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Metarel, an ontology facilitating advanced querying of biomedical knowledge

Ward Blondé UGent (2012)
abstract
Knowledge management has become indispensible in the Life Sciences for integrating and querying the enormous amounts of detailed knowledge about genes, organisms, diseases, drugs, cells, etc. Such detailed knowledge is continuously generated in bioinformatics via both hardware (e.g. raw data dumps from micro‐arrays) and software (e.g. computational analysis of data). Well‐known frameworks for managing knowledge are relational databases and spreadsheets. The doctoral dissertation describes knowledge management in two more recently‐investigated frameworks: ontologies and the Semantic Web. Knowledge statements like ‘lions live in Africa’ and ‘genes are located in a cell nucleus’ are managed with the use of URIs, logics and the ontological distinction between instances and classes. Both theory and practice are described. Metarel, the core subject of the dissertation, is an ontology describing relations that can bridge the mismatch between network‐based relations that appeal to internet browsing and logic‐based relations that are formally expressed in Description Logic. Another important subject of the dissertation is BioGateway, which is a knowledge base that has integrated biomedical knowledge in the form of hundreds of millions of network‐based relations in the RDF format. Metarel was used to upgrade the logical meaning of these relations towards Description Logic. This has enabled to build a computer reasoner that could run over the knowledge base and derive new knowledge statements.
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author
promoter
UGent and Martin Kuiper
organization
alternative title
Metarel, een ontologie voor doorgedreven bevraging van biomedische kennis
year
type
dissertation (monograph)
subject
keyword
Logic, RDF, Knowledge Management, Semantic Web, Relation, Ontology
pages
XVI, 226 pages
publisher
Ghent University. Faculty of Bioscience Engineering
place of publication
Ghent, Belgium
defense location
Gent : Faculteit Bio-ingenieurswetenschappen (A0.030)
defense date
2012-06-22 14:00
ISBN
9789059895324
language
English
UGent publication?
yes
classification
D1
copyright statement
I have retained and own the full copyright for this publication
id
2913369
handle
http://hdl.handle.net/1854/LU-2913369
date created
2012-06-20 11:49:56
date last changed
2012-06-21 09:03:59
@phdthesis{2913369,
  abstract     = {Knowledge management has become indispensible in the Life Sciences for integrating and querying the enormous amounts of detailed knowledge about genes, organisms, diseases, drugs, cells, etc. Such detailed knowledge is continuously generated in bioinformatics via both hardware (e.g. raw data dumps from micro\unmatched{2010}arrays) and software (e.g.  computational analysis  of  data).  Well\unmatched{2010}known  frameworks  for  managing knowledge  are  relational databases and spreadsheets. The doctoral dissertation describes knowledge management in two more  recently\unmatched{2010}investigated  frameworks:  ontologies  and the  Semantic  Web. Knowledge statements like {\textquoteleft}lions live in Africa{\textquoteright} and {\textquoteleft}genes are located in a cell nucleus{\textquoteright} are managed  with the  use  of  URIs,  logics  and  the  ontological  distinction  between  instances and  classes.  Both  theory  and  practice are  described.  Metarel,  the  core  subject  of  the dissertation,  is  an  ontology  describing  relations  that  can bridge  the  mismatch  between network\unmatched{2010}based  relations  that appeal  to  internet  browsing  and  logic\unmatched{2010}based  relations  that are formally expressed in Description Logic. Another important subject of the dissertation is BioGateway, which is a knowledge base that has integrated biomedical knowledge in the form of hundreds of millions of network\unmatched{2010}based relations in the RDF format. Metarel was used to upgrade the logical meaning of these relations towards Description Logic. This has enabled to build a computer reasoner that could run over the knowledge base and derive new knowledge statements.},
  author       = {Blond{\'e}, Ward},
  isbn         = {9789059895324},
  keyword      = {Logic,RDF,Knowledge Management,Semantic Web,Relation,Ontology},
  language     = {eng},
  pages        = {XVI, 226},
  publisher    = {Ghent University. Faculty of Bioscience Engineering},
  school       = {Ghent University},
  title        = {Metarel, an ontology facilitating advanced querying of biomedical knowledge},
  year         = {2012},
}

Chicago
Blondé, Ward. 2012. “Metarel, an Ontology Facilitating Advanced Querying of Biomedical Knowledge”. Ghent, Belgium: Ghent University. Faculty of Bioscience Engineering.
APA
Blondé, W. (2012). Metarel, an ontology facilitating advanced querying of biomedical knowledge. Ghent University. Faculty of Bioscience Engineering, Ghent, Belgium.
Vancouver
1.
Blondé W. Metarel, an ontology facilitating advanced querying of biomedical knowledge. [Ghent, Belgium]: Ghent University. Faculty of Bioscience Engineering; 2012.
MLA
Blondé, Ward. “Metarel, an Ontology Facilitating Advanced Querying of Biomedical Knowledge.” 2012 : n. pag. Print.