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Balancing Self and Non-self in Biological Processes

Explore the complexities of self and non-self interactions in biological processes, from single organisms to multi-species interactions. Distinguish between cell killing and cell adhesion phenomena. Addressing representation issues in cellular physiological processes and the ambiguity of gene product functions. Propose solutions to clarify single or multi-organism processes in annotations.

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Balancing Self and Non-self in Biological Processes

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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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