International Workshop on Genomic Databases (IWGD´07)
August 29-31, 2007 Rio de Janeiro, Brazil

Many bioinformatics projects use a set of chained software packages, which produce and consume a significant amount of data. Besides accessing distributed public databases, most projects also maintain their data in local files or, most often, in databases. They usually constitute independent initiatives leading to redundant efforts and proprietary solutions, which lack standard formats and terminology, making interoperability with other resources a hard task. In order to address this issue, general database schemas capable of storing a comprehensive scope of genomic information for a wide range of interests have been proposed. GUS and CHADO are the most relevant initiatives for this purpose. Although many projects in areas such as Genomics, Post-genomics and Bioinformatics have been supported by government agencies in Brazil, there is still little discussion on standards, interoperability and integration issues. Besides, as the number of bioinformatics projects grows, new data management issues emerge, such as projects and experiments management, workflow support to programs executions, ontology driven querying and resource integration, data mediation and distribution, data provenance, data mining, etc.

The IWGD is one of the first workshops to be organized in Brazil focusing on genomic databases. It is organized by the BiowebDB consortium ( and it is intended to bring together researchers working on issues related to designing, managing, integrating, accessing and exploring genomic databases, giving them the opportunity to present and to discuss their research in a constructive and motivating atmosphere.

Invited speakers

 Kimmen Sjolander 
Susan Davidson
Julian Gough
Kathy Wu
Topics of Interest

The workshop seeks to provide a forum for these topics of interest, but not limited to:

Biological Databases
Biological Data Integration
Biological Data Mining
Biological Data Visualization
Biological Information Extraction and Retrieval
Biological Knowledge Bases
Biological Knowledge Representation and Inference
Biological Data Distribution
Biological Knowledge Discovery and Learning
Molecular Sequence Databases
Phylogeny Databases Systems
Biology databases

Poster Submission

Authors are invited to submit original, unpublished research work for a poster
session to [email protected] with the subject "IWGD 2007". English is the
workshop official language. To present a poster at the workshop, authors must
submit an abstract (*.RTF format) on the topic or theme to be discussed.
Abstracts should use Times New Roman 12 fonts and be no longer than 2 A4 pages
(1 inch to each margin), where:

1st page will contain only:
Title of the abstract
Authors and their filiation
Body of the abstract
2nd page will contain only:
References should follow the BMC Bioinformatics format (examples available
at: All
authors who present their posters at the workshop will have their abstracts
published on the conference Web site. All posters will be displayed at the
beginning of the workshop

IWGD poster session provides space on a poster board that is 1.20m wide and
1.80m high. If you are sizing your poster for a use other than a conference
poster session or for easy transportation, you can set the dimensions to any
size you like. Just remember that you will be able to print single-sheet
posters up to 1.18m wide and 1.78m high.

Important Dates

Abstract submission deadline - June, 29th 2007.
Notification to authors - July, 15th2007.

Workshop Chairs

Alberto M. R. Dávila, FIOCRUZ RJ, Brazil, davila AT
Marta Mattoso, COPPE Sistemas - UFRJ, Brazil, marta AT

Organizing Committee

Maria Luiza Campos, DCC/NCE; UFRJ, Brazil, mluiza AT
Guilherme de Oliveira, FIOCRUZ MG, Brazil oliveira AT
Maria Claudia Cavalcanti, IME RJ, Brazil, yoko AT
Fernanda Baião - UNIRIO, Brazil, fernanda.baiao AT

Supported by:

Fogarty International Center
Oswaldo Cruz Foundation
Banco do Brasil

Accepted posters

Database of Repetitive Elements from the genome of Anopheles gambiae.

Rita Daniela Fernández Medina 1, Cláudio José Struchiner 1, José Marcos Ribeiro 2.

1 Escola Nacional de Saúde Pública, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil

2 Laboratory of Malaria and Vector Research. NIAID, NIH. Rockville, MD 20852 USA

Semantic Web Reasoning: Novel Paradigms for Knowledge Modelling in Bioinformatics

Filippo Menolascina1 2, Stefania Tommasi1, Patrizia Chiarappa1, Angelo

Paradiso1, Giuseppe Mastronardi2, Vitoantonio Bevilacqua2

1 Bioinformatics Research Group, Clinical and Experimental Oncology Lab, NCI 

Bari, Via F. Hahnemann, 10  70126 Bari, Italy

2 Department of Electronics and Electrical Engineering, Polytechnic of Bari,

Via E. Orabona, 4 [UTF-8?]â?? 70125 Bari, Italy

Corresponding author: [email protected]

The use of OC identifier tool selecting optimal clones in finished genomes as an alternative to synthesis of primers for DNA Microarray analysis

Mauricio E Cantão1, 2, João E Ferreira1, Eliana G M Lemos2

1 Institute of Mathematics and Statistics - USP, São Paulo, SP, Brazil

2 Faculty of Agrarian and Veterinary Sciences - UNESP, Jaboticabal, SP, Brazil

An environment for managing and executioning gene expression experiments with microarrays

Vinicius Von Held1, Milton Moraes 2, Alberto Dávila 3, Marta Mattoso 1

1 System and Computer Engineering Program, COPPE/UFRJ

2 Biochemistry and Molecular Biology Departament, FIOCRUZ/RJ

3 Mycobacteriosis Departamento, FIOCRUZ/RJ


Margarita Ramona Ruiz Olazar1, Eugenius Kaszcurewicz1, Benjamín Barán Cegla2

1 Federal University of Rio de Janeiro/COPPE

2 National University of Asunción, Asunción [UTF-8?]â?? Paraguay

Bioinformatics scientific workflows: management, persistence and provenance

Luciano Digiampietri1, Roger Barga2 and Nolan Li3

1 Institute of Computing, University of Campinas

2 Technical Computing @ Microsoft, Microsoft Research

3 Department of Computer Science, Johns Hopkins University

Impact of 16S rDNA sequence heterogeneity and redundancy on the phylogeny, diversity and identification of bacteria of the order Firmicutes.

Ferreira, N. S.; Vianez-Junior, J. L. G.; Novaes, M.N.; Santos, V.B.S;

Direito, I.C.N. & Macrae, A.

Departamento de Microbiologia Geral, IMPPG [UTF-8?]â?? UFRJ

Traceability and provenance in genomic annotation

Luciano Digiampietri1, Claudia Bauzer Medeiros1 and Joao Setubal2

1Institute of Computing, University of Campinas

2Virginia Bioinformatics Institute, Virginia Tech

Capturing Provenance Data from Workflows into the Genomic Unified Schema

Amanda Mattos, Marta Mattoso

PESC , COPPE, Federal University of Rio de Janeiro

STINGRAY: System for Integrated Genomic Resources and Analysis

Glauber Wagner126, Kary Soriano1, Henrique C. L . Jucá1, Kele Belloze3,

Diogo Antonio Tschoeke12, Guilherme Arthur Geronimo2, Felipe F.

Albrecht, Marta Mattoso5, Maria Claudia Cavalcanti3, Maria Luiza

Machado4, Edmundo Carlos Grisard2, Alberto M. R. Dávila1*

1. IOC / FIOCRUZ / RJ; 2. CCB / UFSC / SC; 3. IME / RJ; 4.NCE / UFRJ / RJ; 5.COPPE / UFRJ / RJ; 6.ACBS / UNOESC / SC

Ternary matrices: a new platform to integrate genomic and proteomic data.

Fabio Passetti 1,2 and Paulo Sergio Lopes de Oliveira 1

1. Laboratory of Computational Biology, Laboratory of Genetics and Molecular

Cardiology, Heart Institute (InCor), HCFMUSP, Brazil. 2. Laboratory of

Bioinformatics and Computational Biology, Clinical Research Service, Research

Coordination, Instituto Nacional de Câncer (INCA), Brazil.

Selection of Predictive Genes from Cancer DNA Microarrays Using Evolutionary and Recursive Models.

Marcelo Ribeiro Alves1 and Flavio Fonseca Nobre1.

1 Biomedical Engineering Department, Alberto Luiz Coimbra Institute, Federal

University of Rio de Janeiro, Rio de Janeiro, Brazil.

Genomics Databases and Webservices for Phylogenetics Studies

Luciana Matos1, Kary A. C S. Ocaña2, Marta Mattoso1, Alberto Dávila2

1 COPPE/Federal University of Rio de Janeiro, 2 IOC/Fiocruz

BioAgents: A Multiagent System for Manual Annotation on Genome Sequencing Projects

Richardson S. Lima1, Célia G. Ralha1, Maria Emilia M. T. Walter1, Hugo W.

Schneider1, Anderson G. F. Pereira1 and Marcelo M. Brígido2

Computer Science Department, 2Biology Institute

University of Brasilia

Campus Universitário Darcy Ribeiro Caixa Postal 4466 ? CEP 70.919-970

Brasília, Brazil

An Improved Annotation System based on XML Databases and Ontologies

Marcus V. C. Teixeira, Mauro Biajiz e Ricardo R. Ciferri

Federal University of São Carlos, Computer Science Department, São Carlos, Brazil

Capturing Ontology_based Annotation History

Kele T. Belloze1, Maria Claudia Cavalcanti 1, Renata M. Araujo2, Felipe F. Albrecht1, Alberto M. R. Dávila3

1Instituto Militar de Engenharia, 2UNIRIO, 3Instituto Oswaldo Cruz

SchistoDB : An integrated Schistosoma mansoni database

Zerlotini A1, Moraes RLV1, Heiges M2, Wang H2, Stahl AO2, Kissinger JC2, Oliveira GC1

1. FIOCRUZ / IRR Instituto René Rachou

2. University of Georgia / The Center for Tropical & Emerging Global Diseases

Applying Information Science and Terminology Theories to Ontologies Integration Strategies

Maria Luiza Machado Campos1, Maria Luiza de Almeida Campos2 ,

Linair Maria Campos2, Débora Constantino1

1 - Universidade Federal do Rio de Janeiro - Departamento de Ciência da Computação

Núcleo de Computação Eletrônica

2 - Universidade Federal Fluminense - IBICT

Biological Sequence Index

Cristian Tristão, Sérgio Lifschitz

Departamento de Informática Pontifícia Universidade Católica

22453-900 Rio de Janeiro, Brasil

Allocation Partitioned Replicated Database for BLAST in Computer Cluster

Daniel Xavier, Sérgio Lifschitz

Departamento de Informática Pontifícia Universidade Católica

22453-900 Rio de Janeiro, Brasil