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The use of Ontology in Organising and Managing Protein Family Resources

The use of Ontology in Organising and Managing Protein Family Resources. Katy Wolstencroft, University Of Manchester. Overview. Research communities working on specific protein families Family Resource – central focus for the community Problems communities tend to be small

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The use of Ontology in Organising and Managing Protein Family Resources

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  1. The use of Ontology in Organising and Managing Protein Family Resources Katy Wolstencroft, University Of Manchester

  2. Overview • Research communities working on specific protein families • Family Resource – central focus for the community Problems • communities tend to be small • Difficult to sustain resources for small number of people - funding – community input / consistency

  3. Protein Family Test Cases • Protein Phosphatases: Original test family dephosphorylation, involved in control and communication. http://www.bioinf.man.ac.uk/phosphabase • ABC Transporters: (GSK Pennsylvania) transport of biological molecules through cells and organelles. Both implicated in human disease

  4. Solutions From Ontology? • General biological data problems * Nomenclature and free text data • Sustainability • Consistency and ambiguity Problems associated with both data extraction and data retrieval

  5. GO Accessible Resources GO – “de facto standard” – description of gene products Biological Resources – annotating data to GO terms

  6. Domain-specific Ontology GO allows efficient collection of biological data from heterogeneous sources – not rich enough to describe a whole protein family domain • How should the information be stored? • What information should be stored?

  7. Protein Phosphatase Inhibitors - protein inhibition, transcriptional repression Activators - protein activation, transcriptional activation Domain Structure Disease Association Genetic Localisation Tissue Expression Enzyme - substrates/ products Cofactor/prosthetic group/molecule required for activation ABC Transporters Inhibitors - protein inhibition, transcriptional repression Activators - protein activation, transcriptional activation Domain Structure Disease Association Genetic Localisation Tissue Expression Transported substrates Requirements

  8. PhosphaBase PhosphaBase Doamin Ontology DAML+OIL description logic Relational Database – MySql User interface – Java Servlet Free access over the internet MySQL and Java free Java platform independent ABC Transporters ABC Domain Ontology DAML+OIL description logic Relational Database - Oracle User Interface – Ontology driven interface Internal Company Use Limited access System Requirements

  9. System Architecture

  10. Architecture Advantages /Disadvantages • Sustainability – Data capture can be automated. • Diagnostics– Classification of ‘unknown’ proteins. *Major application in annotation of new genomes* • Accessibilityand Portability– Free availability over the Internet. All software freely available Issues • Maintenance –automation and use of ontology reduces human intervention but the ontology needs occasional maintenance • Standards –DAML+OIL ontology. Need to migrate to OWL, but OWL does not currently allow qualified number restrictions

  11. Diagnostics Automated Classification Andersen et al (2001) Mol. Cell. Biol.21 7117-36

  12. Automated Classification DAML+OIL Ontology Domain Architecture ‘rules’ for group membership

  13. Automated Classification Unknown Sequences InterPro Smart Domain Architecture

  14. Automated Classification Unknown Sequences DAML+OIL Ontology InterPro Smart Domain Architecture ‘rules’ for group membership Domain Architecture Classification Reasoner

  15. Summary • Two rich and useful resources for the phosphatase and ABC transporter research communities • A sustainable resource with automatic classification capabilities • Generic Model – A robust model could be extended to build similar resources for other protein families in the future Ontology technology – powerful tool in managing biological data

  16. Next Steps Phosphorylation Ontology • Control of Phosphorylation mediated by both phosphatases and kinases • Collaboration - Protein Kinase Resource (UCSD) to describe whole phosphorylation events phosphatase Pi Phospho protein protein kinase

  17. Phosphorylation Ontology Goals • Use ontology technology to capture whole phosphorylation events • Description of phosphorylation events in the cell and the biological pathways they affect • Produce phosphorylation resource useful to phosphatase and kinase community and wider.

  18. Acknowledgements Supervisors: Andy Brass, Robert Stevens Advisor and Phosphatase Biologist: Lydia Tabernero GSK: Robin McEntire and the IKM group Funding: Medical Research Council

  19. Screen Shots

  20. Query Result

  21. Query Result - Continued

  22. InteractionBetween Resources • Pand K substrates / inhibitors activators of one another • Common Substrates • Common inhibitors/ activators • Same biological pathways • Same diseases P K Substrates Inhibitors/Activators Biological Pathways Diseases

  23. Proposed Architecture Biological Pathways Emerging Standards/ontologies BioPax / PathOS PhosphaBase Ontology PKR Ontology Gene Ontology

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