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==Tools and Software 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 ==Talks/Presentations== * McCusker J., McGuinness, D. "[[owl:sameAs Considered Harmful to Provenance - CSHALS|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 - CSHALS|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. ==Publications== * [[Jim McCusker|Jim McCusker]], J. Phillips, A. Beltran, A. Finkelstein, and M. Krauthammer, “[http://www.biomedcentral.com/1471-2105/10/S10/S2 Semantic web data warehousing for caGrid],” BMC Bioinformatics, vol. 10, 2009, p. S2. * S. Szpakowski, [[Jim McCusker|Jim McCusker]], and M. Krauthammer, “[http://www.la-press.com/using-semantic-web-technologies-to-annotate-and-align-microarray-desig-a1460 Using Semantic Web Technologies to Annotate and Align Microarray Designs],” Cancer Informatics, vol. 8, 2009. * S. Xu, [[Jim McCusker|Jim McCusker]], and M. Krauthammer, “[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/17/1968 Yale Image Finder (YIF): a new search engine for retrieving biomedical images],” Bioinformatics, vol. 24, Sep. 2008, pp. 1968-1970. * S. Xu, [[Jim McCusker|Jim McCusker]], M. Schultz, and M. Krauthammer, “Improving OCR Performance in Biomedical Literature Retrieval through Preprocessing and Postprocessing,” 2008. * S. Xu, [[Jim McCusker|Jim McCusker]], and M. Krauthammer, “Exploring the use of image text for biomedical literature retrieval.,” AMIA... Annual Symposium proceedings/AMIA Symposium. AMIA Symposium, AMIA Annu Symp Proc, 2008, p. 1186. ==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.
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