Introduction
BMC Bioinformatics 2008 9(Suppl 4):S1
Published on: 25 April 2008
Volume 9 Supplement 4
A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications
Research
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
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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...
BMC Bioinformatics 2008 9(Suppl 4):S2
Published on: 25 April 2008
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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...
BMC Bioinformatics 2008 9(Suppl 4):S3
Published on: 25 April 2008
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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...
BMC Bioinformatics 2008 9(Suppl 4):S4
Published on: 25 April 2008
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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...
BMC Bioinformatics 2008 9(Suppl 4):S5
Published on: 25 April 2008
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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....
BMC Bioinformatics 2008 9(Suppl 4):S6
Published on: 25 April 2008
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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...
BMC Bioinformatics 2008 9(Suppl 4):S7
Published on: 25 April 2008
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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....
BMC Bioinformatics 2008 9(Suppl 4):S8
Published on: 25 April 2008
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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...
BMC Bioinformatics 2008 9(Suppl 4):S9
Published on: 25 April 2008
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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 ...
BMC Bioinformatics 2008 9(Suppl 4):S10
Published on: 25 April 2008
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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.
BMC Bioinformatics 2008 9(Suppl 4):S11
Published on: 25 April 2008
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Research
Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes
With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms...
BMC Bioinformatics 2008 9(Suppl 4):S12
Published on: 25 April 2008
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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...
BMC Bioinformatics 2008 9(Suppl 4):S13
Published on: 25 April 2008
