Volume

Dagstuhl Seminar Proceedings, Volume 5441



Publication Details

  • published at: 2006-02-21
  • Publisher: Schloss-Dagstuhl - Leibniz Zentrum für Informatik

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Document
05441 Abstracts Collection – Managing and Mining Genome Information: Frontiers in Bioinformatics

Authors: Jacek Blazewicz, Johann Christoph Freytag, and Martin Vingron


Abstract
From 30.10.05 to 04.11.05, the Dagstuhl Seminar 05441 ``Managing and Mining Genome Information: Frontiers in Bioinformatics'' was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.

Cite as

Jacek Blazewicz, Johann Christoph Freytag, and Martin Vingron. 05441 Abstracts Collection – Managing and Mining Genome Information: Frontiers in Bioinformatics. In Managing and Mining Genome Information: Frontiers in Bioinformatics. Dagstuhl Seminar Proceedings, Volume 5441, pp. 1-17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2006)


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@InProceedings{blazewicz_et_al:DagSemProc.05441.1,
  author =	{Blazewicz, Jacek and Freytag, Johann Christoph and Vingron, Martin},
  title =	{{05441 Abstracts Collection – Managing and Mining Genome Information: Frontiers in Bioinformatics}},
  booktitle =	{Managing and Mining Genome Information: Frontiers in Bioinformatics},
  pages =	{1--17},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5441},
  editor =	{Jacek Blazewicz and Johann Christoph Freytag and Martin Vingron},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05441.1},
  URN =		{urn:nbn:de:0030-drops-4765},
  doi =		{10.4230/DagSemProc.05441.1},
  annote =	{Keywords: Biological data management, semantic knowledge, ontologies, large-scale data mining, functional genomics}
}
Document
05441 Executive Summary – Managing and Mining Genome Information: Frontiers in Bioinformatics

Authors: Jacek Blazewicz, Johann Christoph Freytag, and Martin Vingron


Abstract
This report summarizes the important aspects of the workshop on "Managing and Mining Genome Information: Frontiers in Bioinformatics" which took place October 31st until November 4th, 2005. Twenty five Participants came from six different countries representing various "branches" of the bioinformatics community. The presentations ranged from describing highly theoretical models to presenting prototypes or systems for managing and mining data in bioinformatics.

Cite as

Jacek Blazewicz, Johann Christoph Freytag, and Martin Vingron. 05441 Executive Summary – Managing and Mining Genome Information: Frontiers in Bioinformatics. In Managing and Mining Genome Information: Frontiers in Bioinformatics. Dagstuhl Seminar Proceedings, Volume 5441, pp. 1-7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2006)


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@InProceedings{blazewicz_et_al:DagSemProc.05441.2,
  author =	{Blazewicz, Jacek and Freytag, Johann Christoph and Vingron, Martin},
  title =	{{05441 Executive Summary – Managing and Mining Genome Information: Frontiers in Bioinformatics}},
  booktitle =	{Managing and Mining Genome Information: Frontiers in Bioinformatics},
  pages =	{1--7},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5441},
  editor =	{Jacek Blazewicz and Johann Christoph Freytag and Martin Vingron},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05441.2},
  URN =		{urn:nbn:de:0030-drops-4759},
  doi =		{10.4230/DagSemProc.05441.2},
  annote =	{Keywords: Biological data management, semantic knowledge, ontologies, large-scale data mining, functional genomics}
}
Document
Semantic browsing of pathway ontologies and biological networks with RDFScape (working paper)

Authors: Andrea Splendiani


Abstract
Studying biological organisms at the systems level is a complex task. Computational approaches require structured representations of existing biological knowledge. This necessity has prompted the development of formal representations of specific areas of knowledge, resulting in ontologies such as Gene Ontology and BioPAX. However, only part of this formalized knowledge is exploited for the interpretation of experimental data. Specifically, it is common to use the association between entities and annotations, like genes and functions, while the structure of the annotation is not considered beyond some common features as inheritance. This is partly due to a lack of tools and methods that bridge resources related to ontologies to the ones related to data analysis. Here we present a platform that merges a semantic web toolkit with a widely adopted modular tool for systems biology investigation. We demonstrate how in this environment it is possible to query ontologies not only as a list of annotations but as a knowledge base from which new information can be derived. We also show how this knowledge can be integrated with biological data.

Cite as

Andrea Splendiani. Semantic browsing of pathway ontologies and biological networks with RDFScape (working paper). In Managing and Mining Genome Information: Frontiers in Bioinformatics. Dagstuhl Seminar Proceedings, Volume 5441, pp. 1-24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2006)


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@InProceedings{splendiani:DagSemProc.05441.3,
  author =	{Splendiani, Andrea},
  title =	{{Semantic browsing of pathway ontologies and biological networks with RDFScape (working paper)}},
  booktitle =	{Managing and Mining Genome Information: Frontiers in Bioinformatics},
  pages =	{1--24},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5441},
  editor =	{Jacek Blazewicz and Johann Christoph Freytag and Martin Vingron},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05441.3},
  URN =		{urn:nbn:de:0030-drops-4746},
  doi =		{10.4230/DagSemProc.05441.3},
  annote =	{Keywords: Pathways, Semantic Web, Ontologies, Microarrays}
}

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