Volume 9 Supplement 4

A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications


Edited by Paolo Romano, Michael Schroeder, Nicola Cannata and Roberto Marangoni

Seventh International Workshop on Network Tools and Applications in Biology (NETTAB 2007). Go to conference site.

Pisa, Italy

12-15 June 2007

  1. Research

    Terminologies for text-mining; an experiment in the lipoprotein metabolism domain

    The engineering of ontologies, especially with a view to a text-mining use, is still a new research field. There does not yet exist a well-defined theory and technology for ontology construction. Many of the o...

    Dimitra Alexopoulou, Thomas Wächter, Laura Pickersgill, Cecilia Eyre and Michael Schroeder

    BMC Bioinformatics 2008 9(Suppl 4):S2

    Published on: 25 April 2008

  2. Research

    Ontology-guided data preparation for discovering genotype-phenotype relationships

    Complexity and amount of post-genomic data constitute two major factors limiting the application of Knowledge Discovery in Databases (KDD) methods in life sciences. Bio-ontologies may nowadays play key roles i...

    Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli and Marie-Dominique Devignes

    BMC Bioinformatics 2008 9(Suppl 4):S3

    Published on: 25 April 2008

  3. Research

    Ontology-based, Tissue MicroArray oriented, image centered tissue bank

    Tissue MicroArray technique is becoming increasingly important in pathology for the validation of experimental data from transcriptomic analysis. This approach produces many images which need to be properly ma...

    Federica Viti, Ivan Merelli, Andrea Caprera, Barbara Lazzari, Alessandra Stella and Luciano Milanesi

    BMC Bioinformatics 2008 9(Suppl 4):S4

    Published on: 25 April 2008

  4. Research

    AMMO-Prot: amine system project 3D-model finder

    Amines are biogenic amino acid derivatives, which play pleiotropic and very important yet complex roles in animal physiology. For many other relevant biomolecules, biochemical and molecular data are being accu...

    Ismael Navas-Delgado, Raúl Montañez, Almudena Pino-Ángeles, Aurelio A Moya-García, José Luis Urdiales, Francisca Sánchez-Jiménez and José F Aldana-Montes

    BMC Bioinformatics 2008 9(Suppl 4):S5

    Published on: 25 April 2008

  5. Research

    RDFScape: Semantic Web meets Systems Biology

    The recent availability of high-throughput data in molecular biology has increased the need for a formal representation of this knowledge domain. New ontologies are being developed to formalize knowledge, e.g....

    Andrea Splendiani

    BMC Bioinformatics 2008 9(Suppl 4):S6

    Published on: 25 April 2008

  6. Research

    Stochastic models for the in silico simulation of synaptic processes

    Research in life sciences is benefiting from a large availability of formal description techniques and analysis methodologies. These allow both the phenomena investigated to be precisely modeled and virtual ex...

    Andrea Bracciali, Marcello Brunelli, Enrico Cataldo and Pierpaolo Degano

    BMC Bioinformatics 2008 9(Suppl 4):S7

    Published on: 25 April 2008

  7. Research

    On deducing causality in metabolic networks

    Metabolic networks present a complex interconnected structure, whose understanding is in general a non-trivial task. Several formal approaches have been developed to support the investigation of such networks....

    Chiara Bodei, Andrea Bracciali and Davide Chiarugi

    BMC Bioinformatics 2008 9(Suppl 4):S8

    Published on: 25 April 2008

  8. Research

    Reconstructing networks of pathways via significance analysis of their intersections

    Significance analysis at single gene level may suffer from the limited number of samples and experimental noise that can severely limit the power of the chosen statistical test. This problem is typically appro...

    Mirko Francesconi, Daniel Remondini, Nicola Neretti, John M Sedivy, Leon N Cooper, Ettore Verondini, Luciano Milanesi and Gastone Castellani

    BMC Bioinformatics 2008 9(Suppl 4):S9

    Published on: 25 April 2008

  9. Research

    GraphFind: enhancing graph searching by low support data mining techniques

    Biomedical and chemical databases are large and rapidly growing in size. Graphs naturally model such kinds of data. To fully exploit the wealth of information in these graph databases, a key role is played by ...

    Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, Dmitry Skripin and Dennis Shasha

    BMC Bioinformatics 2008 9(Suppl 4):S10

    Published on: 25 April 2008

  10. Research

    PARPST: a PARallel algorithm to find peptide sequence tags

    Protein identification is one of the most challenging problems in proteomics. Tandem mass spectrometry provides an important tool to handle the protein identification problem.

    Sara Brunetti, Elena Lodi, Elisa Mori and Maria Stella

    BMC Bioinformatics 2008 9(Suppl 4):S11

    Published on: 25 April 2008

  11. Research

    GeneFisher-P: variations of GeneFisher as processes in Bio-jETI

    PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply a se...

    Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen, Alexander Sczyrba, Sven Hartmeier and Robert Giegerich

    BMC Bioinformatics 2008 9(Suppl 4):S13

    Published on: 25 April 2008