Integration challenges in gene expression data management

Bioinformatics: Managing Scientific Data

Volumn , Issue , 2003, Pages 277-301

  Markowitz, Victor M ^a   Campbell, John ^a   Chen, I Min A ^a   Kosky, Anthony ^a   Palaniappan, Krishna ^a   Topaloglou, Thodoros ^a  

^a Gene Logic Inc Data Management Systems ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33745611937     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-155860829-0/50012-7     Document Type: Chapter

References (20)

1. Lockhart D.J., Winzeler A.E. Genomics, Gene Expression, and DNA Arrays. Nature 2000, 405:827-836.
2. Gene Logic Products, http://www.genelogic.com/products.htm. See GeneExpress product line and Genesis Enterprise software.
3. Lockhart D.J., Dong H., Byrne M.C., et al. Expression Monitoring by Hybridization to High-Density Oligonucleotide Arrays. Nature Biotechnology 1996, 14:1675-1680.
4. Markowitz V.M., Topaloglou T. Applying Data Warehousing Concepts to Gene Expression Data Management. Proceedings of the 2nd IEEE International Symposium on Bioinformatics and Bioengineering 2001, 65-72. IEEE Computer Society, Bethesda, MD.
5. Brazma A., Hingamp P., Quackenbush L Minimum Information About a Microarray Experiment (MIAME): Towards Standards for Microarray Data. Nature Genetics 2001, 29(no. 4):365-371.
6. Human Gene Nomenclature Database, http://www.gene.ucl.ac.uk/nomenclature/.
7. Affymetrix GeneChip Analysis Suite User Guide 2000.
8. Irizarry R.A., Bolstad B., Collin F., et al. Summaries of Affymetrix GeneChip Probe Level Data. Nucleic Acids Research 2003, 31(no. 4).
9. Li C., Wong W. Model-Based Analysis of Oligonucleotide Arrays: Expression Index Computation and Outlier Detection. Proceedings of the National Academy of Science 1998, 98:31-36.
10. Affymetrix. Affymetrix Analysis Data Model. http://www.affymetrix.com/support/.
11. SNOMED. Systematized Nomenclature for Medicine, http://www.snomed.org/.
12. The Gene Ontology Consortium Gene Ontology: Tool for the Unification of Biology. Nature Genetics 2000, 25:25-29. http://www.geneontology.org.
13. Markowitz V.M., Chen I.A., Kosky A. Gene Expression Data Management: A Case Study. Proceedings of the 8th International Conference on Extending Database Technology (EDBT) 2002, 722-731. from the series Lecture Notes in Computer Science, Springer-Verlag, Heidelberg, Germany. C.S. Jensen, K.G. Jeffery, L. Pokorny (Eds.).
14. Hill A.A., Brown E.L., Whitley M.Z., et al. Evaluation of Normalization Procedures for Oligonucleotide Array Data Based on Spiked cRNA Controls. Genome Biology 2001, 2(no. 12). 0055.1-0055.13. http://www.genomebiology.eom/2001/2/12/research/0055.
15. Hoaglin D.C., Mosteller F., Tukey J.W. Understanding Robust and Exploratory Data Analysis 1983, John Wiley, New York.
16. Eckman B.A., Kosky A.S., Laroco A.L. Extending Traditional Query-Based Integration Approaches for Functional Characterization of Post-Genomic Data. Bioinformatics 2001, 17(no. 7):587-601.
17. Davidson S.B., Crabtree J., Brunk B., et al. K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources. IBM Systems Journal 2001, 40(no. 2):512-531.
18. Presentations. Third International Meeting on Microarray Data Standards, Annotations, Ontologies, and Databases 2001, Stanford University, Palo Alto, CA. http://www.mgedsourceforye.net/ontologies/index.php.
19. Pearson H. Biology's Name Game. Nature 2001, 417:631-632.
20. Markowitz V.M., Chen I.A., Kosky A., et al. OPM: Object-Protocol Model Data Management Tools. Bioinformatics: Databases and Systems 1999, 187-199. Kluwer Academic, Boston. S.I. Letovsky (Ed.).