Bioinformatics for Glycan Expression

Integrated Technology Resource for Biomedical Glycomics: Technological Research and Development Project IV, A Project funded by NIH

Publications

Presentations

• Keynote: Amit Sheth, What can semantics do for Bioinformatics, the Fifth National Russian Research Conference (RCDL) , Saint Petersburg, Russia, October 29-31, 2003. Abstract Presentation (ppt ) Best viewed as power point in slide show
• Keynote: Amit Sheth, Semantics-Powered Bioinformatics: What, Why and How of Semantic Search, Integration, Processes and Analytics, Workshop on Semantic Web Technologies for Searching and Retrieving, Scientific Data ,  October 20, 2003, Sanibel Island, Florida, USA.
• Will York at the workshop on glycobiology informatics at the recent meeting of the Society for Glycobiology in San Diego. (ppt)
• Amit Sheth, "Semantic empowerment of Life Science Applications," Cincinnati Children Hospital & Medical Center, October 6, 2006, and Microsoft eScience Workshop, October 14, 2006. presentation (ppt)

Journal Papers

• Satya S. Sahoo, Christopher J. Thomas, Amit P. Sheth, Cory Henson, William S. York, GLYDE - An expressive XML standard for the representation of glycan structure, Carbohydr Res. 2005 Dec 30;340(18):2802-7. Epub 2005 Oct 20. PMID: 16242678
• James A. Atwood III, Satya S. Sahoo, Gerardo Alvarez-Manilla,Daniel B. Weatherly, Kumar Kolli, Ron Orlando and William S. York"Simple modification of a protein database for mass spectral identification of N-linked glycopeptides" Rapid Commun. Mass Spectrom. 2005; 19: 1-5

Conference Publications

• Christopher J. Thomas, Amit P. Sheth, William S. York, "Modular Ontology Design Using Canonical Building Blocks in the Biochemistry Domain". In Proceedings of the International Conference on Formal Ontology in Information Systems (FOIS). IOS Press, November 2006. Paper (pdf)
• Satya S. Sahoo, Christopher J. Thomas, Amit P. Sheth, William S. York, Samir Tartir, "Knowledge Modeling and its Application in Life Sciences: A Tale of two Ontologies", 15th International World Wide Web Conference, Edinburgh, Scotland, May 23 - May 26, 2006 (Acceptance Rate: 11%). Paper (pdf)
• Satya S. Sahoo, Amit P. Sheth, William S. York, John A. Miller, "Semantic Web Services for N-glycosylation Process", International Symposium on Web Services for Computational Biology and Bioinformatics, VBI, Blacksburg, VA, May 26-27, 2005. Abstract (pdf)

Book Chapters

• Christopher Thomas and Amit Sheth, "On the Expressiveness of the Languages for the Semantic Web - Making a Case for 'A Little More", in E. Sanchez (Editor), "Fuzzy Logic and the Semantic Web", Elsevier, March 2006
  Paper (pdf)
• Satya S. Sahoo and Amit Sheth, "Bioinformatics applications of Web Services, Web Processes and role of Semantics", Semantic Web Processes and Their Applications. J. Cardoso, A. Sheth, Editors. Springer, 2006 (in print)
• Satya S. Sahoo, Amit Sheth, Blake Hunter and William S. York, "SemBOWSER - adding Semantics to biological Web services registry", in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, Edited by Christopher J. O. Baker and Kei-Hoi Cheung. Springer, 2006 (in print)

Workshop Papers

• W.S. York, A. Sheth, K. Kochut, J. Miller, C. Thomas, K. Gomadam, S. Sahoo, M. Nagarajan, X. Yi "Semantic Integration of Glycomics Data and Information,"Human Disease Glycomics/Proteome Initiative 1st Workshop 2004: Functional Glycomics in Disease, Osaka, Japan
  Abstract (pdf), Presentation (ppt)
• Amit Sheth, William York, Christopher Thomas, Meenakshi Nagarajan, John A. Miller, Krys Kochut, Satya S. Sahoo, Xiaochuan Yi, "Semantic Web technology in support of Bioinformatics for Glycan Expression,"W3C Workshop on Semantic Web for Life Sciences, 27-28 October 2004, Cambridge, Massachusetts USA. Paper (pdf), Presentation (ppt)

Demonstration Papers/ Posters

• Sahoo Satya S., Hunter B, Sheth A, York WS, Semantic Biological Web Services Registry, Annual Symposium on Computational and Systems Biology, Athens, GA November 11, 2005
• Alvarez-Manilla, G., Atwood, J. III, Sahoo, S.S., Guo, Y., Warren, N.L., York, W.S., Orlando, R., and Pierce, M. 2005. Tools for glycoproteomic analysis: size-exclusion chromatography facilitates identification of tryptic glycopeptides with N-linked glycosylation sites. (Annual Conference of the Society for Glycobiology, November 9-12.) Glycobiology 15:1208
• Satya S. Sahoo, James A. Atwood III, Cory Henson, Amit Sheth, Ron Orlando, William S. York. (2006). "ProPreO - An ontology for high-throughput glycoproteomics". Presented at the Second Annual Georgia Glycoscience Symposium.
• Christopher Thomas, William S. York, Amit Sheth. (2006). "GlycO - a Focused Glycomics Domain Ontology". Presented at the Second Annual Georgia Glycoscience Symposium.

Technical Reports

• Satya S. Sahoo, Christopher Thomas, Amit P. Sheth, William S. York, GlycO and ProPreO: A case study of two deep domain life sciences ontologies LSDIS lab Technical Report, UGA, September 2005

Funding: Bioinformatics of Glycan Expression (one of the four components of the "Integrated Technology Resource for Biomedical Glycomics," appox. $6 million+), National Institute of Health, July 1, 2003 - June 30, 2008.