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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 ToolBioSysBio 200925 March 2009
Allyson Lister, Matthew Pocock, Anil WipatCISBAN, Newcastle Universityhttp://www.cisban.ac.uk http://saint-annotate.sourceforge.net [email protected] 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