Linking biological databases semantically for knowledge discovery

Sudha Ram, Kunpeng Zhang, Wei Wei

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

Many important life sciences questions are aimed at studying the relationships and interactions between biological functions/processes and biological entities such as genes. The answers may be found by examining diverse types of biological/genomic databases. Finding these answers, however, requires accessing, and retrieving data, from diverse biological data sources. More importantly, sophisticated knowledge discovery processes involve traversing through large numbers of inherent links among various data sources. Currently, the links among data are either implemented as hyperlinks without explicitly indicating their meanings and labels, or hidden in a seemingly simple text format. Consequently, biologists spend numerous hours identifying potentially useful links and following each lead manually, which is time-consuming and error-prone. Our research is aimed at constructing semantic relationships among all biological entities. We have designed a semantic model to categorize and formally define the links. By incorporating ontologies such as Gene or Sequence ontology, we propose techniques to analyze the links embedded within and among data records, to explicitly label their semantics, and to facilitate link traversal, querying, and data sharing. Users may then ask complicated and ad hoc questions and even design their own workflow to support their knowledge discovery processes. In addition, we have performed an empirical analysis to demonstrate that our method can not only improve the efficiency of querying multiple databases, but also yield more useful information.

Original languageEnglish (US)
Title of host publicationAdvances in Conceptual Modeling - Challenges and Opportunities - ER 2008 Workshops CMLSA, ECDM, FP-UML, M2AS, RIGiM, SeCoGIS, WISM, Proceedings
Pages22-32
Number of pages11
DOIs
StatePublished - Dec 1 2008
Event27th International Conference on Conceptual Modeling, ER 2008 Workshops: CMLSA, ECDM, FP-UML, M2AS, RIGiM, SeCoGIS, WISM - Barcelona, Spain
Duration: Oct 20 2008Oct 23 2008

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5232 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other27th International Conference on Conceptual Modeling, ER 2008 Workshops: CMLSA, ECDM, FP-UML, M2AS, RIGiM, SeCoGIS, WISM
CountrySpain
CityBarcelona
Period10/20/0810/23/08

Keywords

  • Conceptual modeling
  • Ontology
  • Semantics

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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  • Cite this

    Ram, S., Zhang, K., & Wei, W. (2008). Linking biological databases semantically for knowledge discovery. In Advances in Conceptual Modeling - Challenges and Opportunities - ER 2008 Workshops CMLSA, ECDM, FP-UML, M2AS, RIGiM, SeCoGIS, WISM, Proceedings (pp. 22-32). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5232 LNCS). https://doi.org/10.1007/978-3-540-87991-6-4