GeMCore, a Knowledge Base Dedicated to Mapping Mammalian Genomes

  • Gisèle Bronner
  • Bruno Spataro
  • Christian Gautier
  • François Rechenmann
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2066)


Representing genomic mapping knowledge is a complex process due to the diversity of experimental approaches. The lack of obvious equivalence between different kinds of maps1 makes it difficult to use them simultaneously or in a cooperative way. Furthermore, comparative mapping is not limited to map comparison, it also implies the comparison of the elements they are composed of. Comparison thus implies the combination of different computational objects, corresponding to different levels of information. However, from the user’s point of view, systems devoted to comparative mapping should appear to process queries in a homogeneous manner, whatever the objects they imply. We propose a data model that integrates mapping data, genetical data and sequences and takes into account the specific constraints resulting from the comparison of maps between and within different species.


Comparative Mapping Gene Symbol Hierarchy Class Biological Element Mouse Genome Database 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 1.
    Andersson, L., Archibald, A., Ashburner, M., Audun, S., Barendse, W., Bitgood, J., Bottema, C., Broad, T., Brown, S., Burt, D., Charlier, C., Copeland, N., Davis, S., Davisson, M., Edwards, J., Eggen, A., Elgar, G., Eppig, JT., Franklin, I., Grewe, P., Gill, T. 3RD, Graves, J.A., Hawken, R., Hetzel, J., Womack, J., et al.: Comparative genome organization of vertebrates. The first international workshop on comparative genome organization. Mamm. Genome 7 (1996) 717–734CrossRefGoogle Scholar
  2. 2.
    Rouault, J.P., Kuwabara, P.E., Sinilnikova, O.M., Duret, L., Thierry-Mieg, D., Billaud, M.: Regulation of dauer larva development in Caenorhabditis elegans by daf-18, a homologue of the tumour suppressor PTEN. Current Biology 9 (1999) 329–332Google Scholar
  3. 3.
    Spataro, B., Gautier, C.: Analyse comparative des genomes humains et murins avec l’interface GeMME. Recueil des actes, 1ères Journées Ouvertes: Biologie, Mathématiques, Informatique, 3-5 mai 2000, Montpellier-G. Caraux, O. Gascuel, M.F. Sagot (eds.) (2000) 55–64Google Scholar
  4. 4.
    Bernardi, G.: Isochores and the evolutionary genomics of vertebrates. Gene 241 (2000) 3–17CrossRefGoogle Scholar
  5. 5.
    Matassi, G., Sharp, P., Gautier, C.: Chromosomal location effects on gene sequence evolution in mammals. Current Biology 9 (1999) 786–791CrossRefGoogle Scholar
  6. 6.
    Letovsky, S.: GDB: integrating genomic maps. In: S. Letovsky (ed.) Bioinformatics: Databases and Systems. Kluwer Academic Publishers, Boston, Dortrecht, London (1999) 85–98Google Scholar
  7. 7.
    Eppig, J.T., Richardson, J.E., Blake, J.A., Davisson, M.T., Kadin, J.A., Rinwald, M.: The mouse genome database and the gene expression database: genotype to phenotype. In: S. Letovsky (ed.) Bioinformatics: Databases and Systems. Kluwer Academic Publishers, Boston, Dortrecht, London (1999) 119–128Google Scholar
  8. 8.
    Collins, A., Frezal, J., Teague, J., Morton, N.E.: A metric map of humans:23,500 loci in 850 bands. Proc. Natl. Acad. Sci. USA 93 (1996) 14771–14775CrossRefGoogle Scholar
  9. 9.
    Scott, A.F., Amberger, J., Brylawski, B., McKusick, V.A.: OMIM: online mendelian. inheritance in man. In: S. Letovsky (ed.) Bioinformatics: Databases and Systems. Kluwer Academic Publishers, Boston, Dortrecht, London (1999) 77–84Google Scholar
  10. 10.
    Achard, F., Cussat-Blanc, C., Viara, E., Barillot, E.: The new Virgil database: a service of rich links. Bioinformatics 14 (1998) 342–348CrossRefGoogle Scholar
  11. 11.
    Pruitt, K.D., Katz, K.S., Sicotte, H., Maglott, D.R.: Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet. 16 (2000) 44–47CrossRefGoogle Scholar
  12. 12.
    Thompson, J.D., Higgins, D.G., T.J., Gibson.: CLUSTALW, improving the sensitivity of progressive multiple alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acid. Res 22 (1994) 4673–4680CrossRefGoogle Scholar
  13. 13.
    Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. J Mol Biol. 215 (1990) 403–410Google Scholar
  14. 14.
    Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389–3402CrossRefGoogle Scholar
  15. 15.
    Duret, L., Perrière, G., Gouy, M.: HOVERGEN: comparative analysis of homologous vertebrate genes. In: S. Letovsky (ed.) Bioinformatics: Databases and Systems. Kluwer Academic Publishers, Boston, Dortrecht, London (1999) 21–36Google Scholar
  16. 16.
    Wada, Y., Yasue, H.: Development of an animal genome database and its search system-Comput. Applied Biosci. 12 (1996) 231–235Google Scholar
  17. 17.
    Biaudet, V., Samson, F., Bessieres, P.: Micado-a network oriented database for microbial genomes-Comput. Applied Biosci., 13 (1997) 431–438Google Scholar
  18. 18.
    Thierry-Mieg, J., Thierry-Mieg, D., and Stein, L.: ACEDB: The ACE Database Manager. In: S. Letovsky (ed.) Bioinformatics: Databases and Systems. Kluwer Academic Publishers, Boston, Dortrecht, London (1999) 265–278Google Scholar
  19. 19.
    Durbin, R., Thierry-Mieg, J.: The ACeDB genome database. In: Suhai, S. (ed.) Computational Methods in Genome Research, Plenum Press, New-York (1994) 45–55Google Scholar
  20. 20.
    Flanders, D.J., Weng, S., Petel, F.X., Cherry, J.M.: AtDB, the Arbidopsis thaliana database, and graphical web display of progress by the Arbidopsis genome initiative. Nucleic Acids Res. 26 (1998) 80–84CrossRefGoogle Scholar
  21. 22.
    Fasman, K.H., Letovsky, S.I., Cottingham, R.W., Kingsbury, D.T.: Improvements to the GDB human genome database-Nucleic Acids Res. 24 (1996) 57–63CrossRefGoogle Scholar
  22. 23.
    Gouy, M., Gautier, C., attimonelli, M., Lanave, C., di Paola, G.: ACNUC-a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage. CABIOS 1 (1985) 167–172Google Scholar
  23. 24.
    Page, M., Gensel, J., Capponi, C., Bruley, C., Genoud, P., Ziebelin, D.: Representation des connaissances au moyen de classes et d’associations: le système AROM. Conf. langage et modèles à objet (LMO’00), Mt Saint-Hilaire, CA (2000) 91–106Google Scholar
  24. 25.
    Allen, J.F.: Maintaining knowledge about temporal intervals-Comm. of the ACM 26 (1983) 832–843zbMATHCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2001

Authors and Affiliations

  • Gisèle Bronner
    • 1
    • 2
  • Bruno Spataro
    • 1
  • Christian Gautier
    • 1
  • François Rechenmann
    • 2
  1. 1.Laboratoire de Biométrie et Biologie Évolutive, UMR ― CNRS 5558Université Claude Bernard Lyon1Villeurbanne cedexFrance
  2. 2.INRIA Rhône AlpesSt MartinFrance

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