Saint: A Lightweight Model Annotation and Data Integration ToolBioSysBio 200925 March 2009

Allyson Lister, Matthew Pocock, Anil WipatCISBAN, Newcastle Universityhttp://www.cisban.ac.uk http://saint-annotate.sourceforge.net helpdesk@cisban.ac.ukThis presentation is licensed by Allyson Lister under Creative Commons BY-SA 2.5

Linking Biology to Models Limitations of Current Techniques Saint Aids Model Annotation

Retrieving Annotation Automatically Selection of Annotation

Future Work

http://sbgn.org/Documents/Examples

BiologicalModels

http://sbml.org/SBML_Software_Guide/SBML_Software_Matrix

What is SBML?

SBML is a standard format SBML is widely used (100+ tools) SBML

Represents the mathematical model Enables linking to the underlying biology

What do we know about “actin”? Protein (UniProt) Interactions (Pathway Commons, STRING) Reactions and Parameters (SABIO-RK, BRENDA,

KEGG) Vocabulary (SBO, GO)

Minimal Content (MIRIAM)

What InformationIs Needed?

Information isEverywhere

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 theModel

Checkingthe SBML Model

Checkingthe SBML Model

Detail of SaintDisplay

ChoosingAnnotation

ChoosingAnnotation

ChoosingAnnotation

ChoosingAnnotation

Querying

Querying RemoteData Sources

Not All Names areInformative

Choosing Contentfor the Model

Customizing theNew Annotation

Cdc13

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

Future Work

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

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

Funding for CISBAN provided by BBSRC/EPSRC grant ref BB/C008200/1

http://saint-annotate.sourceforge.net

Thank you!

Funding for CISBAN provided by BBSRC/EPSRC grant ref BB/C008200/1

xkcd.com

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