An Architectural Design of Open Genome Services

Umetsu, Ryo; Ohki, S; Fukuzaki, Akinobu; Konagaya, Akihiko; Shinbara, Daisuke; Saito, Masataka; Watanabe, Kentaro; Kitagawa, T.; Hoshino, Teppei

doi:10.1142/9789812772503_0008

Cited by 6 publications

(3 citation statements)

References 2 publications

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“…BLAST may return very similar but unimportant sequences such as EST (expressed sequence tag) or annotated sequences. We therefore require filtering processes that are able to eliminate redundant and irrelevant data from the computational results [22]. A bioinformatics service ontology is therefore needed in order for the community to make use of and share bioinformatics workflows.…”

Section: Superstructure For Biomedical Knowledge Creationmentioning

confidence: 99%

THE GRID AS A “Ba” FOR BIOMEDICAL KNOWLEDGE CREATION

Konagaya¹

2006

Grid Computing in Life Sciences

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Data-driven biology, typified by the Human Genome Project, has produced an enormous amount of experimental data, including data on genomes, transcriptomes, proteomes, interactomes, and phenomes. The next pursuit in genome science concentrates on elucidating relations among the data. Key to understanding these relations are bio-networks that incorporate information on protein-protein interactions, metabolic pathways, signal transduction pathways, and gene regulatory networks. Development of these bio-networks, however, requires biomedical knowledge of life phenomena in order to add biological interpretations. In this sense, data creation and knowledge creation play complementary roles in the development of genome science. As for knowledge creation, Ikujiro Nonaka proposed the importance of "ba", that is, a time and place in which people share knowledge and work together as a community. Grid computing offers great potential to extend the concept of "ba" to networks, especially in terms of deepening the understanding and use of bio-networks by means of sharing explicit knowledge represented by ontology, mathematical simulation models and bioinformatics workflows.

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Section: Superstructure For Biomedical Knowledge Creationmentioning

confidence: 99%

THE GRID AS A “Ba” FOR BIOMEDICAL KNOWLEDGE CREATION

Konagaya¹

2006

Grid Computing in Life Sciences

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“…Sharing of unpublished data is also important in promoting collaborative research among institutions, as well as sharing of public databases, bioinformatics tools and web services [2][3][4][5][6][7]. Biological knowledge, such as ontology and metadata, also plays an important role in analysis of experimental data and integrating genome-wide OMICS data including genome, transcriptome, proteome, and other types of data [8,9].…”

Section: Introductionmentioning

confidence: 99%

Retraction: Changing from computing grid to knowledge grid in life‐science grid

Talukdar¹,

Konar²,

Datta³

et al. 2011

Biotechnology Journal

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“…The web services also enable us to develop location-free bioinformatics workflows without worrying about computation resources and the maintenance costs of databases and tools 2 [10].…”

Section: Introductionmentioning

confidence: 99%

OBIGrid: towards the 'Ba' for sharing resources, services and knowledge for bioinformatics

Konagaya

2006

Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID'06)

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Open Bioinformatics Grid (OBIGrid) was established in 2002 for sharing the bioinformatics environment including computational resources, public databases, and bioinformatics application tools over the Internet. Grid is one of the most attractive cyber infrastructures for achieving scalability in the computation power and data storage necessary for bioinformatics. Grid also plays the role of 'Ba', the basis of virtual organizations in which people share time and place to work together. 'Ba' can extend beyond the boundaries of current grid computing by utilizing web service technologies for sharing databases, tools, and knowledge distributed all over the world.However, many issues regarding the widespread use of the web services have been raised, such as the semantic gap between bioinformatics workflows and the application programming interfaces provided by web services. The key to solving such issues is the bioinformatics ontology employed to establish interoperability among biological databases and bioinformatics application tools used by the web services. This paper proposes a design of bioinformatics ontology based on triadic relations among input-output data, commands, and databases, and demonstrates its feasibility in the automatic generation of bioinformatics workflows.

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An Architectural Design of Open Genome Services

Cited by 6 publications

References 2 publications

THE GRID AS A “Ba” FOR BIOMEDICAL KNOWLEDGE CREATION

THE GRID AS A “Ba” FOR BIOMEDICAL KNOWLEDGE CREATION

Retraction: Changing from computing grid to knowledge grid in life‐science grid

OBIGrid: towards the 'Ba' for sharing resources, services and knowledge for bioinformatics

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