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.

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.