Advertisement

Neuroinformatics for C. elegans: Relating Mind and Body in Wormbase

  • Nansheng Chen
  • Raymond Y. N. Lee
  • Zeynep F. Altun
  • Thomas Boulin
  • Paul W. Sternberg
  • Lincoln D. Stein

Abstract

In this chapter, we have described how neuroscience data for the nematode C. elegans are deposited to and accessed from database. Research on neuroscience of C. elegans has attracted tremendous attention primarily because of its simple nervous system with 302 neurons. Data generated by comprehensive reconstruction and other efforts were initially deposited to and retrieved from ACeDB. More recently, Wormbase was created, which allows users to access data remotely and easily.

Key words

C. elegans ACeDB Wormbase Database Neuroscience Wiring Gene Ontology 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Selected References

  1. Albert P.S. and Riddle D.L., 1983. Developmental alterations in sensory neuroanatomy of the Caenorhabditis elegans dauer larva. J. Comp. Neurol. 219, 461–481.PubMedCrossRefGoogle Scholar
  2. Alberts, B., 1997. Preface. In C. elegans II (editors: D.L. Riddle, T. Blumenthal, B.J. Meyer and J.R. Priess). pp XI–XIV.Google Scholar
  3. Albertson D.G. and Thomson J.N., 1976. The pharynx of Caenorhabditis elegans. Philos. Trans. R. Soc. Lond. B Biol. Sci. 275, 299–325PubMedCrossRefGoogle Scholar
  4. Brenner, S., 1997 Preface. In C. elegans II (editors: D.L. Riddle, T. Blumenthal, B.J. Meyer and J.R. Priess). pp XV–XVII.Google Scholar
  5. Chalfie M. and White J. 1988 In The Nematode Caenorhabditis elegans. pp 337–391.Google Scholar
  6. Durbin, R.M., 1987. Studies on the development and organization of the nervous system of Caenorhabditis elegans, Ph.D. thesis, King’s College, Cambridge.Google Scholar
  7. Durbin, R.M. and Thierry-Mieg J., 1991. A C. elegans database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov.Google Scholar
  8. Goodman M.B., Hall D.H., Avery L., and Lockery S.R., 1998. Active Currents Regulate Sensitivity and Dynamic Range in C. elegans Neurons, Neuron 20,763–772.PubMedCrossRefGoogle Scholar
  9. Hall D.H., 1977. The posterior nervous system of Caenorhabditis elegans, Ph.D. thesis, California Institute of Technology.spivnGoogle Scholar
  10. Lewis J.A. and Hodgkin J.A., 1997. Specific neuroanatomical changes in chemosensory mutants of the nematode Caenorhabditis elegans. J. Comp. Neurol. 172, 489–510.CrossRefGoogle Scholar
  11. Mori, I. (1999). Genetics of chemotaxis and thermotaxis in the nematode caenorhabditis elegans. Annu. Rev. Genet. 33, 399–422PubMedCrossRefGoogle Scholar
  12. Rand and Nonet, 1997. Neurotransmitter assignments for specific neurons. In C. elegans II (editors: D.L. Riddle, T. Blumenthal, BJ. Meyer and J.R. Priess). pp 1049–1052.Google Scholar
  13. Riddle, DL, Blumenthal, T, Meyer, BJ, and Priess JR, 1997. Introduction to C. elegans. In C. elegans II (editors: D.L. Riddle, T. Blumenthal, BJ. Meyer and J.R. Priess). pp 1–22.Google Scholar
  14. Stein L.D., Sternberg, P., Durbin, R., Thierry-Mieg J, and Spieth, J., 2001. WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucl. Acids. Res. 29, 82–86.PubMedCrossRefGoogle Scholar
  15. Stein L. D. and Thierry-Mieg J., 1998. Scriptable access to the C. elegans genome sequence and other ACEDB databases. Genome Research. 8(12), 1308–1315.PubMedGoogle Scholar
  16. Stein L.D., 1999. Internet access to the C. elegans genome [Internet] Trends in Genetics, 15, 10, 425–427.PubMedCrossRefGoogle Scholar
  17. Sternberg, P. W., 2001. Working in the post-genomic C. elegans world. Cell 105, 173–176.PubMedCrossRefGoogle Scholar
  18. Sulston J.E. and White J.G., 1980. Regulation and cell autonomy during postembryonic development of Caenorhabditis elegans. Dev. Biol. 78, 577–597.PubMedCrossRefGoogle Scholar
  19. Wall, L., Christiansen, T., Orwant, J., 2000. Programming Perl, 3rd edition. O’Reilly Press.spivnGoogle Scholar
  20. Ward S., Thomson N., White J.G., and Brenner S., 1975. Electron microscopical reconstruction of the anterior sensory anatomy of the nematode Caenorhabditis elegans. J. Comp. Neurol. 160, 313–337.PubMedCrossRefGoogle Scholar
  21. Ware R.W., Clark D., Crossland K., and Russell R.L., 1975. The nerve ring of the nematode Caenorhabditis elegans: Sensory input and motor output. J. Comp. Neurol. 162, 71–110.CrossRefGoogle Scholar
  22. White J.G., Southgate E., Thomson J.N., and Brenner S., 1976. The structure of the ventral nerve cord of Caenorhabditis elegans. Philos. Trans. R. Soc. Lond. B Biol. Sci. 275, 327–348.PubMedCrossRefGoogle Scholar
  23. White J.G., Southgate E., Thomson J.N., and Brenner S., 1986. The structure of the nervous system of the nematode C. elegans. Philos. Trans. R. Soc. Lond. B Biol. Sci. 314, 1–340.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2003

Authors and Affiliations

  • Nansheng Chen
    • 1
  • Raymond Y. N. Lee
    • 2
    • 3
  • Zeynep F. Altun
    • 4
  • Thomas Boulin
    • 5
  • Paul W. Sternberg
    • 2
    • 3
  • Lincoln D. Stein
    • 1
  1. 1.Cold Spring Harbor LaboratoryUSA
  2. 2.Division of BiologyHoward Hughes Medical InstituteUSA
  3. 3.Institute of TechnologyPasadenaUSA
  4. 4.Department of NeuroscienceAlbert Einstein College of MedicineUSA
  5. 5.Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUSA

Personalised recommendations