Date post: | 02-Nov-2014 |
Category: |
Technology |
Upload: | allyson-lister |
View: | 1,443 times |
Download: | 0 times |
Annotation of SBML Models Through Rule-Based Semantic Integration
Bio-Ontologies SIG, ISMB 200928 June 2009
Allyson Lister, Phillip Lord, Matthew Pocock, Anil WipatCISBAN and Newcastle University
http://www.cisban.ac.uk/RBM [email protected]
Presentation slides covered under the CC-BY-SA 2.5
Telomeres and Ageing
Image: Public Domain, NASA, from http://commons.wikimedia.org/wiki/File:Telomere_caps.gif
Checkpoint response to telomere uncapping in budding yeast
Proctor et al. [1]
Image and Model: [1]
What is SBML?
Standard formatWidely used (100+ tools)Represents the mathematical modelEnables linking to the underlying biology
Model Annotation Life Cycle
Get dataRead literature
(Re)build modelParameterise
Run and test model
Examine results
Challenges in Model Annotation
Knowledge in lots of places Hard for a single modeller to retrieve all
available knowledge Most existing data integration tools are not
suitable for modellers’ needs Many integration methods are purely syntactic
Rule-Based Mediation
A core ontology, which is a semantically-rich description of the research domain of interest
A set of source ontologies, which are syntactic translations of data formats into OWL
Resolution of syntactic and semantic heterogeneity occurs separately
Can use existing, independent ontologies
Where is the knowledge?
Data Source Number of Rules
BioGRID 17
Pathway Commons 11
UniProtKB 11
Input data sources: UniProtKB, BioGRID, Pathway CommonsData can end up in SBML format via MFO [2]
How are the data sources integrated?
UniprotKB
BioGRID
PathwayCommons
XML
XML
OWL
OWL
OWLTelomereOntology
Instances
Resolvesyntactic
heterogeneity
Resolvesemantic
heterogeneity
Reviews of integration types [3-6] Reviews for ontology mapping [7-11]
Retrievedata
MFO
Exportto
SBML
Achieving the XML to OWL Conversion
The XMLTab plugin for Protégé quickly creates classes and instances from XML
Provides syntactic transformation of data But, not multiple XML files May not be in active development
Syntactic Ontologies →Telomere Ontology
Rules written in SWRL Queries over the telomere ontology are written
in SQWRL SWRLTab and Jess are used to run these rules
and queries While writing rules/queries is mainly manual,
running them is automatic Semantic value is added to the information by
mapping it to a semantically-rich core ontology
Mappings from UniProtKB
upkb:Text(?l, ?value) ˄
upkb:locationSlot(?s, ?l) ˄
swrlb:equal(?value, “Nucleus”) →
tuo:Nucleus(?l)
What is RAD9?
Tell me about something called ‘rad9’ Results could be added back to the existing
model Cross-references SBO annotations Compartment localisations Recommended name
These results allow the addition of information required by the MIRIAM guidelines
What interacts with RAD9?
In Proctor et al., there are four interacting partners with RAD9Two were identified within the model, and were found by querying the telomere ontologyOf the unknown partners, one was provisionally identified as MEC1.
Summary
SBML models require large amounts of data to be mathematically and biologically complete
A two-step integration “rule-based mediation” helps model annotation
Off-the-shelf technology was used Eases the task of fulfilling MIRIAM guidelines SWRL rules were used to populate our semantically-rich
telomere ontology SQWRL was used for querying We found new knowledge that the modeller was not
aware of
Phillip Lord, Matthew Pocock, Anil Wipat
Carole Proctor (10.1098/rsif.2006.0148)
Tom Kirkwood
Reviewers and conference organisers
Funding for CISBAN provided by BBSRC/EPSRC grant ref BB/C008200/1
http://www.cisban.ac.uk/RBM
Thank you!
Funding for CISBAN provided by BBSRC/EPSRC grant ref BB/C008200/1
xkcd.com
References
1. CJ Proctor, DA Lydall, RJ Boys, et al. Modelling the checkpoint response to telomere uncapping in budding yeast. Journal of The Royal Society Interface, Vol. 4, No. 12. (22 February 2007), pp. 73-90.
2. AL Lister, M Pocock, A Wipat, Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models. Journal of Integrative Bioinformatics, Vol. 4, No. 3. (2007), 80.
3. Stephan Philippi and Jacob Kohler. Addressing the problems with life-science databases for traditional uses and systems biology. Nature Reviews Genetics, 7(6):482–488, May 2006
4. W. Sujansky. Heterogeneous database integration in biomedicine. J Biomed Inform, 34(4):285–298, August 2001.
5. Lincoln D Stein. Integrating biological databases. Nat Rev Genet, 4(5):337–345, May 2003.
6. R. Alonso-Calvo et al. An agent- and ontology-based system for integrating public gene, protein, and disease databases. J Biomed Inform, 40(1):17–29, February 2007.
References
7. Marie C. Rousset and Chantal Reynaud. Knowledge representation for information integration. Inf. Syst., 29(1):3–22, 2004.
8. Li Xu and David W. Embley. Combining the Best of Global-as-View and Local-as-View for Data Integration. In Anatoly E. Doroshenko, Terry A. Halpin, Stephen W. Liddle, Heinrich C. Mayr, Anatoly E. Doroshenko, Terry A. Halpin, Stephen W. Liddle, and Heinrich C. Mayr, editors, ISTA, volume 48 of LNI, pages 123–136. GI, 2004.
9. Natalya F. Noy and Mark A. Musen. The PROMPT suite: interactive tools for ontology merging and mapping. Int. J. Hum.-Comput. Stud., 59(6):983–1024, December 2003.
10. Holger Wache et al. Ontology-based integration of information — a survey of existing approaches. In H. Stuckenschmidt, editor, Proceedings of the IJCAI’01 Workshop on Ontologies and Information Sharing, Seattle, Washington, USA, Aug 4-5, pages 108–117, 2001.
11. Jinguang Gu, Baowen Xu, and Xinmeng Chen. An XML query rewriting mechanism with multiple ontologies integration based on complex semantic mapping. Information Fusion, 9(4):512–522, October 2008.
Small Print
This presentation is covered under the CC-BY-SA 2.5 (http://creativecommons.org/licenses/by-sa/2.5/ ) license and can be found on slideshare at: http://www.slideshare.net/allysonlister/annotation-of-sbml-models-through-rulebased-semantic-integration
The ontologies created by the authors are covered under the CC-BY 3.0 license, and external ontologies are governed under their own licensing requirements (specifically, SBO, which is covered under the Artistic License as defined on its SourceForge project site at http://sourceforge.net/projects/sbo/).
END