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Standards, exchange, and databases

Standards, exchange, and databases. Lena Strömbäck lestr@ida.liu.se Department of Computer and Information Science Linköping University. Tertiary str. PDB. DNA seq. GenBank. …. Signaling pathway. Protein seq. SPAD. SWISS-PROT. Secondary str. Taxonomy. PROSITE. AmiGO. Motivation.

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Standards, exchange, and databases

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  1. Standards, exchange, and databases Lena Strömbäck lestr@ida.liu.seDepartment of Computer and Information ScienceLinköping University

  2. Tertiary str. PDB DNA seq. GenBank … Signaling pathway Protein seq. SPAD SWISS-PROT Secondary str. Taxonomy PROSITE AmiGO Motivation INSULIN

  3. XML Standards for Molecular Interactions

  4. What do the standards contain? • Information about objects: • Proteins/Complexes • Genes/DNA • Other molecules • Interaction information • Information about experiments • Kind of experiment • Evidence of the experiment • More ….

  5. Representation of objects

  6. BioPAX

  7. Representation of interactions

  8. BioPAX

  9. Comparison: • S.1 Find all concepts common for the standards?

  10. Summary of standards

  11. Comparison: • S.1 Find all concepts common for the standards? • S.2 For each concept how does it correspond to concepts in other standards. Same concept, sub concept or is it instantiated in several places with different conditions.

  12. Type of objects

  13. Interaction types

  14. Comparison: • S.1 Find all concepts common for the standards? • S.2 For each concept how does it correspond to concepts in other standards. Same concept, sub concept or is it instantiated in several places with different conditions. • S.3 For each of the concept pairs check how they occur in comparison to each other, i.e. side by side or as sub concepts of each other. Compare between the standards.

  15. Interactor Id Names Xref Interactortype Compartment Organism Sequence

  16. Overall semantic structure

  17. Future possibilities Further study of standards Bio-enabling XML technology Tools for matching Thanks!

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