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.
Saint: A Lightweight Model Annotation and Data Integration Tool
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. Linking Biology to Models
Limitations of Current Techniques
Saint Aids Model Annotation
Retrieving Annotation Automatically
Selection of Annotation
Future Work
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. 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?
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?
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. 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. 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. Thank you!
xkcd.com
F
Funding for CISBAN provided by BBSRC/EPSRC grant ref BB/C008200/1
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