James McCusker

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James McCusker
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Jim McCusker works on Biomedical Semantics. His current interests are data and provenance interoperability in life sciences. He has worked as a software developer for 11 years in bioinformatics, high performance computing, data mining, natural language processing, and supply chain auditing.


Erickson, J.S., Chastain, K., McCusker, J., Fry, Z., Yan, R., and McGuinness, D.L. 2014. Technical Report: Identifying First Responder Communities through Social Network Analysis of Disaster-Related Traffic.
McCusker, J., Solanki, K., Chang, C., Dumontier, M., Dordick, J., and McGuinness, D.L. 2014. A Nanopublication Framework for Systems Biology and Drug Repurposing. In Proceedings of CSHALS 2014 (February 26-28 2014, Boston, MA).
McCusker, J., Lebo, T., Krauthammer, M.O., and McGuinness, D.L. 2013. Next Generation Cancer Data Discovery, Access, and Integration Using Prizms and Nanopublications. In Proceedings of Ninth International Conference on Data Integration in the Life Sciences (July 11-12 2013, Montreal, Quebec).
Erickson, J.S., McCusker, J., McGuinness, D.L., Fry, Z., Chastain, K., and Yan, R. 2013. Technical Report: Requirements Gathering through First Responder Social Network Analysis.
Seyed, P., Lebo, T., Patton, E.W., McCusker, J., and McGuinness, D.L. 2013. SemantEco: A Next- Generation Web Observatory.
McCusker, J., McGuinness, D.L., Lee, J., Thomas, C., Courtney, P., Tatalovich, Z., Contractor, N., Morgan, G.D., and Shaikh, A.R. 2013. Towards Next Generation Health Data Exploration: A Data Cube-based Investigation into Population Statistics for Tobacco. In Proceedings of Hawaii International Conference on System Sciences 2013 (January 7-10 2013, Grand Wailea, Maui, Hawaii).
Michaelis, J., McGuinness, D.L., Chang, C., Luciano, J.S., McCusker, J., and Hendler, J. 2012. Applying Multidimensional Navigation and Explanation in Semantic Dataset Summarization. In Proceedings of ISWC 2012 (November 11-15 2012, Boston, MA).
McCusker, J., Lee, J., Thomas, C., and McGuinness, D.L. 2012. Public Health Surveillance Using Global Health Explorer. In Proceedings of SATBI+SWIM at ISWC 2012 (November 12 2012, Boston, MA).
McCusker, J., Lebo, T., Graves, A., DiFranzo, D., Pinheiro, P., and McGuinness, D.L. 2012. Functional Requirements for Information Resource Provenance on the Web. In Proceedings of International Provenance and Annotation Workshop 2012 (June 18-22 2012, Santa Barbara, California).
McCusker, J., Lebo, T., Chang, C., Pinheiro, 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).
McCusker, J., Lebo, T., Ding, L., Chang, C., Pinheiro, 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).
McGuinness, D.L., Shaikh, A.R., Moser, R., Hesse, B.W., Morgan, G.D., Jacobs, 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, pages 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, US).
Halpin, H., Hayes, P.J., McCusker, J., McGuinness, D.L., and Thompson, H.S. 2010. When owl:sameAs isn’t the Same: An Analysis of Identity in Linked Data. In Proceedings of ISWC 2010 (November 7-11 2010, Shanghai, China).
McCusker, J. and McGuinness, D.L. 2010. Provenance of High Throughput Biomedical Experiments. In Proceedings of International Provenance and Annotation Workshop 2010 (June 15-16 2010, Hefner Alumni House, Rensselaer Polytechnic Institute, Troy, NY, US).
McCusker, J. and McGuinness, D.L. 2010. Towards Identity in Linked Data. In Proceedings of OWLED 2010 (June 21-22 2010).

  • 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.
  • 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.


  • 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.

Open Source Projects

  • 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.

Professional Service

Peer Reviews

  • International Provenance and Annotations Workshop (IPAW) 2012
  • Journal of Web Semantics
  • Bioinformatics
  • Drug Discovery Today

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.