liu.seSearch for publications in DiVA
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Towards transparent access to multiple biological databanks
Linköping University, Department of Computer and Information Science, IISLAB. Linköping University, The Institute of Technology.ORCID iD: 0000-0002-9084-0470
Linköping University, Department of Computer and Information Science, IISLAB. Linköping University, The Institute of Technology.
2003 (English)In: Proceedings of the first Asia-Pacific Bioinformatics Conference, Adelaide, Australia, 2003, Vol. 33, 53-60 p.Conference paper, Published paper (Refereed)
Abstract [en]

Nowadays, biologists use a number of large biological databanks to find relevant information for their research. Users of these databanks face a number of problems. One problem is that users are required to have good knowledge about the contents, implementations and conceptual models of many databanks to be able to ask precise and relevant questions. Further, the terminology that is used in the different databanks may be different. Also, when asking complex queries to multiple databanks, users need to construct a query plan on their own possibly leading to poor performance or not even obtaining results. To alleviate these problems we define an architecture for systems that deal with these problems by allowing for a transparent and integrated way to query the multiple sources. The contribution of this paper is threefold. First, we describe a study of current biological databanks. Then, we propose a base query language that contains operators that should be present in any query language for biological databanks. Further, we present an architecture for a system supporting such a language and providing integrated access to the highly distributed and heterogeneous environment of biological databanks.

Place, publisher, year, edition, pages
2003. Vol. 33, 53-60 p.
National Category
Engineering and Technology
Identifiers
URN: urn:nbn:se:liu:diva-14032OAI: oai:DiVA.org:liu-14032DiVA: diva2:22494
Available from: 2006-09-28 Created: 2006-09-28 Last updated: 2015-02-18
In thesis
1. Integration of Biological Data
Open this publication in new window or tab >>Integration of Biological Data
2006 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Data integration is an important procedure underlying many research tasks in the life sciences, as often multiple data sources have to be accessed to collect the relevant data. The data sources vary in content, data format, and access methods, which often vastly complicates the data retrieval process. As a result, the task of retrieving data requires a great deal of effort and expertise on the part of the user. To alleviate these difficulties, various information integration systems have been proposed in the area. However, a number of issues remain unsolved and new integration solutions are needed.

The work presented in this thesis considers data integration at three different levels. 1) Integration of biological data sources deals with integrating multiple data sources from an information integration system point of view. We study properties of biological data sources and existing integration systems. Based on the study, we formulate requirements for systems integrating biological data sources. Then, we define a query language that supports queries commonly used by biologists. Also, we propose a high-level architecture for an information integration system that meets a selected set of requirements and that supports the specified query language. 2) Integration of ontologies deals with finding overlapping information between ontologies. We develop and evaluate algorithms that use life science literature and take the structure of the ontologies into account. 3) Grouping of biological data entries deals with organizing data entries into groups based on the computation of similarity values between the data entries. We propose a method that covers the main steps and components involved in similarity-based grouping procedures. The applicability of the method is illustrated by a number of test cases. Further, we develop an environment that supports comparison and evaluation of different grouping strategies.

The work is supported by the implementation of: 1) a prototype for a system integrating biological data sources, called BioTRIFU, 2) algorithms for ontology alignment, and 3) an environment for evaluating strategies for similarity-based grouping of biological data, called KitEGA.

Place, publisher, year, edition, pages
Institutionen för datavetenskap, 2006. 20 p.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1035
Keyword
Datalogi, integration, grouping, databases, ontologies, biological data, ioinformatics, KitEGA, Datalogi
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-7484 (URN)91-85523-28-3 (ISBN)
Public defence
2006-09-25, Visionen, Hus B, Campus Valla, Linköpings universitet, Linköping, 13:15 (English)
Opponent
Supervisors
Available from: 2006-09-28 Created: 2006-09-28 Last updated: 2017-08-15Bibliographically approved

Open Access in DiVA

No full text

Other links

Link to articleLink to Ph.D. Thesis

Authority records BETA

Lambrix, PatrickJakoniené, Vaida

Search in DiVA

By author/editor
Lambrix, PatrickJakoniené, Vaida
By organisation
IISLABThe Institute of Technology
Engineering and Technology

Search outside of DiVA

GoogleGoogle Scholar

urn-nbn

Altmetric score

urn-nbn
Total: 76 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf