Semantics-driven modelling of user preferences for information retrieval in the biomedical domain

Abstract

A large amount of biomedical and genomic data are currently available on the Internet. However, data are distributed into heterogeneous biological information sources, with little or even no organization. Semantic technologies provide a consistent and reliable basis with which to confront the challenges involved in the organization, manipulation and visualization of data and knowledge. One of the knowledge representation techniques used in semantic processing is the ontology, which is commonly defined as a formal and explicit specification of a shared conceptualization of a domain of interest. The work presented here introduces a set of interoperable algorithms that can use domain and ontological information to improve information-retrieval processes. This work presents an ontology-based information-retrieval system for the biomedical domain. This system, with which some experiments have been carried out that are described in this paper, is based on the use of domain ontologies for the creation and normalization of lightweight ontologies that represent user preferences in a determined domain in order to improve information-retrieval processes.

Keywords:

• Ontology
• thesauri
• information retrieval
• Semantic Web

Acknowledgements

This work was possible due to the Spanish Ministry for Science and Innovation under project SeCloud TIN2010-18650, and the Spanish Ministry for Industry, Tourism and Commerce under project TSI-020302-2011-15.

Declaration of Interest: The authors report no conflict of interest.

Notes

Health Care and Life Sciences Interest Group, http://www.w3.org/2001/sw/hcls/

HCLS Banff 2007 demo, http://esw.w3.org/topic/HCLS/Banff2007Demo

BioPortal, http://www.bioontology.org/tools/portal/bioportal.html

GeneOntology http://www.geneontology.org/

MGED http://mged.sourceforge.net/

SBML http://sbml.org/Documents

BioPax http://www.biopax.org/

BioCyc http://biocyc.org/

Reactome http://www.reactome.org/ReactomeGWT/entrypoint.html

TextPresso http://www.textpresso.org/

GeneWays http://anya.igsb.anl.gov/Geneways/GeneWays.html

TAMBIS http://www.cs.man.ac.uk/~stevensr/tambis/

HyBrow http://www.hybrow.org/

http://dublincore.org/documents/dces/

http://bioportal.bioontology.org/ontologies

This ontology has been developed by Alexandra Bulzan and can be accessed in the following URL http://bioportal.bioontology.org/ontologies/40202