chemistry and Chemical Biology); Torsten Schwede (University of Basel, Swiss Institute of Bioinfomatics & Biozentrum); Konstantin Arnold (University of Basel, Swiss Institute of Bioinfomatics & Biozentrum); Florian Kiefer (University of Basel, Swiss Institute of Bioinfomatics & Biozentrum); Lorenza Bordoli (University of Basel, Swiss Institute of Bioinfomatics & Biozentrum); Michael Podvinec (University of Basel, Swiss Institute of Bioinfomatics & Biozentrum); Jurgen Kopp (Heidelberg University, Biochemie-Zentrum); Paul D. Adams (Lawrence Berkeley National Laboratory, Physical Biosciences Division); Lester G. Carter (Lawrence Berkeley National Laboratory, Physical Biosciences Division); Wladek Minor (University of Virginia, Department of Molecular Physiology and Biological Physics); Rajesh Nair (Columbia University, Department of Biochemistry & Molecular Biophysics); Joshua La Baer (University Medical School, Harvard Institute of Proteomics & Department of Biological Chemistry and Molecular Pharmacology); Helen M. Berman (Rutgers, The State University of New Jersey, Department Chemistry and Chemical Biology); |
| Short Abstract: The PSI Structural Genomics Knowledgebase (PSI SGKB: http://kb.psi-structuralgenomics.org/) is designed to turn the products of the Protein Structure Initiative into knowledge that is important for understanding living systems and disease. A description of how this resource can be used for enabling biological research will be presented. |
| Long Abstract: Click Here |
| Poster E10 |
| Establishment and public release of integrated Clinical Omics Database (iCOD) with clinical and molecular biological information for systems pathological research. |
| Hiroshi Mizushima- Tokyo Medical And Dental University |
| Yasen Mahmut (Tokyo Medical and Dental University, Information Center for Medical Sciences); Ken Miyaguchi (Tokyo Medical and Dental University, Information Center for Medical Sciences); Kaoru Mogushi (Tokyo Medical and Dental University, Information Center for Medical Sciences); Kazuro Shimokawa (Tokyo Medical and Dental University, Information Center for Medical Sciences); Hiroshi Tanaka (Tokyo Medical and Dental University, Information Center for Medical Sciences); |
| Short Abstract: Development of “TMDU Clinical Omics Database” has been conducted by integrating OMICS information and clinical information. We currently collected 500+ cases including hepatic, colon, and oral cancer. Database now can be accessed at http://omics.tmd.ac.jp/. This would be the first integrated clinical database with both clinical and molecular biological information. |
| Long Abstract: Click Here |
| Poster E11 |
| The Roche Mutome Database |
| Jan Küntzer- Roche Diagnostics GmbH |
| Stefan Klostermann (Roche Diagnostics GmbH, Pharma Research Penzberg / TR-IB); Helmut Burtscher (Roche Diagnostics GmbH, Pharma Research Penzberg / TR-D3); |
| Short Abstract: We developed an integrative biological information system for the human mutome combining different publicly available databases and Roche in-house applications. The database contains all kind of mutations at the DNA and protein sequence level like substitutions, deletions, insertions, amplification, and chromosomal rearrangements. |
| Long Abstract: Click Here |
| Poster E12 |
| PDB decomposition tool |
| Rafael Ordog- Eotvos Lorand University, PIT Group |
| Zoltán Szabadka (Eotvos Lorand University, PIT Group, Department Of Computer Science); Vince Grolmusz (Eotvos Lorand University, PIT Group, Department Of Computer Science); |
| Short Abstract: We present a fast tool - freely available through a web-interface - for identifying and marking missing atoms and residues in the PDB, as well as automatically decomposing the PDB entries into separate files describing ligands and polypeptide chains. |
| Long Abstract: Click Here |
| Poster E13 |
| jORCA: Making the use of bioinformatics web services easier. |
| Victoria Martin-Requena- University of Málaga |
| Javier Rios (University of Málaga, Computer Architecture); Maximiliano García (University of Málaga, Computer Architecture); Sergio Ramirez (University of Málaga, Computer Architecture); Oswaldo Trelles (University of Málaga, Computer Architecture); |
| Short Abstract: jORCA is a client able to integrate different types of web-services repositories mapping their metadata descriptors over a general virtual definition to support scalable service discovery and to achieve flexible tools intercommunication. jORCA allows executing different invocation protocols and includes interactive features to cover a broad range of users. |
| Long Abstract: Click Here |
| Poster E14 |
| New Features in the UniProt Archive (UniParc) |
| Quan Lin- European Bioinformatics Institute (EBI) |
| Rasko Leinonen (EMBL Outstation, , European Bioinformatics Institute (EBI), ); Richard Côté (EMBL Outstation, , European Bioinformatics Institute (EBI), ); Maria Martin (EMBL Outstation, , European Bioinformatics Institute (EBI), ); Claire O'Donovan (EMBL Outstation, , European Bioinformatics Institute (EBI), ); Rolf Apweiler (EMBL Outstation, , European Bioinformatics Institute (EBI), ); |
| Short Abstract: UniParc is the most comprehensive protein sequence database available. We have extended its functionality by adding TaxId and NCBI gi numbers, by giving the reasons as why some proteins are excluded from UniProtKB and by adding UniProtKB accessions to some sequences that are not identical to a UniProKB sequence. |
| Long Abstract: Click Here |
| Poster E15 |
| Migration of the Pfam database to HMMER3 |
| Robert Finn- Wellcome Trust Sanger Institute |
| Penny Coggill (Wellcome Trust Sanger Institute, Bioinformatics); Jaina Mistry (Wellcome Trust Sanger Institute, Bioinformatics); John Tate (Wellcome Trust Sanger Institute, Bioinformatics); Sean Eddy (Janelia Farm Research Campus, Eddy Group); Alex Bateman (Wellcome Trust Sanger Institute, Bioinformatics); |
| Short Abstract: Pfam, the protein families database, is underpinned by the HMMER software package. In January 2009, a faster, more sensitive version of HMMER was released: HMMER3. The migration of Pfam to HMMER3 has resulted in many important changes to the database, which increases both its scope and its potential use. |
| Long Abstract: Click Here |
| Poster E16 |
| UniProtJAPI: a remote API for accessing UniProt data |
| Samuel Patient- EBI - European Bioinformatics Institute |
| Michael Kleen (EBI, PANDA); Maria Jesus Martin (EBI, PANDA); Rolf Apweiler (EBI, PANDA); |
| Short Abstract: The UniProtJAPI facilitates the integration of UniProt Knowledgebase data into Java-based software applications. The library supports queries and similarity searches that return UniProt entries in the form of Java objects. These objects contain functional annotations or sequence information associated with the entry. UniProtJAPI is available at http://www.ebi.ac.uk/uniprot/remotingAPI/ |
| Long Abstract: Click Here |
| Poster E17 |
| The enzyme information system BRENDA |
| Maurice Scheer- Technische Universität Braunschweig |
| Andreas Grote (Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry); Michael Rother (Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry); Juliane Thiele (Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry); Antje Chang (Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry); Ida Schomburg (Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry); Dietmar Schomburg (Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry); |
| Short Abstract: BRENDA is an enzyme information system. Biochemical and molecular information on all classified enzymes extracted from primary literature is made freely accessible by sophisticated software tools (http://www.brenda-enzymes.org). Recent innovations comprise the inclusion of protein-specific data, the display of active sites in 3D-structure of enzymes and improvements of the textmining. |
| Long Abstract: Click Here |
| Poster E18 |
| SuperToxic: a comprehensive database of toxic compounds |
| Robert Preissner- Charite |
| Ulrike Schmidt (Charite , Institute for Physiology); Swantje Struck (Charite, Institute for Physiology); Bjoern Gruening (Charite, Institute for Physiology); Julia Hossbach (Charite, Institute for Physiology); Ines S. Jaeger (Charite, Institute for Physiology); Elke Michalsky (Charite, Institute for Physiology); Roza Parol (Charite, Institute for Physiology); Ulrike Linequist (Ernst-Moritz-Arndt-University Greifswald, Institute of Pharmacy); Eberhard Teuscher (Ernst-Moritz-Arndt-University Greifswald, Institute of Pharmacy); |
| Short Abstract: The database SuperToxic is a comprehensive collection of 150,000 compounds, classified according to their toxicity based on more than 2 million measurements. \"Toxicity properties\" extracted from SuperToxic, function as a guideline for the toxicological evaluation of unknown substances and their possible biological interactions. |
| Long Abstract: Click Here |
| Poster E19 |
| BioExpert: Biological Knowledge Base Creation through Concept Mapping |
| Andrew Gibson- University of Amsterdam |
| Gerbert Jansen (University of Amsterdam, Academic Medical Center); Antoine van Kampen (University of Amsterdam, Academic Medical Center); Serge Barth (University of Amsterdam, Swammerdam Institute for Life Sciences); Aviral Vatsa (University of Amsterdam, Academic Medical Center); |
| Short Abstract: The BioExpert Project is working towards an environment in which experts can create knowledge bases that focus on specific topics in biology. Our strategy is to capture and represent knowledge using graphical concept maps. We present the pilot ‘Peroxisome Knowledge Base’, which was created using this methodology. |
| Long Abstract: Click Here |
| Poster E20 |
| BioMart and Web Services in InterPro |
| John Maslen- EMBL - European Bioinformatics Institute |
| Philip Jones (EMBL - European Bioinformatics Institute, InterPro Team); Sarah Hunter (EMBL - European Bioinformatics Institute, InterPro Team); |
| Short Abstract: InterPro has introduced a BioMart interface, giving users the ability to generate complex queries over the InterPro data, with highly-customisable control over the results. It also allows the generation of distributed queries with federated databases and web service access to the data via REST and a DAS server. |
| Long Abstract: Click Here |
| Poster E21 |
| EMBRACE web services and Chipster: easy access to up-to-date tools |
| Aleksi Kallio- CSC - The Finnish IT Center for Science |
| Taavi Hupponen (CSC - The Finnish IT Center for Science , -); Petri Klemelä (CSC - The Finnish IT Center for Science , -); Jarno Tuimala (CSC - The Finnish IT Center for Science , -); Eija Korpelainen (CSC - The Finnish IT Center for Science , -); |
| Short Abstract: Substantial amount of novel methods and databases have been produced in the EU-funded EMBRACE network (see EMBRACE Registry for complete list). We integrate the services with our user-friendly analysis software Chipster to make them accessible also to biologists. We also provide new public web services based on Chipster. |
| Long Abstract: Click Here |
| Poster E23 |
| RISSC2: an online interface to study ribosomal intergenic transcribed spacers in prokaryotes |
| Ravindra Pushker- University College Dublin |
| Giuseppe D\\\'Auria (Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia); Francisco Rodriguez-Valera (University of Miguel Hernandez, Department of Microbiology); |
| Short Abstract: RISSC2 is a novel database which contains a) 16S-23S ribosomal ITS present in prokaryotesfrom different environments providing an update to the old RISSC database; b) much shorterribosomal spacers which can be found between 23S and 5S rRNAs. It is available online at http://egg.umh.es/rissc2/. |
| Long Abstract: Click Here |
| Poster E24 |
| Kegg Orthology enrichment with a procedure based on UniRef clusters recruits novel elements to Atlas and Pathways |
| Gabriel Fernandes- Universidade Federal de Minas Gerais |
| J Miguel Ortega (Universidade Federal de Minas Gerais, Biochemistry and Immunology); |
| Short Abstract: Here we report a procedure to enrich information of Kegg Orthology database, initially comprised of 1,248,629 proteins from 846 distinct organisms. Using the information contained in iProClass (PIR) we raised the data to 2,241,188 proteins (1,9 fold enrichment) corresponding to 24,081 distinct genomes. |
| Long Abstract: Click Here |
| Poster E25 |
| Symbiosis: a Web-based framework for managing and analysing high throughput metabolomic data |
| Fady Mohareb- Bioinformatics Group |
| Conrad Bessant (Bioinformatics Group, Cranfield Health); George Nychas (Microbiology & Biotechnology Lab of Food, Agricultural University of Athens); |
| Short Abstract: The Symbiosis-EU framework is a Web-based research platform that allows users to store, manipulate, and analyse experimental high-throughput –omic data. The framework also provides means for performing statistical analysis through a choice of data analysis pipelines mainly for metabolomic data, but the system is continuously updated to support other platforms. |
| Long Abstract: Click Here |
| Poster E26 |
| XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources |
| Kam Dahlquist- Loyola Marymount University |
| Alexandrea Alphonso (Loyola Marymount University, Biology); Derek Smith (Loyola Marymount University, Electrical Engineering & Computer Science); Chad Villaflores (Loyola Marymount University, Biology); John Dionisio (Loyola Marymount University, Electrical Engineering &Computer Science); |
| Short Abstract: XMLPipeDB is an open source suite of Java-based tools for automatically building relational databases from an XML schema (XSD). We have used it to generate GenMAPP Gene Databases containing UniProt and Gene Ontology data for several microorganisms and plants. Other common bioinformatics XML formats were tested for compatibility with XMLPipeDB. |
| Long Abstract: Click Here |
| Poster E28 |
| An Overview of the BioExtract Server – a Distributed, Web Based Application for Bioinformatic Analysis |
| Carol Lushbough- University of South Dakota |
| Volker Brendel (Iowa State University, the Department of Genetics, Development and Cell Biology and Department of Statistics); |
| Short Abstract: The BioExtract Server (http://bioextract.org) is a Web-based data integration application designed to aid researchers in the development of computational workflows. It allows users, via a Web browser, to query multiple data sources, save query results as searchable data sets, execute local and Web-accessible analytic tools, and create computational workflows. |
| Long Abstract: Click Here |
| Poster E29 |
| iRefIndex |
| Sabry Razick- University Of Oslo |
| Ian Donaldson (Group leader, Biotechnology Centre ofOslo); George Magklaras (Senior Computer Systems Engineer, The Biotechnology Centre of Oslo); |
| Short Abstract: None On File |
| Long Abstract: Click Here |
| Poster E30 |
| ELIXIR Bioinformatics User Survey |
| Sandrine Palcy- Université Bordeaux 2 |
| Antoine de Daruvar (Université Bordeaux 2 , Centre de Bioinformatique de Bordeaux); |
| Short Abstract: The Bioinformatics User survey has been carried out for the European Life sciences Infrastructure for Biological Information (ELIXIR) project. Participation of 804 individual research groups and subsequent analysis of the collected information provided insights for a better understanding of the user community needs and priorities in respect to bioinformatics infrastructures. |
| Long Abstract: Click Here |
| Poster E31 |
| Hyperlink Management System for creating maintenance-free hyperlinks to major biological databases. |
| Tadashi Imanishi- AIST |
| Hajime Nakaoka (JBIC, Research and Development); |
| Short Abstract: We developed the Hyperlink Management System for automatically updating and maintaining hyperlinks among major public databases for human genes and proteins, enabling maintenance-free hyperlinks. We also developed the ID Converter System for converting data IDs of major biological databases. These systems are freely available at http://biodb.jp/. |
| Long Abstract: Click Here |
| Poster E32 |
| A database supporting Quantitaive aspects of Plant Breeding |
| Richard Finkers- WUR |
| Roeland Voorrips (WUR, Plant breeding); |
| Short Abstract: Support of databases for Quantitative breeding research are getting more important. We developed an database focusing at storage of marker and trait data. A set of tools were implemented in a web-based front-end which aims at integrative analysis and visualization of the stored information. |
| Long Abstract: Click Here |
| Poster E33 |
| SoyXpress: A soybean transcriptome database |
| Martina Stromvik- McGill University |
| Kei Chin Cheng (McGill University, Plant Science); |
| Short Abstract: In order to explore the soybean transcriptome we developed SoyXpress, a MySQL database (http://soyxpress.agrenv.mcgill.ca/). Affymetrix microarray data are linked with ESTs, metabolic pathways, GO terms and SwissProt keywords. Currently SoyXpress houses microarray data comparing transgenic and conventional soybean cultivars, as well as a section on common soybean virus sequence data. |
| Long Abstract: Click Here |
| Poster E34 |
| The Ibidas data integration and accession platform |
| Jan Bot- TU Delft |
| Marc Hulsman (TU Delft, Bioinformatics); Marcel Reinders (TU Delft, Bioinformatics); |
| Short Abstract: Ibidas provides a python-based software environment for querying biologicaldata, with support for multiple input types such as databases, text files or web services. It can be used from within widely used analysis tools such as R and Matlab, and is easily extendible. |
| Long Abstract: Click Here |
| Poster E35 |
| CliquePOINT: A tool for analysis the complex information from a protein-protein interaction network |
| Sheng-An Lee- National Taiwan University |
| Yun-Yan Yang (National Taiwan University, Department of Computer Science and Information Engineering); Yu-Lun Kuo (National Taiwan University, Department of Computer Science and Information Engineering); Cheng-Yan Kao (National Taiwan University, Department of Computer Science and Information Engineering); Chi-Ying Huang (National Yang-Ming University, Institute of Clinical Medicine); |
| Short Abstract: CliquePoint was developed to evaluate the complex information, three parts of dataset in CliquePoint (i.e., protein-protein interaction, complex, and tissue expression dataset) are utilized. The concept of clique and interologs as a comparative strategy to assign reliable experimental datasets and to explicitly reveal potential PPIs and complexes in a species. |
| Long Abstract: Click Here |
| Poster E36 |
| A Virtual Library for BITS Meetings |
| Paolo Romano- National Cancer Research Institute |
| Achille Zappa (National Cancer Research Institute, Bioinformatics); Mariangela Miele (National Cancer Research Institute, Bioinformatics); Stefania Parodi (National Cancer Research Institute, Bioinformatics); |
| Short Abstract: Grey literature may include data of extreme interest. The Virtual Library for BITS Meetings includes 669 scientific contributions from 10 meetings of the Bioinformatics Italian Society. It is available at http://bioinformatics.istge.it/bits_library/. Contributions can be searched by author, title and contents, listed by meeting and topic, and downloaded in PDF. |
| Long Abstract: Click Here |
| Poster E37 |
| Community intelligence applied to gene annotation: The Gene Wiki and BioGPS |
| Andrew Su- GNF |
| Jon Huss, III (GNF, Computational Discovery); Chunlei Wu (GNF, Computational Discovery); Camilo Orozco (GNF, Computational Discovery); Jason Boyer (GNF, Computational Discovery); James Goodale (GNF, Computational Discovery); Serge Batalov (GNF, Computational Discovery); Tim Vickers (Washington University, School of Medicine); Faramarz Valafar (San Diego State University, Computer Science); |
| Short Abstract: Recently, we introduced two community intelligence initiatives aimed at accelerating gene annotation and gene portal development, called the Gene Wiki and BioGPS, respectively. We present details on the design on these two resources, as well as usage statistics showing substantial usage and contributions by the scientific community. |
| Long Abstract: Click Here |
| Poster E39 |
| InterMine – open source data warehouse and query interface |
| Richard Smith- Cambridge University |
| Adrian Carr (University of Cambridge, Cambridge Systems Biology Centre); Sergio Contrino (University of Cambridge, Cambridge Systems Biology Centre); Rachel Lyne (University of Cambridge, Cambridge Systems Biology Centre); Julie Sullivan (University of Cambridge, Cambridge Systems Biology Centre); Dan Tomlinson (University of Cambridge, Cambridge Systems Biology Centre); Xavier Watkins (University of Cambridge, Cambridge Systems Biology Centre); Matthew Wakeling (University of Cambridge, Cambridge Systems Biology Centre); Gos Micklem (University of Cambridge, Cambridge Systems Biology Centre); |
| Short Abstract: InterMine is an open-source system for building query-optimised data warehouses. It supports data integration from standard biological formats and makes it easy to add your own data. A sophisticated web application provides flexible access for users to create custom queries, use templates and operate on lists. |
| Long Abstract: Click Here |
| Poster E40 |
| Custom Databases and Queries for PFAM, GO, and GOA: Exploratory analysis of protein and function relations |
| Mark Fenner- Norwich University |
| No additional authors |
| Short Abstract: For exploratory problems that build and manipulate sets of elements from large biological databases, local access is a practical necessity. We present a small suite of tools which balance speed and convenience for exploring PFAM, GO, and GOA within Python. Exploratory results can be directly processed by further Python-based workflows. |
| Long Abstract: Click Here |
| Poster E41 |
| The ELIXIR Database Provider Survey |
| Andrew Lyall- EMBL- European Bioinformatics Institute |
| Christopher Southan (EMBL- European Bioinformatics Institute, Elixir Database Survey Coordinator); Graham Cameron (EMBL- European Bioinformatics Institute, Associate Director); |
| Short Abstract: A major survey of biomolecular resources has been carried out for the European Life sciences Infrastructure for Biological Information (ELIXIR) project. From 531 European databases contacted 208 have completed the questionnaire. Information about location, data, funding, usage and other statistics of database operation will be outlined in this poster |
| Long Abstract: Click Here |
| Poster E42 |
| Annotating drugs and metabolites with their chemical class |
| Roman Eisner- University of Alberta |
| Russ Greiner (University of Alberta, Computing Science); Craig Knox (University of Alberta, Computing Science); Joseph Cruz (University of Alberta, Computing Science); David Wishart (University of Alberta, Computing Science); |
| Short Abstract: We annotate the compounds in the HMDB and Drugbank with their chemical class. Using machine-learning, structural similarity methods, and manual curation, we assign chemical class to these compounds. The chemical class makes for more searchable databases, and can aid in further annotation of compounds. |
| Long Abstract: Click Here |
| Poster E43 |
| The ArrayExpress Atlas – a semantically enriched multispecies atlas of gene expression |
| Tony Burdett- European Bioinformatics Institute |
| Helen Parkinson (European Bioinformatics Institute, Microarray); Ele Holloway (European Bioinformatics Institute, Microarray); Tomasz Adamusiak (European Bioinformatics Institute, Microarray); Ibrahim Emam (European Bioinformatics Institute, Microarray); Pavel Kurnosov (European Bioinformatics Institute, Microarray); James Malone (European Bioinformatics Institute, Microarray); Gabriella Rustici (European Bioinformatics Institute, Microarray); Alvis Brazma (European Bioinformatics Institute, Microarray); Misha Kapushesky (European Bioinformatics Institute, Microarray); |
| Short Abstract: The ArrayExpress Atlas is a semantically enriched database of meta-analytical summary statistics over the ArrayExpress Warehouse. Users can query for condition-specific gene expression across multiple gene expression datasets. |
| Long Abstract: Click Here |
| Poster E44 |
| UniProt Automatic Annotation |
| Michael Kleen- EMBL-EBI The European Bioinformatics Institute |
| Ricardo Antunes (EBI - Panda, EMBL-EBI The European Bioinformatics Institute); Maria-Jesus Martin (EBI - Panda, EMBL-EBI The European Bioinformatics Institute); Rolf Apweiler (EBI - Panda, EMBL-EBI The European Bioinformatics Institute); |
| Short Abstract: The UniProt Automatic Annotation Project automatically annotates protein entries in the unreviewed TrEMBL section of the UniProtKnowledgebase(UniProtKB). The system is used to create rules based on the annotation in the reviewed Swiss-Prot section of UniProtKB. Theserules are then applied in each release to enrich the TrEMBL section with general annotations. |
| Long Abstract: Click Here |
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