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. 2004 Mar;5(2):148–155. doi: 10.1002/cfg.389

The ESF Programme on Functional Genomics Workshop on ‘Data Integration in Functional Genomics: Application to Biological Pathways’

Pierre-Alain Binz 1,2,✉, Henning Hermjakob 3, Paul van der Vet 4
PMCID: PMC2447351  PMID: 18629067

Abstract

We report from the second ESF Programme on Functional Genomics workshop on Data Integration, which covered topics including the status of biological pathways databases in existing consortia; pathways as part of bioinformatics infrastructures; design, creation and formalization of biological pathways databases; generating and supporting pathway data and interoperability of databases with other external databases and standards. Key issues emerging from the discussions were the need for continued funding to cover maintenance and curation of databases, the importance of quality control of the data in these resources, and efforts to facilitate the exchange of data and to ensure the interoperability of databases.

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Selected References

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  1. Binz Pierre-Alain, Martin Annette, Taussig Mike, de Daruvar Antoine. Conference Report: The ESF Programme on Integrated Approaches for Functional Genomics. Workshop on 'Data Integration in Functional Genomics and Proteomics'. Comp Funct Genomics. 2002;3(1):16–21. doi: 10.1002/cfg.134. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Choi Claudia, Krull Mathias, Kel Alexander, Kel-Margoulis Olga, Pistor Susanne, Potapov Anatolij, Voss Nico, Wingender Edgar. TRANSPATH--a high quality database focused on signal transduction. Comp Funct Genomics. 2004;5(2):163–168. doi: 10.1002/cfg.386. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Kärst Uwe, Realis Consortium REALIS: postgenomic analysis of Listeria Monocytogenes. Comp Funct Genomics. 2002;3(1):32–34. doi: 10.1002/cfg.137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Lisacek F., Chichester C., Gonnet P., Jaillet O., Kappus S., Nikitin F., Roland P., Rossier G., Truong L., Appel R. Shaping biological knowledge: applications in proteomics. Comp Funct Genomics. 2004;5(2):190–195. doi: 10.1002/cfg.379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Medjahed Djamel, Lemkin Peter F., Smythers Gary W., Munroe David J. Looking for cancer clues in publicly accessible databases. Comp Funct Genomics. 2004;5(2):196–200. doi: 10.1002/cfg.378. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Nasi Sergio. From databases to modelling of functional pathways. Comp Funct Genomics. 2004;5(2):179–183. doi: 10.1002/cfg.375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Romano Paolo, Aresu Ottavia, Assunta Manniello Maria, Parodi Barbara. Interoperability of CABRI Services and Biochemical Pathways Databases. Comp Funct Genomics. 2004;5(2):169–172. doi: 10.1002/cfg.376. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Schoof H., Ernst R., Mayer K. F. X. The PlaNet Consortium: a network of European plant databases connecting plant genome data in an integrated biological knowledge resource. Comp Funct Genomics. 2004;5(2):184–189. doi: 10.1002/cfg.374. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Schoof Heiko, Ernst Rebecca, Nazarov Vladimir, Pfeifer Lukas, Mewes Hans-Werner, Mayer Klaus F. X. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics. Nucleic Acids Res. 2004 Jan 1;32(DATABASE):D373–D376. doi: 10.1093/nar/gkh068. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Schoof Heiko. Towards Interoperability in Genome Databases: The MAtDB (MIPS Arabidopsis Thaliana Database) Experience. Comp Funct Genomics. 2003;4(2):255–258. doi: 10.1002/cfg.278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Schoof Heiko, Zaccaria Paolo, Gundlach Heidrun, Lemcke Kai, Rudd Stephen, Kolesov Grigory, Arnold Roland, Mewes H. W., Mayer Klaus F. X. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res. 2002 Jan 1;30(1):91–93. doi: 10.1093/nar/30.1.91. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Wittig Ulrike, Weidemann Andreas, Kania Renate, Peiss Christian, Rojas Isabel. Classification of chemical compounds to support complex queries in a pathway database. Comp Funct Genomics. 2004;5(2):156–162. doi: 10.1002/cfg.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. van Beek Johannes H. G. M. Data integration and analysis for medical systems biology. Comp Funct Genomics. 2004;5(2):201–204. doi: 10.1002/cfg.385. [DOI] [PMC free article] [PubMed] [Google Scholar]

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