Standards, exchange, and databases

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Standards, exchange, and databases

• Lena Strömbäck
• lestr_at_ida.liu.seDepartment of Computer and
  Information ScienceLinköping University

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Motivation
INSULIN
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XML Standards for Molecular Interactions
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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 .

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Representation of objects
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BioPAX
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Representation of interactions
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BioPAX
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Comparison

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

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Summary of standards
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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.

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Type of objects
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Interaction types
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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.

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Interactor Id Names Xref
Interactortype Compartment Organism
Sequence
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Overall semantic structure
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Future possibilities

• Further study of standards
• Bio-enabling XML technology
• Tools for matching

Thanks!