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we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base.
Satya Sahoo, Olivier Bodenreider, Joni Rutter, Karen Skinner, Amit Sheth. An Ontology-Driven Semantic Mashup of Gene and Biological Pathway Information: Application to the Domain of Nicotine Dependence. 2008 ;.
This paper illustrates how Semantic Web technologies (especially RDF
Satya Sahoo, Olivier Bodenreider, Joni Rutter, Karen Skinner, Amit Sheth. An Ontology-Driven Semantic Mashup of Gene and Biological Pathway Information: Application to the Domain of Nicotine Dependence. 2008 ;.
text mining
Delroy Cameron, Pablo Mendes, Amit Sheth, Krishnaprasad Thirunarayan, Ramakanth Kavuluru, Olivier Bodenreider. Semantic Predications for Complex Information Needs in Biomedical Literature. 2011 IEEE International Conference on Bioinformatics and Biomedicine. Atlanta, GA: IEEE; 2011.
Delroy Cameron, Ramakanth Kavuluru, Olivier Bodenreider, Pablo Mendes, Amit Sheth, Krishnaprasad Thirunarayan. Semantic Predications for Complex Information Needs in Biomedical Literature. In 5th International Conference on Bioinformatics and Biomedicine (BIBM2011). Atlanta GA: 2011 IEEE International Conference on Bioinformatics and Biomedicine; 2011.  (471.3 KB)
Swanson's Hypothesis
Delroy Cameron, Olivier Bodenreider, Hima Yalamanchili, Tu Danh, Sreeram Vallabhaneni, Krishnaprasad Thirunarayan, Amit Sheth, Thomas Rindflesch. A Graph-Based Recovery and Decomposition of Swanson's Hypothesis using Semantic Predications. Journal of Biomedical Informatics. 2013 ;46(2):238-251.  (915.51 KB)
Subgraph Creation
Delroy Cameron, Olivier Bodenreider, Hima Yalamanchili, Tu Danh, Sreeram Vallabhaneni, Krishnaprasad Thirunarayan, Amit Sheth, Thomas Rindflesch. A Graph-Based Recovery and Decomposition of Swanson's Hypothesis using Semantic Predications. Journal of Biomedical Informatics. 2013 ;46(2):238-251.  (915.51 KB)
sparql
Vinh Nguyen, Olivier Bodenreider, Amit Sheth. Don't like RDF Reification? Making Statements about Statements using Singleton Property. 23rd International conference on World Wide Web (WWW '14). New York, NY: ACM; 2014. p. 759-770.  (382.61 KB)
Singleton Property
Vinh Nguyen, Olivier Bodenreider, Amit Sheth. Don't like RDF Reification? Making Statements about Statements using Singleton Property. 23rd International conference on World Wide Web (WWW '14). New York, NY: ACM; 2014. p. 759-770.  (382.61 KB)
Semantic Web and SPARQL and Gene Ontology and Entrez Gene and path queries. and Data integration and Resource DescriptionFramework
Amit Sheth, Satya S. Sahoo, Olivier Bodenreider, Kelly Zeng. An experiment in integrating large biomedical knowledge resources with RDF: Application to associating genotype and phenotype information. In Workshop on Health Care and Life Sciences Data Integration for the Semantic Web at WWW2007; 2007.  (246.22 KB)
Semantic Web and Knowledge Exploration
Vinh Nguyen, Olivier Bodenreider, Todd Minning, Amit Sheth. The Knowledge Driven Exploration of Integrated Biomedical Knowledge Sources Facilitates the Generation of New Hypotheses. In 1st International Conference on Linked Science. Bonn, Germany: Linked Science workshop, ISWC; 2011.  (138.82 KB)
Semantic Web
Vinh Nguyen, Olivier Bodenreider, Amit Sheth. Don't like RDF Reification? Making Statements about Statements using Singleton Property. 23rd International conference on World Wide Web (WWW '14). New York, NY: ACM; 2014. p. 759-770.  (382.61 KB)
Satya Sahoo, Kelly Zeng, Olivier Bodenreider, Amit Sheth. From "Glycosyltransferase" to "Congenital Muscular Dystrophy": Integrating Knowledge from NCBI Entrez Gene and the Gene Ontology. 2007 ;.
Semantic relatedness
Delroy Cameron, Ramakanth Kavuluru, Thomas Rindflesch, Amit Sheth, Krishnaprasad Thirunarayan, Olivier Bodenreider. Context-driven automatic subgraph creation for literature-based discovery. Journal of Biomedical Informatics. 2015 ;54:141-157.  (2.37 MB)
semantic provenance
Satya S. Sahoo, Krishnaprasad Thirunarayan, Olivier Bodenreider, Pascal Hitzler, Amit Sheth. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. In SSDBM2010. The 22nd International Conference on Scientific and Statistical Database Management (SSDBM) 2010; 2010.  (810.08 KB)
semantic predications
Delroy Cameron, Olivier Bodenreider, Hima Yalamanchili, Tu Danh, Sreeram Vallabhaneni, Krishnaprasad Thirunarayan, Amit Sheth, Thomas Rindflesch. A Graph-Based Recovery and Decomposition of Swanson's Hypothesis using Semantic Predications. Journal of Biomedical Informatics. 2013 ;46(2):238-251.  (915.51 KB)
Delroy Cameron, Pablo Mendes, Amit Sheth, Krishnaprasad Thirunarayan, Ramakanth Kavuluru, Olivier Bodenreider. Semantic Predications for Complex Information Needs in Biomedical Literature. 2011 IEEE International Conference on Bioinformatics and Biomedicine. Atlanta, GA: IEEE; 2011.
Delroy Cameron, Ramakanth Kavuluru, Olivier Bodenreider, Pablo Mendes, Amit Sheth, Krishnaprasad Thirunarayan. Semantic Predications for Complex Information Needs in Biomedical Literature. In 5th International Conference on Bioinformatics and Biomedicine (BIBM2011). Atlanta GA: 2011 IEEE International Conference on Bioinformatics and Biomedicine; 2011.  (471.3 KB)
Semantic mashup
Karen Skinner, Joni Rutter, Amit Sheth, Olivier Bodenreider, Satya S. Sahoo. An Ontology-driven Semantic Mash-up of Gene and Biological Pathway Information: Application to the Domain of Nicotine Dependence. Journal of Biomedical Informatics. 2008 ;:752-765.  (617.43 KB)
Semantic Bioinformatics
Karen Skinner, Joni Rutter, Amit Sheth, Olivier Bodenreider, Satya S. Sahoo. An Ontology-driven Semantic Mash-up of Gene and Biological Pathway Information: Application to the Domain of Nicotine Dependence. Journal of Biomedical Informatics. 2008 ;:752-765.  (617.43 KB)
Semantic Associations and Background Knowledge and Semantic Predications and Subgraph Creation and Swanson&#39
Delroy Cameron, Olivier Bodenreider, Hima Yalamanchili, Tu Danh, Sreeram Vallabhaneni, Krishnaprasad Thirunarayan, Amit Sheth, Thomas C. Rindflesch. A Graph-Based Recovery and Decomposition of Swanson's Hypothesis using Semantic Predications. 2012.  (915.51 KB)
semantic associations
Delroy Cameron, Olivier Bodenreider, Hima Yalamanchili, Tu Danh, Sreeram Vallabhaneni, Krishnaprasad Thirunarayan, Amit Sheth, Thomas Rindflesch. A Graph-Based Recovery and Decomposition of Swanson's Hypothesis using Semantic Predications. Journal of Biomedical Informatics. 2013 ;46(2):238-251.  (915.51 KB)
s Hypothesis and Literature-Based Discovery (LBD)
Delroy Cameron, Olivier Bodenreider, Hima Yalamanchili, Tu Danh, Sreeram Vallabhaneni, Krishnaprasad Thirunarayan, Amit Sheth, Thomas C. Rindflesch. A Graph-Based Recovery and Decomposition of Swanson's Hypothesis using Semantic Predications. 2012.  (915.51 KB)
RDF reification
Satya S. Sahoo, Krishnaprasad Thirunarayan, Olivier Bodenreider, Pascal Hitzler, Amit Sheth. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. In SSDBM2010. The 22nd International Conference on Scientific and Statistical Database Management (SSDBM) 2010; 2010.  (810.08 KB)
Vinh Nguyen, Olivier Bodenreider, Amit Sheth. Don't like RDF Reification? Making Statements about Statements using Singleton Property. 23rd International conference on World Wide Web (WWW '14). New York, NY: ACM; 2014. p. 759-770.  (382.61 KB)
rdf
Vinh Nguyen, Olivier Bodenreider, Amit Sheth. Don't like RDF Reification? Making Statements about Statements using Singleton Property. 23rd International conference on World Wide Web (WWW '14). New York, NY: ACM; 2014. p. 759-770.  (382.61 KB)
Satya Sahoo, Kelly Zeng, Olivier Bodenreider, Amit Sheth. From "Glycosyltransferase" to "Congenital Muscular Dystrophy": Integrating Knowledge from NCBI Entrez Gene and the Gene Ontology. 2007 ;.
question answering
Delroy Cameron, Pablo Mendes, Amit Sheth, Krishnaprasad Thirunarayan, Ramakanth Kavuluru, Olivier Bodenreider. Semantic Predications for Complex Information Needs in Biomedical Literature. 2011 IEEE International Conference on Bioinformatics and Biomedicine. Atlanta, GA: IEEE; 2011.
Delroy Cameron, Ramakanth Kavuluru, Olivier Bodenreider, Pablo Mendes, Amit Sheth, Krishnaprasad Thirunarayan. Semantic Predications for Complex Information Needs in Biomedical Literature. In 5th International Conference on Bioinformatics and Biomedicine (BIBM2011). Atlanta GA: 2011 IEEE International Conference on Bioinformatics and Biomedicine; 2011.  (471.3 KB)
Provenir ontology and Provenance context entity and Biomedical knowledge repository and Context theory and RDF reification
Satya Sahoo, Olivier Bodenreider, Krishnaprasad Thirunarayan, Pascal Hitzler, Amit Sheth. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. Scientific and Statistical Database Management (SSDBM 2010). Heidelberg, Germany; 2010. p. 461-470.  (534.62 KB)
Provenir ontology
Satya S. Sahoo, Krishnaprasad Thirunarayan, Olivier Bodenreider, Pascal Hitzler, Amit Sheth. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. In SSDBM2010. The 22nd International Conference on Scientific and Statistical Database Management (SSDBM) 2010; 2010.  (810.08 KB)
Provenance Management Framework
Satya S. Sahoo, Krishnaprasad Thirunarayan, Olivier Bodenreider, Pascal Hitzler, Amit Sheth. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. In SSDBM2010. The 22nd International Conference on Scientific and Statistical Database Management (SSDBM) 2010; 2010.  (810.08 KB)
Provenance context entity
Satya S. Sahoo, Krishnaprasad Thirunarayan, Olivier Bodenreider, Pascal Hitzler, Amit Sheth. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. In SSDBM2010. The 22nd International Conference on Scientific and Statistical Database Management (SSDBM) 2010; 2010.  (810.08 KB)
Provenance context
Satya S. Sahoo, Krishnaprasad Thirunarayan, Olivier Bodenreider, Pascal Hitzler, Amit Sheth. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. In SSDBM2010. The 22nd International Conference on Scientific and Statistical Database Management (SSDBM) 2010; 2010.  (810.08 KB)
PrOM
Satya S. Sahoo, Krishnaprasad Thirunarayan, Olivier Bodenreider, Pascal Hitzler, Amit Sheth. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. In SSDBM2010. The 22nd International Conference on Scientific and Statistical Database Management (SSDBM) 2010; 2010.  (810.08 KB)
Path clustering
Delroy Cameron, Ramakanth Kavuluru, Thomas Rindflesch, Amit Sheth, Krishnaprasad Thirunarayan, Olivier Bodenreider. Context-driven automatic subgraph creation for literature-based discovery. Journal of Biomedical Informatics. 2015 ;54:141-157.  (2.37 MB)
PACE
Satya S. Sahoo, Krishnaprasad Thirunarayan, Olivier Bodenreider, Pascal Hitzler, Amit Sheth. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. In SSDBM2010. The 22nd International Conference on Scientific and Statistical Database Management (SSDBM) 2010; 2010.  (810.08 KB)
OWL
Satya Sahoo, Olivier Bodenreider, Joni Rutter, Karen Skinner, Amit Sheth. An Ontology-Driven Semantic Mashup of Gene and Biological Pathway Information: Application to the Domain of Nicotine Dependence. 2008 ;.
Nicotine dependence
Karen Skinner, Joni Rutter, Amit Sheth, Olivier Bodenreider, Satya S. Sahoo. An Ontology-driven Semantic Mash-up of Gene and Biological Pathway Information: Application to the Domain of Nicotine Dependence. Journal of Biomedical Informatics. 2008 ;:752-765.  (617.43 KB)
Multi-ontology schema integration
Karen Skinner, Joni Rutter, Amit Sheth, Olivier Bodenreider, Satya S. Sahoo. An Ontology-driven Semantic Mash-up of Gene and Biological Pathway Information: Application to the Domain of Nicotine Dependence. Journal of Biomedical Informatics. 2008 ;:752-765.  (617.43 KB)
Model theoretic semantics
Satya S. Sahoo, Krishnaprasad Thirunarayan, Olivier Bodenreider, Pascal Hitzler, Amit Sheth. Provenance Context Entity (PaCE): Scalable Provenance Tracking for Scientific RDF Data. In SSDBM2010. The 22nd International Conference on Scientific and Statistical Database Management (SSDBM) 2010; 2010.  (810.08 KB)
Meta triples
Vinh Nguyen, Olivier Bodenreider, Amit Sheth. Don't like RDF Reification? Making Statements about Statements using Singleton Property. 23rd International conference on World Wide Web (WWW '14). New York, NY: ACM; 2014. p. 759-770.  (382.61 KB)
Medical Subject Headings (MeSH)
Delroy Cameron, Ramakanth Kavuluru, Thomas Rindflesch, Amit Sheth, Krishnaprasad Thirunarayan, Olivier Bodenreider. Context-driven automatic subgraph creation for literature-based discovery. Journal of Biomedical Informatics. 2015 ;54:141-157.  (2.37 MB)
Literature-based discovery (LBD)
Delroy Cameron, Olivier Bodenreider, Hima Yalamanchili, Tu Danh, Sreeram Vallabhaneni, Krishnaprasad Thirunarayan, Amit Sheth, Thomas Rindflesch. A Graph-Based Recovery and Decomposition of Swanson's Hypothesis using Semantic Predications. Journal of Biomedical Informatics. 2013 ;46(2):238-251.  (915.51 KB)
Delroy Cameron, Ramakanth Kavuluru, Thomas Rindflesch, Amit Sheth, Krishnaprasad Thirunarayan, Olivier Bodenreider. Context-driven automatic subgraph creation for literature-based discovery. Journal of Biomedical Informatics. 2015 ;54:141-157.  (2.37 MB)
literature-based discovery
Delroy Cameron, Pablo Mendes, Amit Sheth, Krishnaprasad Thirunarayan, Ramakanth Kavuluru, Olivier Bodenreider. Semantic Predications for Complex Information Needs in Biomedical Literature. 2011 IEEE International Conference on Bioinformatics and Biomedicine. Atlanta, GA: IEEE; 2011.
Delroy Cameron, Ramakanth Kavuluru, Olivier Bodenreider, Pablo Mendes, Amit Sheth, Krishnaprasad Thirunarayan. Semantic Predications for Complex Information Needs in Biomedical Literature. In 5th International Conference on Bioinformatics and Biomedicine (BIBM2011). Atlanta GA: 2011 IEEE International Conference on Bioinformatics and Biomedicine; 2011.  (471.3 KB)
knowledge integration
Satya Sahoo, Kelly Zeng, Olivier Bodenreider, Amit Sheth. From "Glycosyltransferase" to "Congenital Muscular Dystrophy": Integrating Knowledge from NCBI Entrez Gene and the Gene Ontology. 2007 ;.
information integration
Karen Skinner, Joni Rutter, Amit Sheth, Olivier Bodenreider, Satya S. Sahoo. An Ontology-driven Semantic Mash-up of Gene and Biological Pathway Information: Application to the Domain of Nicotine Dependence. Journal of Biomedical Informatics. 2008 ;:752-765.  (617.43 KB)
Hierarchical agglomerative clustering
Delroy Cameron, Ramakanth Kavuluru, Thomas Rindflesch, Amit Sheth, Krishnaprasad Thirunarayan, Olivier Bodenreider. Context-driven automatic subgraph creation for literature-based discovery. Journal of Biomedical Informatics. 2015 ;54:141-157.  (2.37 MB)
Graph mining
Delroy Cameron, Ramakanth Kavuluru, Thomas Rindflesch, Amit Sheth, Krishnaprasad Thirunarayan, Olivier Bodenreider. Context-driven automatic subgraph creation for literature-based discovery. Journal of Biomedical Informatics. 2015 ;54:141-157.  (2.37 MB)

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