Conference Paper

Algorithms and databases in bioinformatics: towards a proteomic ontology

Magna Graecia Univ., Catanzaro, Italy
DOI: 10.1109/ITCC.2005.63 Conference: Information Technology: Coding and Computing, 2005. ITCC 2005. International Conference on, Volume: 1
Source: IEEE Xplore

ABSTRACT Classification of bioinformatics tools and databases, as well as modelling of biological processes, can help the design of complex in silico experiments. After presenting a survey of bioinformatics algorithms and biological databases, we describe a first design of an ontology for the Proteomics domain. The ontology can be used either to better understand biological processes or to enhance design of distributed bioinformatics applications.

1 Bookmark
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: In this work we revise the layered software architecture for the Knowledge Grid by explicitly introducing the concept of Resourceome, i.e. an “alive” ontology of resources. This approach is necessary to tackle the challenges posed by the “ome” status, reached by the world of bioinformatics resources. The resulting software architecture, a Resourceomic Grid, integrates components to support issues like awareness, discovery, integration and abstraction of resources.
    Future Generation Computer Systems 03/2007; · 2.64 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Semantic Grid applications based on the cooperation of Grid Services need semantic modeling tools and functions to access and manage ontologies stored on the Grid. Although many tools and methodologies exist for ontology editing and management, they often work in a centralized way and are not available on the Grid. The paper proposes a distributed ontology management framework where ontology schema is replicated and instances are distributed among nodes of the Grid. A distributed ontology kernel that offers querying and updating APIs and a graphical query interface for ontology browsing have been fully designed. The kernel leverages distributed data management functions offered by the Grid middleware to store and access ontology fragments. It has been embedded into an ontology-based workflow editor allowing distributed users to design and execute bioinformatics applications. Domain ontologies, partitioned and managed by the ontology kernel, are accessed by the editor enhancing workflow composition. The ontology distribution allows to design a complete application whatever availability of Grid nodes.
    Multiagent and Grid Systems. 01/2006; 2:29-44.


Available from
Jun 3, 2014