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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 Nodulation in plants • Some can be single or multi organism Cell killing Cell adhesion Example • Toxin that inserts into membrane of target organism, causing cell lysis • Annotate to ‘cell killing of cells of other organism’ Representation Problem • ‘cellular physiological process’ must now mean physiological processes occurring in a cell in any organism Problem 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! 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 Solution • Explicitly state whether process is single or multi-organism …but how? Possible solution I • Terms may refer to single or multiorganism process • Represent at annotation stage with ‘self’ qualifier Possible solution I • Protein kil1 involved in killing self cells kil1 cell killing self • Protein tox1 kills plant cells tox1 cell killing 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 Possible solution I All information in annotations; no ontology terms to represent multi-organism processes Would still want terms describing interactions, e.g. nodulation Possible solution II • Add terms for single organism and multiorganism processes under a generic parent 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 Possible solution II All possibilities covered Term explosion! Possible solutions?
