Difference between revisions of "Satya"
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'''Satya S. Sahoo''' <br/> | '''Satya S. Sahoo''' <br/> | ||
| − | Ph.D | + | Ph.D. Computer Science and Engineering<br/> |
| + | [http://knoesis.wright.edu/ Kno.e.sis Center], Wright State University | ||
==Updates== | ==Updates== | ||
| − | + | * I joined the Case Western Reserve University as Assistant Professor in September 2010 ([http://cci.case.edu/cci/index.php/Satya_Sahoo new webpage]) | |
==Research Interests== | ==Research Interests== | ||
| − | I am interested in | + | I am interested in scientific metadata and data management and integration using declarative knowledge representation (ontology), reasoning, and related Semantic Web technologies. I also work on optimizing query performance, for example using materialized views, for queries with both high expression complexity and data complexity.<br/> I have special interest in provenance metadata management in scientific applications. We have developed a provenance management framework with foundational model of provenance, specialized query operators, and implemented a scalable query engine for provenance analysis with a new class of materialized views based on domain semantics. <br/> |
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==Current Projects== | ==Current Projects== | ||
===Provenance Management Framework=== | ===Provenance Management Framework=== | ||
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* '''Provenance Representation''': An upper-level ontology for representation of provenance information called [http://wiki.knoesis.org/index.php/Provenir_Ontology '''provenir''']. | * '''Provenance Representation''': An upper-level ontology for representation of provenance information called [http://wiki.knoesis.org/index.php/Provenir_Ontology '''provenir''']. | ||
* '''Provenance Analysis''': A set of provenance query operators has been defined based on a systematic classification of provenance queries. The provenance classification scheme has been proposed for the first time in provenance research. | * '''Provenance Analysis''': A set of provenance query operators has been defined based on a systematic classification of provenance queries. The provenance classification scheme has been proposed for the first time in provenance research. | ||
| − | * ''' | + | * '''Scalable Query Infrastructure''': A provenance query engine has been implemented to support the provenance query operators over a RDF data store. The query engine uses a new class of materialized views called ''Materialized Provenance View'' (MPV), for optimizing performance of complex queries over large datasets. |
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===Semantics and Services enabled Problem Solving Environment for ''T.cruzi''=== | ===Semantics and Services enabled Problem Solving Environment for ''T.cruzi''=== | ||
| − | Aim: develop and deploy a novel ontology-driven problem-solving environment for T.cruzi. | + | Aim: develop and deploy a novel ontology-driven problem-solving environment for ''T.cruzi''. |
* Ontology Development: Development of two ontologies (a) [http://bioportal.bioontology.org/ontologies/39544 Parasite Life cycle ontology], (b) [http://bioportal.bioontology.org/ontologies/40425 Parasite Experiment ontology]. Both have been released to the National Center for Biomedical Ontologies (NCBO)<br/> | * Ontology Development: Development of two ontologies (a) [http://bioportal.bioontology.org/ontologies/39544 Parasite Life cycle ontology], (b) [http://bioportal.bioontology.org/ontologies/40425 Parasite Experiment ontology]. Both have been released to the National Center for Biomedical Ontologies (NCBO)<br/> | ||
Collaborators: ''Tarleton Research Group, University of Georgia'' and ''The Wellcome Trust Sanger Institute, Cambridge, UK'' | Collaborators: ''Tarleton Research Group, University of Georgia'' and ''The Wellcome Trust Sanger Institute, Cambridge, UK'' | ||
* Parasite Knowledge Repository: Integrated repository in RDF format of gene knockout, strains, proteomics, pathway, and microarray data for query answering in parasite research | * Parasite Knowledge Repository: Integrated repository in RDF format of gene knockout, strains, proteomics, pathway, and microarray data for query answering in parasite research | ||
* Trykipedia: Explore use of Wiki-based platform for collaborative ontology development [http://wiki.knoesis.org/index.php/Trykipedia Trykipedia]<br/> | * Trykipedia: Explore use of Wiki-based platform for collaborative ontology development [http://wiki.knoesis.org/index.php/Trykipedia Trykipedia]<br/> | ||
| + | ==Workshop Series on the Semantic Web and Provenance Management (SWPM)== | ||
| + | Proposed and co-organizing a series of workshops exploring the research issues at the intersection of Semantic Web and Provenance Management. <br/> | ||
| + | *The first workshop [http://wiki.knoesis.org/index.php/SWPM-2009 SWPM'09] was held in conjunction with the International Semantic Web Conference (ISWC) 2009 with a keynote given by [http://www.cs.man.ac.uk/~carole/ Dr. Carole Goble]. <br/> | ||
| + | *The second workshop [http://wiki.knoesis.org/index.php/SWPM-2010 SWPM'10] will be held in conjunction with ISWC'10. The keynote speaker for SWPM'10 is [http://www.cs.rpi.edu/~dlm/ Dr. Deborah McGuinness].<br/> | ||
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==Select Publications== | ==Select Publications== | ||
===Provenance Management Framework=== | ===Provenance Management Framework=== | ||
| − | * S.S. Sahoo, D.B. Weatherly, R. Mutharaju, P. Anantharam, A. Sheth, R.L. Tarleton, “Ontology-driven Provenance Management in eScience: an Application in Parasite Research”, The 8th International Conference on Ontologies, DataBases, and Applications of Semantics, (ODBASE 2009), Vilamoura, Algarve-Portugal, Nov 02 - 04, 2009 | + | * S.S. Sahoo, O. Bodenreider, P. Hitzler, A. Sheth, K., Thirunarayan, “Provenance Context Entity (PaCE): Scalable provenance tracking for scientific RDF data.”,in the 22nd International Conference on Scientific and Statistical Database Management (SSDBM) 2010 [http://knoesis.wright.edu/library/download/ProvenanceTracking_PaCE.pdf pdf] |
| + | * S.S. Sahoo, D.B. Weatherly, R. Mutharaju, P. Anantharam, A. Sheth, R.L. Tarleton, “Ontology-driven Provenance Management in eScience: an Application in Parasite Research”, The 8th International Conference on Ontologies, DataBases, and Applications of Semantics, (ODBASE 2009), Vilamoura, Algarve-Portugal, pp.992-1009, Nov 02 - 04, 2009. [http://knoesis.wright.edu/library/download/ODBASE09_sahoo.pdf pdf] | ||
* S.S. Sahoo, A. Sheth, C. Henson, “Semantic Provenance for eScience: ‘Meaningful’ Metadata to Manage the Deluge of Scientific Data,” IEEE Internet Computing, Web-Scale Workflow Track, M.B. Blake and M. Huhns (Eds.), 12(4), pp.46-54, July-Aug. 2008 [http://knoesis.wright.edu/researchers/satya/pubs/SPF-IC.pdf pdf] | * S.S. Sahoo, A. Sheth, C. Henson, “Semantic Provenance for eScience: ‘Meaningful’ Metadata to Manage the Deluge of Scientific Data,” IEEE Internet Computing, Web-Scale Workflow Track, M.B. Blake and M. Huhns (Eds.), 12(4), pp.46-54, July-Aug. 2008 [http://knoesis.wright.edu/researchers/satya/pubs/SPF-IC.pdf pdf] | ||
* S.S. Sahoo, C. Thomas, A. Sheth, W.S. York and S. Tartir, “Knowledge Modeling and Its Application in Life Sciences: A Tale of Two Ontologies.” 15th International WWW2006 Conference, pp. 317-326, Scotland, May 23–26, 2006. ''(Acceptance Rate: 11%)'' [http://www2006.org/programme/files/pdf/1088.pdf pdf] | * S.S. Sahoo, C. Thomas, A. Sheth, W.S. York and S. Tartir, “Knowledge Modeling and Its Application in Life Sciences: A Tale of Two Ontologies.” 15th International WWW2006 Conference, pp. 317-326, Scotland, May 23–26, 2006. ''(Acceptance Rate: 11%)'' [http://www2006.org/programme/files/pdf/1088.pdf pdf] | ||
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===Scientific Data Integration=== | ===Scientific Data Integration=== | ||
* S.S. Sahoo, O. Bodenreider, J.L. Rutter, K.J. Skinner, A.P. Sheth, “An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence,” Journal of Biomedical Informatics (Special Issue: Semantic Mashup of Biomedical Data), 41(5), 752-765, Oct. 2008 [http://dx.doi.org/10.1016/j.jbi.2008.02.006 pdf] | * S.S. Sahoo, O. Bodenreider, J.L. Rutter, K.J. Skinner, A.P. Sheth, “An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence,” Journal of Biomedical Informatics (Special Issue: Semantic Mashup of Biomedical Data), 41(5), 752-765, Oct. 2008 [http://dx.doi.org/10.1016/j.jbi.2008.02.006 pdf] | ||
| − | * S.S. Sahoo, K. Zeng, O. Bodenreider, A.P. Sheth, “From ‘glycosyltransferase’ to ‘congenital muscular dystrophy’: Integrating knowledge from NCBI Entrez Gene and the Gene Ontology,” Medinfo 2007, Brisbane, Australia, 20-24 August, 2007 | + | * S.S. Sahoo, K. Zeng, O. Bodenreider, A.P. Sheth, “From ‘glycosyltransferase’ to ‘congenital muscular dystrophy’: Integrating knowledge from NCBI Entrez Gene and the Gene Ontology,” Medinfo 2007, Brisbane, Australia, pp. 1260–64, 20-24 August, 2007. [http://mor.nlm.nih.gov:8000/pubs/pdf/2007-medinfo-ss.pdf pdf]<br/> |
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Latest revision as of 23:32, 25 January 2012
Satya S. Sahoo
Ph.D. Computer Science and Engineering
Kno.e.sis Center, Wright State University
Contents
Updates
- I joined the Case Western Reserve University as Assistant Professor in September 2010 (new webpage)
Research Interests
I am interested in scientific metadata and data management and integration using declarative knowledge representation (ontology), reasoning, and related Semantic Web technologies. I also work on optimizing query performance, for example using materialized views, for queries with both high expression complexity and data complexity.
I have special interest in provenance metadata management in scientific applications. We have developed a provenance management framework with foundational model of provenance, specialized query operators, and implemented a scalable query engine for provenance analysis with a new class of materialized views based on domain semantics.
Current Projects
Provenance Management Framework
Provenance is critical metadata to interpret scientific results, validate experimental processes, and associate trust values.
We have defined an end-to-end framework, underpinned by a novel provenance algebra, addressing three important aspects of provenance management:
- Provenance Representation: An upper-level ontology for representation of provenance information called provenir.
- Provenance Analysis: A set of provenance query operators has been defined based on a systematic classification of provenance queries. The provenance classification scheme has been proposed for the first time in provenance research.
- Scalable Query Infrastructure: A provenance query engine has been implemented to support the provenance query operators over a RDF data store. The query engine uses a new class of materialized views called Materialized Provenance View (MPV), for optimizing performance of complex queries over large datasets.
Semantics and Services enabled Problem Solving Environment for T.cruzi
Aim: develop and deploy a novel ontology-driven problem-solving environment for T.cruzi.
- Ontology Development: Development of two ontologies (a) Parasite Life cycle ontology, (b) Parasite Experiment ontology. Both have been released to the National Center for Biomedical Ontologies (NCBO)
Collaborators: Tarleton Research Group, University of Georgia and The Wellcome Trust Sanger Institute, Cambridge, UK
- Parasite Knowledge Repository: Integrated repository in RDF format of gene knockout, strains, proteomics, pathway, and microarray data for query answering in parasite research
- Trykipedia: Explore use of Wiki-based platform for collaborative ontology development Trykipedia
Workshop Series on the Semantic Web and Provenance Management (SWPM)
Proposed and co-organizing a series of workshops exploring the research issues at the intersection of Semantic Web and Provenance Management.
- The first workshop SWPM'09 was held in conjunction with the International Semantic Web Conference (ISWC) 2009 with a keynote given by Dr. Carole Goble.
- The second workshop SWPM'10 will be held in conjunction with ISWC'10. The keynote speaker for SWPM'10 is Dr. Deborah McGuinness.
Select Publications
Provenance Management Framework
- S.S. Sahoo, O. Bodenreider, P. Hitzler, A. Sheth, K., Thirunarayan, “Provenance Context Entity (PaCE): Scalable provenance tracking for scientific RDF data.”,in the 22nd International Conference on Scientific and Statistical Database Management (SSDBM) 2010 pdf
- S.S. Sahoo, D.B. Weatherly, R. Mutharaju, P. Anantharam, A. Sheth, R.L. Tarleton, “Ontology-driven Provenance Management in eScience: an Application in Parasite Research”, The 8th International Conference on Ontologies, DataBases, and Applications of Semantics, (ODBASE 2009), Vilamoura, Algarve-Portugal, pp.992-1009, Nov 02 - 04, 2009. pdf
- S.S. Sahoo, A. Sheth, C. Henson, “Semantic Provenance for eScience: ‘Meaningful’ Metadata to Manage the Deluge of Scientific Data,” IEEE Internet Computing, Web-Scale Workflow Track, M.B. Blake and M. Huhns (Eds.), 12(4), pp.46-54, July-Aug. 2008 pdf
- S.S. Sahoo, C. Thomas, A. Sheth, W.S. York and S. Tartir, “Knowledge Modeling and Its Application in Life Sciences: A Tale of Two Ontologies.” 15th International WWW2006 Conference, pp. 317-326, Scotland, May 23–26, 2006. (Acceptance Rate: 11%) pdf
Scientific Data Integration
- S.S. Sahoo, O. Bodenreider, J.L. Rutter, K.J. Skinner, A.P. Sheth, “An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence,” Journal of Biomedical Informatics (Special Issue: Semantic Mashup of Biomedical Data), 41(5), 752-765, Oct. 2008 pdf
- S.S. Sahoo, K. Zeng, O. Bodenreider, A.P. Sheth, “From ‘glycosyltransferase’ to ‘congenital muscular dystrophy’: Integrating knowledge from NCBI Entrez Gene and the Gene Ontology,” Medinfo 2007, Brisbane, Australia, pp. 1260–64, 20-24 August, 2007. pdf
