Integration and Mining of Genomic Annotations: Experiences and Perspectives in GFINDer Data Warehousing
Many tasks in bioinformatics require the comprehensive evaluation of different types of data, generally available in distributed and heterogeneous data sources. Several approaches, including federated databases, multi databases and mediator based systems, have been proposed to integrate data from multiple sources. Yet, data warehousing seams to be the most adequate when numerous data need to be integrated, efficiently processed, and mined comprehensively. To support biological interpretation of high-throughput gene lists, we previously developed GFINDer (Genome Functional INtegrated Discoverer, http://www.bioinformatics.polimi.it/GFINDer/), a web server that statistically analyzes and mines functional and phenotypic gene annotations sparsely available in numerous databanks to highlight annotation categories significantly enriched or depleted in the considered gene lists. GFINDer includes a data warehouse that integrates gene and protein annotations of several organisms expressed through various controlled terminologies and ontologies. Here, we describe GFINDer data warehouse and discuss the lessons learned in its construction and five-year maintenance and development.
KeywordsGFINDer biomolecular annotation integration data warehousing
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- 2.Lee, T.J., Pouliot, Y., Wagner, V., Gupta, P., Stringer-Calvert, D.W., Tenenbaum, J.D., Karp, P.D.: BioWarehouse: A Bioinformatics Database Warehouse Toolkit. BMC Bioinformatics 7(170), 1–14 (2006)Google Scholar
- 5.Diehn, M., Sherlock, G., Binkley, G., Jin, H., Matese, J.C., Hernandez-Boussard, T., Rees, C.A., Cherry, J.M., Botstein, D., Brown, P.O., Alizadeh, A.A.: SOURCE: A Unified Genomic Resource of Functional Annotations, Ontologies, and Gene Expression Data. Nucleic Acids Res. 31, 219–223 (2003)CrossRefPubMedPubMedCentralGoogle Scholar
- 6.Cadag, E., Louie, B., Myler, P.J., Tarczy-Hornoch, P.: Biomediator Data Integration and Inference for Functional Annotation of Anonymous Sequences. In: Pac. Symp. Biocomput., pp. 343–354 (2007)Google Scholar
- 9.The Gene Ontology Consortium: Gene Ontology: Tool for the Unification of Biology. Nature Genet. 25, 25–29 (2000)Google Scholar
- 11.Masseroli, M., Bellistri, E., Franceschini, A., Pinciroli, F.: Statistical Analysis of Genomic Protein Family and Domain Controlled Annotations for Functional Investigation of Classified Gene Lists. BMC Bioinformatics 8(suppl. 1), 1–10 (2007)Google Scholar
- 12.Ceresa, M., Masseroli, M., Campi, A.: A Web-enabled Database of Human Gene Expression Controlled Annotations for Gene List Functional Evaluation. In: Dittmar, A., Clark, J. (eds.) 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS 2007), pp. 394–397. The Printing House, Stoughton (2007)CrossRefGoogle Scholar