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Semantic eScience

Lead Professor: Peter Fox

Concepts:eScience

Meetings: eScience Meetings

Description:

Science has fully entered a new mode of operation. E-science, defined as a combination of science, informatics, computer science, cyberinfrastructure and information technology is changing the way all of these disciplines do both their individual and collaborative work.

As semantic technologies have been gaining momentum in various e-Science areas (for example, W3C's new interest group for semantic web health care and life science), it is important to offer semantic-based methodologies, tools, middleware to facilitate scientific knowledge modeling, logical-based hypothesis checking, semantic data integration and application composition, integrated knowledge discovery and data analyzing for different e-Science applications.

Partially influenced by the Artificial Intelligence community, the Semantic Web researchers have largely focused on formal aspects of semantic representation languages or general-purpose semantic application development, with inadequate consideration of requirements from specific science areas. On the other hand, general science researchers are growing ever more dependent on the web, but they have no coherent agenda for exploring the emerging trends on the semantic web technologies. It urgently requires the development of a multi-disciplinary field to foster the growth and development of e-Science applications based on the semantic technologies and related knowledge-based approaches.

Projects

MetPetDBA Database for Metamorphic Petrology (MetPetDB)
 Research Areas: X-informatics, Knowledge Provenance, Data Frameworks, Data Science, Semantic eScience
Principal Investigator:
Co Investigator: Peter Fox
Description: MetPetDB is a database for metamorphic petrology that is being designed and built by a global community of metamorphic petrologists in collaboration with computer scientists at Rensselaer Polytechnic Institute as part of the National Cyberinfrastructure Initiative and supported by the National Science Foundation.
Concepts: Data Science, Geophysical Science, eScience, Semantic Web, Data Visualization, Xinformatics, Semantic eScience, Web Science, Semantic Faceted Browse/Search, Semantic Web Services, Provenance
Earth System Grid - Center for Enabling TechnologiesEarth System Grid - Center for Enabling Technologies (ESG-CET)
 Research Areas: Data Frameworks, Semantic eScience
Principal Investigator: and Peter Fox
Sponsor: Scientific Discovery through Advanced Computing
Description: The Earth System Grid (ESG) integrates supercomputers with large-scale data and analysis servers located at numerous national labs and research centers to create a powerful environment for next generation climate research.
Concepts: eScience, Solar Science
OPeNDAPOPeNDAP
 Research Areas: Data Frameworks, Semantic eScience
Sponsor: Tetherless World Constellation
Description: Tasks for various TWC projects related to data access and the OPeNDAP software products.
Concepts: eScience
Ocean Observing Initiative: Cyber-Infrastructure - Semantic PrototypeOcean Observing Initiative: Cyber-Infrastructure - Semantic Prototype (OOI-CI-SP)
 Research Areas: Semantic eScience, Data Frameworks
Principal Investigator: Peter Fox
Sponsor: Woods Hole Oceanographic Institution
Description: Design and Develop a Faceted Browse application to allow scientists to semantically search data related to Ocean Sciences .
Concepts: eScience, Ocean Science, Semantic Faceted Browse/Search
SeSF Project LogoSemantic eScience Framework (SeSF)
 Research Areas: Data Science, Semantic eScience, Data Frameworks
Principal Investigator: Peter Fox
Co Investigator: Deborah L. McGuinness
Sponsor: National Science Foundation Office of Cyberinfrastructure
Description: The goals of this effort is to design and implement a configurable and extensible semantic eScience framework.
Concepts: eScience
SESDI Project LogoSemantically-Enabled Science Data Integration (SESDI)
 Research Areas: Semantic eScience
Principal Investigator: Peter Fox
Co Investigator: Deborah L. McGuinness
Sponsor: National Aeronautics and Space Administration
Description: The vast majority of explorations of the Earth system are limited in their ability to effectively explore the most important (often most difficult) problems because they are forced to interconnect at the data-element, or syntactic, level rather than at a higher scientific, or semantic, level.
Concepts: eScience
Virtual Terrestrial Solar Observatory LogoVirtual Solar Terrestrial Observatory (VSTO)
 Research Areas: Semantic eScience, Data Frameworks
Principal Investigator: Peter Fox
Co Investigator: Deborah L. McGuinness
Sponsor: National Science Foundation
Description: VSTO is a collaborative project between the High Altitude Observatory and Scientific Computing Division of the National Center for Atmospheric Research and McGuinness Associates.
Concepts: Terrestrial Science, eScience, Solar Science
Publications:
McCusker, J., Lebo, T., Chang, C., Pinheiro da Silva, P., and McGuinness, D.L. 2012. Parallel Identities for Managing Open Government Data. IEEE Intelligent Systems
McGuinness, D.L., Shaikh, A.R., Lebo, T., Ding, L., Courtney, P., McCusker, J., Moser, R., Morgan, G.D., Tatalovich, Z., Willis, G., Contractor, N., and Hesse, B.W. 2012. Towards Semantically-Enabled Next Generation Community Health Information Portals: The PopSciGrid Pilot. In Proceedings of Hawaii International Conference on System Sciences 2012 (January 4-7 2012, Grand Wailea, Maui).
Lebo, T., Erickson, J., Ding, L., Graves, A., Williams, G.T., DiFranzo, D., Li, X., Michaelis, J., Zheng, J., Flores, J., Shangguan, Z., McGuinness, D.L., and Hendler, J. 2011. Producing and Using Linked Open Government Data in the TWC LOGD Portal. Linking Government Data
2011. Linking Government Data.
Wang, P., Zheng, J., Fu, L., Patton, E.W., Lebo, T., Ding, L., Luciano, J.S., and McGuinness, D.L. 2011. Next Generation Environmental Informatics as exemplified by the Tetherless World Semantic Water Quality Portal. In Proceedings of AGU Fall Meeting 2011 (December 5-9 2011).
Patton, E.W., Wang, P., Zheng, J., Fu, L., Lebo, T., Ding, L., Liu, Q., Luciano, J.S., and McGuinness, D.L. 2011. Assessing Health Effects of Water Pollution Using a Semantic Water Quality Portal. In Proceedings of 10th International Semantic Web Conference (October 23-27 2011, Bonn, Germany).
McCusker, J., Lebo, T., Ding, L., Chang, C., Pinheiro da Silva, P., and McGuinness, D.L. 2011. Where did you hear that? Information and the Sources They Come From. In Proceedings of International Workshop on Linked Science 2011 (October 14 2011, Bonn, Germany).
Wang, P., Zheng, J., Fu, L., Patton, E.W., Lebo, T., Ding, L., Liu, Q., Luciano, J.S., and McGuinness, D.L. 2011. A Semantic Portal for Next Generation Monitoring Systems. In Proceedings of 10th International Semantic Web Conference (October 23-27 2011, Bonn, Germany).
Zheng, J., Wang, P., Patton, E.W., Lebo, T., Luciano, J.S., and McGuinness, D.L. 2011. A Semantically-Enabled Provenance-Aware Water Quality Portal. In Proceedings of the Environmental Information Management Conference 2011 (September 28-29 2011, Santa Barbara, CA, USA).
Fox, P. 2011. The rise of informatics as a research domain.
Wang, P., Zheng, J., Fu, L., Patton, E.W., Lebo, T., Ding, L., Liu, Q., Luciano, J.S., and McGuinness, D.L. 2011. TWC-SWQP: A Semantic Portal for Next Generation Environmental Monitoring (Technical Report).
McGuinness, D.L., Shaikh, A.R., Moser, R., Hesse, B.W., Morgan, G.D., Augustson, E.M., Hunt, Y., Tatalovich, Z., Willis, G., Blake, K., Courtney, P., Finney, L., Sanders, A., Ding, L., Lebo, T., McCusker, J., Contractor, N., Huang, Y., and Devlin, H. 2011. A Semantically-enabled Community Health Portal for Cancer Prevention and Control. In Proceedings of Web Science Conference 2011 (June 15-17 2011, Koblenz, Germany).
Ding, L., Michaelis, J., McCusker, J., and McGuinness, D.L. 2011. Linked provenance data: A semantic Web-based approach to interoperable workflow traces. Future Generation Computer Systems, pp. 797-805.
McCusker, J., Luciano, J.S., and McGuinness, D.L. 2011. Towards an Ontology for Conceptual Modeling. In Proceedings of International Conference on Biomedical Ontology (July 26-30 2011, Buffalo, NY, USA).
Fox, P. and Hendler, J. 2011. Changing the Equation on Scientific Data Visualization. Science Magazine, pp. 705-708.
Zednik, S., Fox, P., and McGuinness, D.L. 2010. System Transparency, or How I Learned to Worry about Meaning and Love Provenance!. In Proceedings of 3rd International Provenance and Annotation Workshop (June 15-16 2010, ), pp. 165-173.
Benedict, J., McGuinness, D.L., and Fox, P. 2010. A Reusable Semantic Virtual Observatory Platform. In Proceedings of AGU Fall Meeting 2008 (December 15-19 2008, San Francisco, CA).
West, P., Michaelis, J., Fox, P., Zednik, S., and McGuinness, D.L. 2010. Presenting Provenance Based on User Roles: Experiences with a Solar Physics Data Ingest System. In Proceedings of AGU Fall Meeting 2010 (December 13-17 2010, San Francisco, CA).
Rozell, E., Maffei, A., Beaulieu, S., and Fox, P. 2010. A Framework for Integrating Oceanographic Data Repositories. In Proceedings of AGU Fall Meeting 2010 (December 13-17 2010, San Francisco, CA).
McCusker, J. and McGuinness, D.L. 2010. Provenance of High Throughput Biomedical Experiments. In Proceedings of 3rd International Provenance and Annotation Workshop (June 15-16 2010, ).
Michaelis, J., Ding, L., Shangguan, Z., Zednik, S., Huang, R., Pinheiro da Silva, P., Rio, N., and McGuinness, D.L. 2009. Towards Usable and Interoperable Workflow Provenance: Empirical Case Studies Using PML. In Proceedings of First International Workshop on the role of Semantic Web in Provenance Management (October 25 2009).
Zednik, S., Fox, P., McGuinness, D.L., Pinheiro da Silva, P., and Chang, C. 2009. Semantic Provenance for Science Data Products - Application to Image Data Processing. In Proceedings of First International Workshop on the role of Semantic Web in Provenance Management (October 25 2009).
Fox, P., McGuinness, D.L., Cinquini, L., West, P., Garcia, J., Benedict, J., and Middleton, D. 2009. Ontology-supported Scientific Data Frameworks: The Virtual Solar-Terrestrial Observatory Experience. Computers & Geosciences, pp. 724-738.
McGuinness, D.L., Fox, P., Pinheiro da Silva, P., Zednik, S., Rio, N., Ding, L., West, P., and Chang, C. 2008. Annotating and embedding provenance in science data repositories to enable next generation science applications. In Proceedings of AGU Fall Meeting 2008 (December 15-19 2008, San Francisco, CA).
Fox, P., McGuinness, D.L., Garcia, J., Zednik, S., and Ding, L. 2008. Semantic Provenance for Image Data Processing. In Proceedings of Geoinformatics 2008 (June 11-13 2008).
Fox, P., Cinquini, L., McGuinness, D.L., West, P., Garcia, J., Benedict, J., and Zednik, S. 2007. Semantic Web Services for Interdisciplinary Scientific Data Query and Retrieval. In Proceedings of AAAI Workshop on Semantic e-Science 2007 of the Conference on Artificial Intelligence 2007 (July 23 2007July 23 2007, Vancouver, Canada).
McGuinness, D.L., Fox, P., Cinquini, L., West, P., Garcia, J., Benedict, J., and Middleton, D. 2007. A Deployed Semantically-Enabled Interdisciplinary Virtual Observatory. In Proceedings of Conference on Artificial Intelligence 2007 (July 22-26 2007, Vancouver, British Columbia).
McGuinness, D.L., Fox, P., Cinquini, L., West, P., Garcia, J., Benedict, J., and Middleton, D. 2007. The Virtual Solar-Terrestrial Observatory: A Deployed Semantic Web Application Case Study for Scientific Research. In Proceedings of Innovative Applications of Artificial Intelligence Conference 2007 (July 22 2007-July 26 2011, Vancouver, British Columbia).
McGuinness, D.L., Fox, P., Cinquini, L., West, P., Benedict, J., and Garcia, J. 2007. Current and future uses of OWL for Earth and Space science data frameworks: successes and limitations. In Proceedings of OWLED 2007 (June 6-7 2007).
McGuinness, D.L., Fox, P., Cinquini, L., Darnell, J., West, P., Benedict, J., Garcia, J., and Middleton, D. 2006. Ontology-Enabled Virtual Observatories: Semantic Integration in Practice. In Proceedings of ISWC 2006 (November 5-9 2006, Athens, GA, US).

Presentations:
Fox, P. (December 9, 2011). Information Model Driven Semantic Framework Architecture and Design for Distributed Data Repositories. In: AGU Fall Meeting 2011
West, P., Fox, P., Gallagher, J., Potter, N., Halloway, D., & Zednik, S. (December 8, 2011). OPeNDAP Hyrax: An extensible data access framework within the Earth System Grid Federation. In: AGU Fall Meeting 2011
Fox, P., & Maffei, A. (December 7, 2011). Facilitating Next Generation Science Collaboration: Respecting and Mediating Vocabularies with Semantics in Ecosystems Assessments.. In: AGU Fall Meeting 2011
Patton, E., West, P., Greer, R., & Jin, B. (December 7, 2011). Publishing and Editing of Semantically-Enabled Scientific Metadata Across Multiple Web Platforms: Challenges and Experiences. In: AGU Fall Meeting 2011
Maffei, A., Rozell, E., West, P., Zednik, S., & Fox, P. (December 7, 2011). Open Standards and Technologies in the S2S Framework. In: AGU Fall Meeting 2011
Zednik, S., Leptoukh, G., Fox, P., Lynnes, C., West, P., & Ahmad, S. (December 6, 2011). A Semantic Representation of Product Quality and Evidence for Satellite Data. In: AGU Fall Meeting 2011
Fox, P. (September 28, 2011). Semantic Data Frameworks Come of Age. In: Astroinformatics 2011
Fox, P. (September 26, 2011). Informatics takes on data and information quality, uncertainty and bias (in atmospheric science). In: Astroinformatics 2011
Fox, P. (September 4, 2011). Strategic coordination of ICSU data activities. In: 1st ICSU World Data System Conference - Global Data for Global Science
Fox, P. (August 2, 2011). The rise of informatics as a research domain. In: WIRADA Science Symposium 2011
Wang, P., Zheng, J., Fu, L., Patton, E., Lebo, T., Ding, L., Luciano, J., & McGuinness, D. (July 25, 2011). TWC-SWQP: A Semantically-Enabled Provenance-Aware Water Quality Portal .
Zednik, S., Leptoukh, G., Fox, P., Lynnes, C., & Pan, J. (April 8, 2011). Experiences Developing a User-centric Presentation of Provenance for a Web-based Science Data Analysis Tool. In: EGU General Assembly 2011
Rozell, E., Fox, P., Maffei, A., & Zednik, S. (April 6, 2011). A Framework for Earth Science Search Interface Development. In:
McGuinness, D. (March 18, 2011). Linked Data and the Provenance Explosion. In: Second International Colloquium on Data Provenance and Data Management for eScience (DPDM'11)
West, P., Michaelis, J., Fox, P., Zednik, S., & McGuinness, D. (December 17, 2010). Presenting Provenance Based on User Roles: Experiences with a Solar Physics Data Ingest System. In: AGU Fall Meeting 2010
Michaelis, J., Zednik, S., West, P., Fox, P., & McGuinness, D. (December 16, 2010). Extending eScience Provenance with User-Submitted Semantic Annotations, Abstract IN43C-08. In: AGU Fall Meeting 2010
Fox, P. (December 13, 2010). Realities in Science Data and Information - Let's go for translucency. In: AGU Fall Meeting 2010
Zednik, S., Lynnes, C., Fox, P., Leptoukh, G., & Pan, J. (December 13, 2010). A Semantic Provenance-aware Expert Advisory System in a Web-based Science Data Analysis Tool. In: AGU Fall Meeting 2010
Fox, P., & McGuinness, D. (December 18, 2009). The Semantic e-Science Framework. In: AGU Fall Meeting 2009
McGuinness, D., Fox, P., Pinheiro da Silva, P., Zednik, S., Rio, N., Ding, L., West, P., & Chang, C. (December 15, 2008). Annotating and embedding provenance in science data repositories to enable next generation science applications. In: AGU Fall Meeting 2008
Fox, P., McGuinness, D., Garcia, J., Zednik, S., & Ding, L. (June 11, 2008). Semantic Provenance for Image Data Processing. In: Geoinformatics 2008

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