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Self and Non-self

Self and Non-self. Amelia Ireland and Jane Lomax. Self and non-self. Two types of biological process Single organism Two or more organisms Single species Multi-species ‘interaction between organisms’ node. Self and non-self. Some always multi-organism Viral transcription

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Self and Non-self

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  1. Self and Non-self Amelia Ireland and Jane Lomax

  2. Self and non-self • Two types of biological process • Single organism • Two or more organisms • Single species • Multi-species • ‘interaction between organisms’ node

  3. Self and non-self • Some always multi-organism • Viral transcription • Nodulation in plants • Some can be single or multi organism • Cell killing • Cell adhesion

  4. Example • Toxin that inserts into membrane of target organism, causing cell lysis • Annotate to ‘cell killing of cells of other organism’

  5. Representation

  6. Problem • ‘cellular physiological process’ must now mean physiological processes occurring in a cell in any organism

  7. Problem

  8. 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!

  9. 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

  10. Solution • Explicitly state whether process is single or multi-organism …but how?

  11. Possible solution I • Terms may refer to single or multi-organism process • Represent at annotation stage with ‘self’ qualifier

  12. Possible solution I • Protein kil1 involved in killing self cells kil1 cell killing self • Protein tox1 kills plant cells tox1 cell killing

  13. 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

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

  15. Possible solution II • Add terms for single organism and multi-organism processes under a generic parent

  16. 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

  17. Possible solution II • All possibilities covered • Term explosion!

  18. Possible solutions?

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