Change search
ReferencesLink to record
Permanent link

Direct link
SWI-Prolog as a Semantic Web Tool for semantic querying in Bioclipse: Integration and performance benchmarking
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Prof. Jarl Wikberg, Bioclipse group)
2010 (English)Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

The huge amounts of data produced in high-throughput techniques in the life sciences and the need for integration of heterogeneous data from disparate sources in new fields such as Systems Biology and translational drug development require better approaches to data integration. The semantic web is anticipated to provide solutions through new formats for knowledge representation and management. Software libraries for semantic web formats are becoming mature, but there exist multiple tools based on foundationally different technologies. SWI-Prolog, a tool with semantic web support, was integrated into the Bioclipse bio- and cheminformatics workbench software and evaluated in terms of performance against non Prolog-based semantic web tools in Bioclipse, Jena and Pellet, for querying a data set consisting of mostly numerical, NMR shift values, in the semantic web format RDF. The integration has given access to the convenience of the Prolog language for working with semantic data and defining data management workflows in Bioclipse. The performance comparison shows that SWI-Prolog is superior in terms of performance over Jena and Pellet for this specific dataset and suggests Prolog-based tools as interesting for further evaluations.

Place, publisher, year, edition, pages
2010. , 37 p.
Series
UPTEC X, 10 014
Keyword [en]
Semantic Web, Prolog, Bioclipse, RDF, SPARQL, NMR shift, Eclipse, Java
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:uu:diva-146738OAI: oai:DiVA.org:uu-146738DiVA: diva2:398839
Presentation
2010-06-18, B7:101a, Biomedicinskt Centrum, Husargatan 3, Uppsala, 14:33 (English)
Uppsok
Technology
Supervisors
Examiners
Available from: 2011-03-09 Created: 2011-02-19 Last updated: 2011-03-09Bibliographically approved

Open Access in DiVA

fulltext(913 kB)1281 downloads
File information
File name FULLTEXT01.pdfFile size 913 kBChecksum SHA-512
603b8348db54d1cf472c98fa4409f394f0540e7ffaf0231b750440b51005c19b700fcb8d8c8b7c0a31db01ea93007f5ca56310e3cd415738a17d57dfb0f0aa5d
Type fulltextMimetype application/pdf

Search in DiVA

By author/editor
Lampa, Samuel
By organisation
Department of Pharmaceutical Biosciences
Bioinformatics and Systems Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 1281 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Total: 3800 hits
ReferencesLink to record
Permanent link

Direct link