Tetherless World Constellation

James McCusker
Contact Info
Email	mccusj@rpi.edu

Affiliations Move:

	Tetherless World Constellation (TWC)	Website: http://tw.rpi.edu
	Rensselaer Polytechnic Institute (RPI)	Website: http://www.rpi.edu

• James McCusker, and D. McGuinness. “Provenance of High Throughput Biomedical Experiments.” In International Provenance and Annotations Workshop, 1-7, 2010. http://tw.rpi.edu/proj/portal.wiki/images/a/af/IPAW2010_RP_McCusker.pdf.
• James McCusker, and D. L. McGuinness. “Towards identity in linked data.” Proceedings of OWL: Experience and Directions, San Francisco, USA (June 21-22, 2010), http://www. webont. org/owled/2010/papers/owled2010\_submission\_12. pdf (2010): 1-10. http://tw.rpiscrews.us/wiki.tw/images/8/8e/Owled2010-sameas.pdf.
• James McCusker, Joshua A Phillips, Alejandra González Beltrán, Anthony Finkelstein, and Michael Krauthammer. “Semantic web data warehousing for caGrid.” BMC Bioinformatics 10, no. Suppl 10 (2009): S2. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2755823&tool=pmcentrez&rendertype=abstract.
• James McCusker, and D. McGuinness. “Explorations into the Provenance of High Throughput Biomedical Experiments.” Edited by Deborah L McGuinness, James R Michaelis, and Luc Moreau. Provenance and Annotation of Data and Processes 6378 (2010): 120–128. http://www.springerlink.com/index/W10740804446172U.pdf.

• Halpin, Harry, Patrick Hayes, James McCusker, D. Mcguinness, and Henry Thompson. “When owl: sameas isn’t the same: An analysis of identity in linked data.” Edited by Peter F. Patel-Schneider, Yue Pan, Pascal Hitzler, Peter Mika, Lei Zhang, Jeff Z. Pan, Ian Horrocks, and Birte Glimm. The Semantic Web–ISWC 2010 6496 (2010): 305–320. http://www.springerlink.com/index/V24433851K747864.pdf.
• Luciano, Joanne, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Tim Clark, Christine Denney, Christopher Domarew, et al. “The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside.” Journal of Biomedical Semantics. BioMed Central Ltd, May 17, 2011. http://www.jbiomedsem.com/content/2/S2/S1.
• Ding, L., J. Michaelis, James McCusker, and D.L. McGuinness. “Linked provenance data: A semantic Web-based approach to interoperable workflow traces.” Future Generation Computer Systems (2010). http://linkinghub.elsevier.com/retrieve/pii/S0167739X10002049.

• Holford, Matthew E, James McCusker, Kei-Hoi Cheung, and Michael Krauthammer. “Analysis of Cancer Omics Data In A Semantic Web Framework.” In Proceedings of the 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences BerlinGermany December 810 2010, 1-15, 2010.
• Halaban, Ruth, Wengeng Zhang, Antonella Bacchiocchi, Elaine Cheng, Fabio Parisi, Stephan Ariyan, Michael Krauthammer, James McCusker, Yuval Kluger, and Mario Sznol. “PLX4032, a selective BRAFV600E kinase inhibitor, activates the ERK pathway and enhances cell migration and proliferation of BRAFWT melanoma cells.” Pigment cell melanoma research 23, no. 2 (2010): 190-200. http://www.ncbi.nlm.nih.gov/pubmed/20149136.
• Xu, Songhua, James McCusker, and Michael Krauthammer. “Yale Image Finder (YIF): a new search engine for retrieving biomedical images.” Bioinformatics 24, no. 17 (2008): 1968-1970. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18614584.
• S. Szpakowski, James McCusker, and M. Krauthammer, “Using Semantic Web Technologies to Annotate and Align Microarray Designs,” Cancer Informatics, vol. 8, 2009.

Talks/Presentations

• McCusker J., McGuinness, D. "owl:sameAs Considered Harmful to Provenance" ISCB Conference on Semantics in Healthcare & Life Sciences, Feb 24-26 2010.
• McCusker J., McGuinness, D. "Representing Microarray Experiment Metadata Using Provenance Models" ISCB Conference on Semantics in Healthcare & Life Sciences, Feb 24-26 2010.
• McCusker J. "A Model for Comprehensive Biospecimen Lifecycles: From Clinic to Bench and Back" caBIG Tissue Banks and Pathology Tools Workspace Face to Face Meeting, Dec. 9-10 2009; caBIG Architecture Workspace Teleconference, Jan. 22, 2010; NCI LIMS Consortium Monthly Meeting, Feb. 22, 2009.
• McCusker J. "Data Provenance and caGrid" caBIG Architecture & VCDE Joint Workspace Face to Face Meeting, May, 2009.
• Krauthammer M., McCusker J. "MelaGrid: A Data Sharing Framework for Skin Cancer Research" caBIG Architecture & VCDE Joint Workspace Face to Face Meeting, May, 2009.

Projects Move:

	Foresight and Understanding from Scientific Exposition (FUSE) Research Areas: Inference And Trust, Knowledge Provenance, Data Frameworks Principal Investigator: Deborah L. McGuinness Co Investigator: Jim Hendler Sponsor: Intelligence Advanced Research Projects Activity Description: Technical emergence refers to the process whereby innovative ideas, capabilities, applications, and even entirely new fields of study arise, are tested, mature, and, if conditions are favorable, demonstrate feasibility and impact. IARPA’s Foresight and Understanding from Scientific Exposition (FUSE) Program is sponsoring advanced research and development (R&D) to develop automated systems that aid in the systematic, continuous, and comprehensive assessment of technical emergence using information derived from the published scientific, technical, and patent literature. Concepts: Provenance, Semantic Web
	Health on the Web Research Areas: Knowledge Provenance Principal Investigator: Deborah L. McGuinness and Joanne S. Luciano Description: The Tetherless World Constellation's Health on the Web's primary goal is to explore the next generation web technology needed to improve health.
	Population Science Grid (PopSciGrid) Research Areas: Knowledge Provenance Principal Investigator: Deborah L. McGuinness Sponsor: National Science Foundation Description: .
	Semantic Sea Ice Interoperability Initiative (SSIII) Principal Investigator: Mark Parsons, Siri Jodha Singh Khalsa, and Ruth Duerr Co Investigator: Deborah L. McGuinness Sponsor: National Science Foundation Description: SSIII is a National Science Foundation (NSF) funded effort to enhance the interoperability of sea ice data to establish a network of practitioners working to enhance semantic interoperability of all Arctic data. SSIII is a collaborative project between NSIDC and the Rensselaer Polytechnic Institute (RPI) Tetherless World Constellation project. We seek to build on the work initiated under the International Polar Year (IPY) and create a community of practice working to improve interoperability within the Polar Information Commons (PIC), the Sustained Arctic Observing Network (SAON), and broader global systems.

• MAGE-TAB to MAGE-RDF: A tool to convert MAGE-TAB files, a common description format for microarray and gene expression data, into an RDF representation. http://magetab2rdf.googlecode.com
• OWLtoSKOS: A tool for converting OWL ontologies into SKOS (http://www.w3.org/2004/02/skos) ontologies. This allows automated conversion of terminologies into a format that lets instance data directly reference the terms and concepts, simplifies the representations of existing controlled vocabularies and terminology hierarchies, and vastly improves inferencing performance. http://owltoskos.googlecode.com

Scholarships and Awards

• Weissman Family Graduate Fellowship for 2009/2010.

Membership and Conference Chairs

• Member of the World Wide Web Consortium (W3C) Provenance Incubator Group.
• Publicity Co-Chair of International Provenance and Annotation Workshop (IPAW) 2010.

Notable Class Projects

• Semantic E-Science: Arunachalam S., Li X., McCusker J., Milack C. "Environmental Cleanup": Served as modeling expert and provided integration with a large number of existing ontologies.

Key Personnel on Grants and Contracts

• caBIG Architecture Workspace Participant Contract, Yale University, FY 2008, renewed through FY 2009. Tissue Banks and Pathology Tools Architecture Workspace Guide to Mentors, Architecture representative on the Life Sciences Composite Architecture Team (LS-CAT), development of recommendations surrounding provenance standards within caBIG.
• caBIG caTissue Suite 1.1 Adopter Contract, Yale University, FY 2008. Project Manager.