Transcript interactions with other organisms

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?