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1 Semantic Web for Biomedicine
[Ashburner, 2000] Michael Ashburner, Catherine A. Ball, Judith A. Blake, David Botstein,
Heather Butler, J. Michael Cherry, Allan P. Davis, Kara Dolinski, Selina S. Dwight, Janan
T. Eppig, Midori A. Harris, David P. Hill, Laurie Issel-Tarver, Andrew Kasarskis, Suzanna
Lewis, John C. Matese, Joel E. Richardson, Martin Ringwald, Gerald M. Rubin, and
Gavin Sherlock. Gene ontology: tool for the unification of biology. nature genetics,
25:25–29, 2000. Read this paper.
[Yeh et al, 2003] I. Yeh, P. D. Karp, N. F. Noy, & R. B. Altman. Knowledge acquisition,
consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics,
2(January 22):241-8. 2003. Read this paper.
[Neumann et al, 2004] E. K. Neumann, E. Miller, and J. Wilbanks. What the semantic web could
do for the life sciences. Drug Discovery Today: BIOSILICO, 2(6):228{236, 2004. Read
this paper.
[Camon et al, 2004] Evelyn Camon , Michele Magrane , Daniel Barrell , Vivian Lee , Emily
Dimmer , John Maslen , David Binns , Nicola Harte , Rodrigo Lopez , and Rolf Apweiler
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with
Gene Ontology Nucl. Acids Res. 32: D262-D266. D262±D266 Nucleic Acids Research,
2004, Vol. 32, Database issue.
[Neumann , 2005] E. Neumann, A Life Science Semantic Web: Are We There Yet? Sci. STKE
2005, pe22 (2005). Read this paper.
[Mukherjea, 2005] Sougata Mukherjea. 2005. Information retrieval and knowledge discovery
utilising a biomedical Semantic Web. Brief Bioinform 6: 252-262. Read this paper.
[Cheung, 2005] Kei-Hoi Cheung , Kevin Y. Yip , Andrew Smith , Remko deKnikker , Andy
Masiar , and Mark Gerstein. YeastHub: a semantic web use case for integrating data in the
life sciences domain. Bioinformatics 21: i85-i96. Read this paper.
[Bodenreider and Stevens, 2006] Olivier Bodenreider and Robert Stevens. Bio-ontologies: current
trends and future directions. Briefings in Bioinformatics Advance Access published on
September 1, 2006, DOI 10.1093/bib/bbl027. Brief Bioinform 7: 256-274. Read this
paper.
[Stephens et al, 2006] Stephens, S., Morales, A., and Quinlan, M. 2006. Applying Semantic Web
Technologies to Drug Safety Determination. IEEE Intelligent Systems 21, 1 (Jan. 2006),
82-86. Read this paper.
[Gene Ontology Consortium, 2006]Gene Ontology Consortium. The Gene Ontology (GO) project
in 2006. Nucl. Acids Res.,34(suppl. 1):D322–326, 2006. Read this paper.
[Good and Wilkinson, 2006] Benjamin M. Good , and Mark D. Wilkinson. The Life Sciences
Semantic Web is Full of Creeps! Briefings in Bioinformatics Advance Access published
on September 1, 2006, DOI 10.1093/bib/bbl025. Brief Bioinform 7: 275-286. Read this
paper.
[Post et al, 2007] L. J. G. Post, M. Roos, M. S. Marshall, R. van Driel, and T. M. Breit. A semantic
web approach applied to integrative bioinformatics experimentation: a biological use case
with genomics data. Bioinformatics, November 15, 2007; 23(22): 3080 - 3087. Read this
paper.
[Gudivada et al, 2007] Ranga Chandra Gudivada, Xiaoyan A. Qu, Anil G Jegga, Eric K. Neumann,
and Bruce J Aronow. A genome-phenome integrated approach for mining disease-causal
genes using semantic web. In WWW ’07 Workshops: Health Care and Life Sciences Data
Integration for the Semantic Web, 2007. Read this paper.
[Chen et al, 2007] H. Chen, Y. Wang, and Z. Wu. Introduction to semantic e-science in
biomedicine. BMC Bioinformatics, 8(Suppl 3):S1, 2007. Read this paper.
[Smith et al, 2007] Barry Smith1, Michael Ashburner2, Cornelius Rosse3, Jonathan Bard4,
William Bug5, Werner Ceusters6, Louis J Goldberg7, Karen Eilbeck8, Amelia Ireland9,
Christopher J Mungall10, The OBI Consortium11, Neocles Leontis12, Philippe
Rocca-Serra9, Alan Ruttenberg13, Susanna-Assunta Sansone9, Richard H
Scheuermann14, Nigam Shah15, Patricia L Whetzel16 & Suzanna Lewis10. The OBO
Foundry: coordinated evolution of ontologies to support biomedical data integration.
Nature Biotechnology 25, 1251 - 1255 (2007) Read this paper.
[Rubin et al, 2008] Daniel L. Rubin , Nigam H. Shah , and Natalya F. Noy. Biomedical ontologies:
a functional perspective. Briefings in Bioinformatics Advance Access published on
January 1, 2008, DOI 10.1093/bib/bbm059. Brief Bioinform 9: 75-90. Read this paper.
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