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Documents authored by Rebholz-Schuhmann, Dietrich

Document
DOI: 10.4230/DagSemProc.08131.5
Facilitating the development of controlled vocabularies for metabolomics technologies with text mining

Authors: Irena Spasic, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas B. Kell, and Norman W. Paton

Published in: Dagstuhl Seminar Proceedings, Volume 8131, Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives (2008)

Abstract
Background. Many bioinformatics applications rely on controlled vocabularies or ontologies to consistently interpret and seamlessly integrate information scattered across public resources. Experimental data sets from metabolomics studies need to be integrated with one another, but also with data produced by other types of omics studies in the spirit of systems biology, hence the pressing need for vocabularies and ontologies in metabolomics. However, it is time-consuming and non trivial to construct these resources manually. Results. We describe a methodology for rapid development of controlled vocabularies, a study originally motivated by the needs for vocabularies describing metabolomics technologies. We present case studies involving two controlled vocabularies (for nuclear magnetic resonance spectroscopy and gas chromatography) whose development is currently underway as part of the Metabolomics Standards Initiative. The initial vocabularies were compiled manually, providing a total of 243 and 152 terms. A total of 5,699 and 2,612 new terms were acquired automatically from the literature. The analysis of the results showed that full-text articles (especially the Materials and Methods sections) are the major source of technology-specific terms as opposed to paper abstracts. Conclusions. We suggest a text mining method for efficient corpus-based term acquisition as a way of rapidly expanding a set of controlled vocabularies with the terms used in the scientific literature. We adopted an integrative approach, combining relatively generic software and data resources for time- and cost-effective development of a text mining tool for expansion of controlled vocabularies across various domains, as a practical alternative to both manual term collection and tailor-made named entity recognition methods.
Cite as

Irena Spasic, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas B. Kell, and Norman W. Paton. Facilitating the development of controlled vocabularies for metabolomics technologies with text mining. In Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives. Dagstuhl Seminar Proceedings, Volume 8131, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{spasic_et_al:DagSemProc.08131.5,
  author =	{Spasic, Irena and Schober, Daniel and Sansone, Susanna-Assunta and Rebholz-Schuhmann, Dietrich and Kell, Douglas B. and Paton, Norman W.},
  title =	{{Facilitating the development of controlled vocabularies for metabolomics technologies with text mining}},
  booktitle =	{Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8131},
  editor =	{Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.5},
  URN =		{urn:nbn:de:0030-drops-15503},
  doi =		{10.4230/DagSemProc.08131.5},
  annote =	{Keywords: Text mining, ontology, controlled vocabulary, metabolomics}
}
Document
DOI: 10.4230/DagSemProc.08131.1
08131 Executive Summary – Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives

Authors: Michael Ashburner, Ulf Leser, and Dietrich Rebholz-Schuhmann

Published in: Dagstuhl Seminar Proceedings, Volume 8131, Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives (2008)

Abstract
Researchers in Text Mining and researchers active in developing ontological resources provide solutions to preserve semantic information properly, i.e. in ontologies and/or fact databases. Researchers from both fields tend to work independently from each other, but there is a shared interest to profit from ongoing research in the complementary domain. The relatedness of both domains has led to the idea to organize a workshop that brings together members of both research domains.
Cite as

Michael Ashburner, Ulf Leser, and Dietrich Rebholz-Schuhmann. 08131 Executive Summary – Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives. In Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives. Dagstuhl Seminar Proceedings, Volume 8131, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{ashburner_et_al:DagSemProc.08131.1,
  author =	{Ashburner, Michael and Leser, Ulf and Rebholz-Schuhmann, Dietrich},
  title =	{{08131 Executive Summary – Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives}},
  booktitle =	{Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8131},
  editor =	{Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.1},
  URN =		{urn:nbn:de:0030-drops-15234},
  doi =		{10.4230/DagSemProc.08131.1},
  annote =	{Keywords: Text Mining, natural language processing, ontologies, ontology design, machine learning, bioinformatics, medical informatics, knowledge management}
}
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