Self and Non-self

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Self and Non-self

• Amelia Ireland and Jane Lomax

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Self and non-self

• Two types of biological process
• Single organism
• Two or more organisms
• Single species
• Multi-species
• interaction between organisms node

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Self and non-self

• Some always multi-organism
• Viral transcription
• Nodulation in plants
• Some can be single or multi organism
• Cell killing
• Cell adhesion

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Example

• Toxin that inserts into membrane of target
  organism, causing cell lysis
• Annotate to cell killing of cells of other
  organism

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Representation
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Problem

• cellular physiological process must now mean
  physiological processes occurring in a cell in
  any organism

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Problem
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GO Slim

• GO slim term cell death
• apoptosis and cell killing of cells of other
  organism both children
• No way of telling whether gene products are
  suicidal or murderers!

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Problem

• Majority of terms make no reference to whether
  process involves one or multiple organisms
• Most users assume terms are single organism
  processes
• Problems with multi-organism processes under
  single organism processes

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Solution

• Explicitly state whether process is single or
  multi-organism
• but how?

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Possible solution I

• Terms may refer to single or multi-organism
  process
• Represent at annotation stage with self
  qualifier

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Possible solution I

• Protein kil1 involved in killing self cells
• kil1 cell killing self
• Protein tox1 kills plant cells
• tox1 cell killing

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Possible solution I

• Allows obvious relationships such as
• regulation of cell cycle
• viral regulation of cell cycle
• One term fits all solution
• no new terms needed
• no need for cell killing of cells of other
  organism
• No need for interaction between organisms node

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Possible solution I

• All information in annotations no ontology terms
  to represent multi-organism processes
• Would still want terms describing interactions,
  e.g. nodulation

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Possible solution II

• Add terms for single organism and multi-organism
  processes under a generic parent

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Possible solution II

• biological process
• single organism biological process
• cell killing in self
• multi-organism biological process
• cell killing in other organism
• cell killing
• cell killing in self
• cell killing in other organism

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Possible solution II

• All possibilities covered
• Term explosion!

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Possible solutions?