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Towards transparent access to multiple biological databanks
Linköpings universitet, Institutionen för datavetenskap, IISLAB. Linköpings universitet, Tekniska högskolan.ORCID-id: 0000-0002-9084-0470
Linköpings universitet, Institutionen för datavetenskap, IISLAB. Linköpings universitet, Tekniska högskolan.
2003 (Engelska)Ingår i: Proceedings of the first Asia-Pacific Bioinformatics Conference, Adelaide, Australia, 2003, Vol. 33, s. 53-60Konferensbidrag, Publicerat paper (Refereegranskat)
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.

Ort, förlag, år, upplaga, sidor
2003. Vol. 33, s. 53-60
Nationell ämneskategori
Teknik och teknologier
Identifikatorer
URN: urn:nbn:se:liu:diva-14032OAI: oai:DiVA.org:liu-14032DiVA, id: diva2:22494
Tillgänglig från: 2006-09-28 Skapad: 2006-09-28 Senast uppdaterad: 2015-02-18
Ingår i avhandling
1. Integration of Biological Data
Öppna denna publikation i ny flik eller fönster >>Integration of Biological Data
2006 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
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.

Ort, förlag, år, upplaga, sidor
Institutionen för datavetenskap, 2006. s. 20
Serie
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1035
Nyckelord
Datalogi, integration, grouping, databases, ontologies, biological data, ioinformatics, KitEGA, Datalogi
Nationell ämneskategori
Teknik och teknologier
Identifikatorer
urn:nbn:se:liu:diva-7484 (URN)91-85523-28-3 (ISBN)
Disputation
2006-09-25, Visionen, Hus B, Campus Valla, Linköpings universitet, Linköping, 13:15 (Engelska)
Opponent
Handledare
Tillgänglig från: 2006-09-28 Skapad: 2006-09-28 Senast uppdaterad: 2017-08-15Bibliografiskt granskad

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