Saint: A Lightweight Model Annotation and Data Integration Tool

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A talk given by Allyson Lister at BioSysBio (http://conferences.theiet.org/biosysbio/) in March 2009. Describes Saint, a lightweight model annotation and data integration tool. You can find out more at http://saint-annotate.sourceforge.net. CellML support is coming soon.

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Saint: A Lightweight Model Annotation and Data Integration Tool

  1. 1. Saint: A Lightweight Model Annotation and Data Integration Tool BioSysBio 2009 25 March 2009 Allyson Lister, Matthew Pocock, Anil Wipat CISBAN, Newcastle University http://www.cisban.ac.uk http://saint-annotate.sourceforge.net helpdesk@cisban.ac.uk
  2. 2.  Linking Biology to Models  Limitations of Current Techniques  Saint Aids Model Annotation  Retrieving Annotation Automatically  Selection of Annotation  Future Work
  3. 3. Biological Models http://sbgn.org/Documents/Examples
  4. 4.  SBML is a standard format  SBML is widely used (100+ tools) S  SBML  Represents the mathematical model  Enables linking to the underlying biology What is SBML? http://sbml.org/SBML_Software_Guide/SBML_Software_Matrix
  5. 5.  What do we know about “actin”?  Protein (UniProt) P  Interactions (Pathway Commons, STRING) I  Reactions and Parameters (SABIO-RK, BRENDA, K KEGG)  Vocabulary (SBO, GO) V  Minimal Content (MIRIAM) M What Information Is Needed?
  6. 6. Information is Everywhere
  7. 7. Saint Makes Integration Easier
  8. 8.  Saint is lightweight  Easy-to-use  Pick and choose from suggested annotation  Move on to next task quickly  Saint is useful as  A first-pass annotation tool  Add annotation to existing model What is Saint?
  9. 9. How Saint Helps
  10. 10. Loading the Model
  11. 11. Checking the SBML Model
  12. 12. Checking the SBML Model
  13. 13. Detail of Saint Display
  14. 14. Choosing Annotation
  15. 15. Choosing Annotation
  16. 16. Choosing Annotation
  17. 17. Choosing Annotation
  18. 18. Querying
  19. 19. Querying Remote Data Sources
  20. 20. Not All Names are Informative
  21. 21. Choosing Content for the Model
  22. 22. Cdc13 Customizing the New Annotation
  23. 23.  Saint discovers links between a mathematical model and the underlying biology  Saint automatically queries many databases  Saint makes models more meaningful and useful  Saint saves time for the modeller Summary
  24. 24.  More data sources  Use of species types  Better support for non-systematic names  Find a way to add software source attribution to the SBML model  Incorporation of SBGN for better display Future Work
  25. 25. http://saint-annotate.sourceforge.net  Neil Wipat, Matthew Pocock  Carole Proctor (10.1098/rsif.2006.0148), Graham Smith, and all the CISBAN modellers  Tom Kirkwood  Sarah Keating, Camille Laibe, Michael Hucka, Akiya Jouraku, Nicolas Le Novere, and the rest of the SBML and BioModels communites and mailing lists  Phil Lord F Funding for CISBAN provided by BBSRC/EPSRC grant ref BB/C008200/1
  26. 26.  Thank you! xkcd.com F Funding for CISBAN provided by BBSRC/EPSRC grant ref BB/C008200/1
  27. 27. Small Print  The image of the database cylinders is LGPL and can be found at http://commons.wikimedia.org/wiki/File:Crystal_Clear_app_database.png The “user” image is licensed under the CC-BY- SA 2.5 and can be found at http://commons.wikimedia.org/wiki/File:User_icon_2.svg This presentation is licensed by Allyson Lister under Creative Commons BY-SA 2.5

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