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

 Linking Biology to Models
 Limitations of Current Techniques
 Saint Aids Model Annotation
 Retrieving Annotation Automatically
 Selection of Annotation
 Future Work

Biological
Models
http://sbgn.org/Documents/Examples

 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

 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?

Information is
Everywhere

Saint Makes
Integration Easier

 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?

How Saint Helps

Loading the
Model

Checking
the SBML Model

Checking
the SBML Model

Detail of Saint
Display

Choosing
Annotation

Choosing
Annotation

Choosing
Annotation

Choosing
Annotation

Querying

Querying Remote
Data Sources

Not All Names are
Informative

Choosing Content
for the Model

Cdc13
Customizing the
New Annotation

 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

 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

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

 Thank you!
xkcd.com
F
Funding for CISBAN provided by BBSRC/EPSRC grant ref BB/C008200/1

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