Skip to main content

From Published Expression and Phenotype Data to Structured Knowledge: The Arabidopsis Gene Net Supplementary Database and Its Applications

  • Conference paper
Knowledge Processing and Data Analysis (KPP 2007, KONT 2007)

Abstract

We report on the development progress of the AGNS (Arabidopsis gene net supplementary) database and a AGNS-based information system for automation of research on the morphogenesis of Arabidopsis thaliana (L.), a well-known model plant in system biology.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Aitken, S.: Formalizing concepts of species, sex and development stage in anatomical ontologies. Bioinformatics 21, 2773–2779 (2005)

    Article  Google Scholar 

  2. Bard, J.B., Rhee, S.Y.: Ontologies in biology: design, applications and future challenges. Nat. Rev. Genet. 5, 213–222 (2004)

    Article  Google Scholar 

  3. Berardini, T.Z., et al.: Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. V. 135, 745–755 (2004)

    Article  Google Scholar 

  4. Bodenreider, O., et al.: Biomedical ontologies. In: Altman, R.B., Dunker, A.K., Hunter, L., Jung, T.A., Klein, T.E. (eds.) Proceedings of Pacific Symposium on Biocomputing, pp. 76–78. World Scientific, Singapore (2005)

    Google Scholar 

  5. Carland, F.M., McHale, N.A.: LOP1: a gene involved in auxin transport and vascular patterning in Arabidopsis. Development 122(6), 1811–1819 (1996)

    Google Scholar 

  6. Karp, P.D.: An ontology for biological function based on molecular interactions. Bioinformatics 16, 269–285 (2000)

    Article  Google Scholar 

  7. Lynn, K., et al.: The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene. Development 126, 469–481 (1999)

    Google Scholar 

  8. Mironova, V.V., Poplavsky, A.S., Ponomaryov, D.K., Omelianchuk, N.A.: Ontology of Arabidopsis Genenet Supplementary Database(AGNS): Cross references to TAIR ontology. In: Proc. Bioinformatics of Genome Regulation and Structure, pp. 209–212 (2005)

    Google Scholar 

  9. Plant Ontology Consortium, http://www.plantontology.org

  10. Vincent, P., et al.: The Plant Ontology Consortium and plant ontologies. Comparative and Functional Genomics 3(2), 137–142 (2002)

    Article  Google Scholar 

  11. Jaiswal, P., et al.: Plant ontology (PO): a controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics 6(7-8), 388–397 (2006)

    Article  Google Scholar 

  12. The PubMed database, http://www.ncbi.nlm.nih.gov/pubmed/

  13. Smith, B., et al.: On the application of formal principles to life science data: a case study in the gene ontology. In: Rahm, E. (ed.) Database Integration in the Life Sciences, pp. 79–94. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  14. Smith, B., et al.: Relations in biomedical ontologies. Genome Biology 6 (2005), http://genomebiology.com/2005/6/5/R46

  15. Smith, B.: Mereotopology: A theory of parts and boundaries. Data and Knowledge Engineering 20, 287–303 (1996)

    Article  MATH  Google Scholar 

  16. TAIR The Arabidopsis Information Resource, http://www.arabidopsis.org

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Ponomaryov, D. et al. (2011). From Published Expression and Phenotype Data to Structured Knowledge: The Arabidopsis Gene Net Supplementary Database and Its Applications. In: Wolff, K.E., Palchunov, D.E., Zagoruiko, N.G., Andelfinger, U. (eds) Knowledge Processing and Data Analysis. KPP KONT 2007 2007. Lecture Notes in Computer Science(), vol 6581. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-22140-8_7

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-22140-8_7

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-22139-2

  • Online ISBN: 978-3-642-22140-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics